8IC4

Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- mouse under cold temperature

PDB DOI: https://doi.org/10.2210/pdb8IC4/pdb
EM Map EMD-35354: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Mus musculus
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-02-10 Released: 2024-09-18
Deposition Author(s): Shin, Y.-C., Liao, M.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- mouse under cold temperature

Shin, Y.-C., Liao, M.

To be published.

Macromolecule Content

Total Structure Weight: 566.82 kDa
Atom Count: 31,638
Modelled Residue Count: 3,804
Deposited Residue Count: 4,813
Unique protein chains: 24

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial	A [auth D]	463	Mus musculus	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q91WD5 (Mus musculus) Explore Q91WD5 Go to UniProtKB: Q91WD5
IMPC: MGI:2385112
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91WD5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 6	B [auth J]	172	Mus musculus	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for P03925 (Mus musculus) Explore P03925 Go to UniProtKB: P03925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03925
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4L	C [auth K]	98	Mus musculus	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for P03903 (Mus musculus) Explore P03903 Go to UniProtKB: P03903
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03903
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 5	D [auth L]	607	Mus musculus	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for P03921 (Mus musculus) Explore P03921 Go to UniProtKB: P03921
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03921
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4	E [auth M]	459	Mus musculus	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for P03911 (Mus musculus) Explore P03911 Go to UniProtKB: P03911
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03911
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 2	F [auth N]	345	Mus musculus	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for P03893 (Mus musculus) Explore P03893 Go to UniProtKB: P03893
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03893
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	G [auth O]	355	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99LC3 (Mus musculus) Explore Q99LC3 Go to UniProtKB: Q99LC3
IMPC: MGI:1914523
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99LC3
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein, mitochondrial	H [auth U]	156	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9CR21 (Mus musculus) Explore Q9CR21 Go to UniProtKB: Q9CR21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CR21
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	I [auth X]	172	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DCJ5 (Mus musculus) Explore Q9DCJ5 Go to UniProtKB: Q9DCJ5
IMPC: MGI:1915625
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9DCJ5
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11	J [auth Y]	143	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for G5E814 (Mus musculus) Explore G5E814 Go to UniProtKB: G5E814
IMPC: MGI:1917125
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G5E814
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial	K [auth c]	76	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9CQY9 (Mus musculus) Explore Q9CQY9 Go to UniProtKB: Q9CQY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQY9
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C2	L [auth d]	120	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9CQ54 (Mus musculus) Explore Q9CQ54 Go to UniProtKB: Q9CQ54
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQ54
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5	M [auth e]	106	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99LY9 (Mus musculus) Explore Q99LY9 Go to UniProtKB: Q99LY9
IMPC: MGI:1890889
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99LY9
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1	N [auth f]	57	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0DN34 (Mus musculus) Explore P0DN34 Go to UniProtKB: P0DN34
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DN34
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial	O [auth g]	151	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for O09111 (Mus musculus) Explore O09111 Go to UniProtKB: O09111
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O09111
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial	P [auth h]	189	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQH3 (Mus musculus) Explore Q9CQH3 Go to UniProtKB: Q9CQH3
IMPC: MGI:1913296
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQH3
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6	Q [auth i]	128	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q3UIU2 (Mus musculus) Explore Q3UIU2 Go to UniProtKB: Q3UIU2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3UIU2
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial	R [auth j]	105	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9CPU2 (Mus musculus) Explore Q9CPU2 Go to UniProtKB: Q9CPU2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CPU2
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3	S [auth k]	104	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9CQZ6 (Mus musculus) Explore Q9CQZ6 Go to UniProtKB: Q9CQZ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQZ6
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	T [auth l]	186	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D6J5 (Mus musculus) Explore Q9D6J5 Go to UniProtKB: Q9D6J5
IMPC: MGI:1914514
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9D6J5
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4	U [auth m]	129	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9CQC7 (Mus musculus) Explore Q9CQC7 Go to UniProtKB: Q9CQC7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQC7
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Reference Sequence

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	V [auth n]	179	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQJ8 (Mus musculus) Explore Q9CQJ8 Go to UniProtKB: Q9CQJ8
IMPC: MGI:1913468
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CQJ8
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7	W [auth o]	137	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9CR61 (Mus musculus) Explore Q9CR61 Go to UniProtKB: Q9CR61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CR61
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10	X [auth p]	176	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9DCS9 (Mus musculus) Explore Q9DCS9 Go to UniProtKB: Q9DCS9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9DCS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain CA [auth L] SDF format, chain HA [auth M] SDF format, chain JA [auth Y] SDF format, chain KA [auth d] SDF format, chain LA [auth h] MOL2 format, chain CA [auth L] MOL2 format, chain HA [auth M] MOL2 format, chain JA [auth Y] MOL2 format, chain KA [auth d] MOL2 format, chain LA [auth h]	CA [auth L], HA [auth M], JA [auth Y], KA [auth d], LA [auth h]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain CA [auth L] Focus chain HA [auth M] Focus chain JA [auth Y] Focus chain KA [auth d] Focus chain LA [auth h] Interactions & Density Focus chain CA [auth L] Focus chain HA [auth M] Focus chain JA [auth Y] Focus chain KA [auth d] Focus chain LA [auth h]
3PE (Subject of Investigation/LOI) Query on 3PE Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain BA [auth L] SDF format, chain EA [auth L] SDF format, chain FA [auth M] SDF format, chain GA [auth M] SDF format, chain MA [auth i] SDF format, chain NA [auth m] SDF format, chain Y [auth D] SDF format, chain Z [auth J] MOL2 format, chain AA [auth L] MOL2 format, chain BA [auth L] MOL2 format, chain EA [auth L] MOL2 format, chain FA [auth M] MOL2 format, chain GA [auth M] MOL2 format, chain MA [auth i] MOL2 format, chain NA [auth m] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth J]	AA [auth L] BA [auth L] EA [auth L] FA [auth M] GA [auth M] AA [auth L], BA [auth L], EA [auth L], FA [auth M], GA [auth M], MA [auth i], NA [auth m], Y [auth D], Z [auth J]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain AA [auth L] Focus chain BA [auth L] Focus chain EA [auth L] Focus chain FA [auth M] Focus chain GA [auth M] Focus chain MA [auth i] Focus chain NA [auth m] Focus chain Y [auth D] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth L] Focus chain EA [auth L] Focus chain FA [auth M] Focus chain GA [auth M] Focus chain MA [auth i] Focus chain NA [auth m] Focus chain Y [auth D] Focus chain Z [auth J]
EHZ (Subject of Investigation/LOI) Query on EHZ Download Ideal Coordinates CCD File SDF format, chain OA [auth n] MOL2 format, chain OA [auth n]	OA [auth n]	~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate C₂₅ H₄₉ N₂ O₉ P S JYSKQPQRUCZFIQ-REWPJTCUSA-N		Interactions Focus chain OA [auth n] Interactions & Density Focus chain OA [auth n]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain IA [auth O] MOL2 format, chain IA [auth O]	IA [auth O]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain IA [auth O] Interactions & Density Focus chain IA [auth O]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth L] MOL2 format, chain DA [auth L]	DA [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth L] Interactions & Density Focus chain DA [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-09-18

Deposition Author(s):

Shin, Y.-C.

Liao, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	RO1 DK081418
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	RO1 DK089883

Revision History (Full details and data files)

Version 1.0: 2024-09-18
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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8IC4

Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- mouse under cold temperature

Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- mouse under cold temperature

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

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Entity ID: 4

UniProt

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Entity ID: 5

UniProt

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Entity ID: 6

UniProt

Entity Groups

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Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

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Entity ID: 13

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

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Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

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Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19