3DTU

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides complexed with deoxycholic acid

PDB DOI: https://doi.org/10.2210/pdb3DTU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cereibacter sphaeroides
Expression System: Cereibacter sphaeroides
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2008-07-15 Released: 2008-09-16
Deposition Author(s): Qin, L., Mills, D.A., Buhrow, L., Hiser, C., Ferguson-Miller, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.212
R-Value Work: 0.184
R-Value Observed: 0.184

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A conserved steroid binding site in cytochrome C oxidase.

Qin, L., Mills, D.A., Buhrow, L., Hiser, C., Ferguson-Miller, S.

(2008) Biochemistry 47: 9931-9933

PubMed: 18759498 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/bi8013483
Primary Citation of Related Structures:
3DTU

PubMed Abstract:
Micromolar concentrations of the bile salt deoxycholate are shown to rescue the activity of an inactive mutant, E101A, in the K proton pathway of Rhodobacter sphaeroides cytochrome c oxidase. A crystal structure of the wild-type enzyme reveals, as predicted, deoxycholate bound with its carboxyl group at the entrance of the K path. Since cholate is a known potent inhibitor of bovine oxidase and is seen in a similar position in the bovine structure, the crystallographically defined, conserved steroid binding site could reveal a regulatory site for steroids or structurally related molecules that act on the essential K proton path.

Organizational Affiliation

Biochemistry and Molecular Biology Department, Michigan State University, East Lansing, Michigan 48824, USA.

Macromolecule Content

Total Structure Weight: 198.95 kDa
Atom Count: 13,976
Modelled Residue Count: 1,592
Deposited Residue Count: 1,656
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, C	566	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: ctaD EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P33517 (Cereibacter sphaeroides) Explore P33517 Go to UniProtKB: P33517
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33517
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, D	262	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: ctaC, coxII, ctaB EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q03736 (Cereibacter sphaeroides) Explore Q03736 Go to UniProtKB: Q03736
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03736
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEA Query on HEA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain O [auth A]	N [auth A], O [auth A], PA [auth C], QA [auth C]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth C] Focus chain QA [auth C]
DMU Query on DMU Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	AB [auth D] E [auth A] F [auth A] G [auth A] H [auth A] AB [auth D], E [auth A], F [auth A], G [auth A], H [auth A], IA [auth C], JA [auth C], X [auth B], Y [auth B]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain AB [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain X [auth B] Focus chain Y [auth B]
DXC Query on DXC Download Ideal Coordinates CCD File SDF format, chain RA [auth C] MOL2 format, chain RA [auth C] mmCIF format, chain RA [auth C]	RA [auth C]	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID C₂₄ H₄₀ O₄ KXGVEGMKQFWNSR-LLQZFEROSA-N		Interactions Focus chain RA [auth C] Interactions & Density Focus chain RA [auth C]
TRD Query on TRD Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain HB [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain GA [auth B] SDF format, chain IB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain IB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain HB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain IB [auth D]	EA [auth B] FA [auth B] FB [auth D] GA [auth B] GB [auth D] EA [auth B], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HB [auth D], IB [auth D], P [auth A], Q [auth A], R [auth A], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	TRIDECANE C₁₃ H₂₈ IIYFAKIEWZDVMP-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
HTO Query on HTO Download Ideal Coordinates CCD File SDF format, chain HA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain HA [auth B]	HA [auth B]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain HA [auth B] Interactions & Density Focus chain HA [auth B]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EB [auth D]	BA [auth B], CA [auth B], DA [auth B], DB [auth D], EB [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EB [auth D] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EB [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain OA [auth C] SDF format, chain M [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain M [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain M [auth A]	M [auth A], OA [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Focus chain OA [auth C] Interactions & Density Focus chain M [auth A] Focus chain OA [auth C]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain I [auth A] SDF format, chain KA [auth C] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain Z [auth B]	AA [auth B] BB [auth D] CB [auth D] I [auth A] KA [auth C] AA [auth B], BB [auth D], CB [auth D], I [auth A], KA [auth C], Z [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain I [auth A] Focus chain KA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain I [auth A] Focus chain KA [auth C] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain MA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth C]	K [auth A], MA [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain MA [auth C] Interactions & Density Focus chain K [auth A] Focus chain MA [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain LA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth C]	J [auth A], LA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain LA [auth C] Interactions & Density Focus chain J [auth A] Focus chain LA [auth C]
OH Query on OH Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain NA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth C]	L [auth A], NA [auth C]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain NA [auth C] Interactions & Density Focus chain L [auth A] Focus chain NA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.212
R-Value Work: 0.184
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.243	α = 90
b = 132.052	β = 90
c = 167.966	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 1.3: 2023-08-30
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-09
Changes: Data collection, Structure summary