9FNN

Cryo-EM structure of the c-di-GMP-saturated 'crown'less Bcs macrocomplex for cellulose secretion in E. coli

PDB DOI: https://doi.org/10.2210/pdb9FNN/pdb
EM Map EMD-50599: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-10 Released: 2024-10-16
Deposition Author(s): Anso, I., Krasteva, P.V.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for synthase activation and cellulose modification in the E. coli Type II Bcs secretion system.

Anso, I., Zouhir, S., Sana, T.G., Krasteva, P.V.

(2024) Nat Commun

DOI: https://doi.org/10.1038/s41467-024-53113-8

Macromolecule Content

Total Structure Weight: 783.24 kDa
Atom Count: 23,714
Modelled Residue Count: 2,895
Deposited Residue Count: 6,948
Unique protein chains: 7

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulose synthase catalytic subunit [UDP-forming]	A	908	Escherichia coli	Mutation(s): 0 Gene Names: bcsA, yhjO, yhjP, b3533, JW5665 EC: 2.4.1.12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic di-GMP-binding protein	B, K [auth X], L [auth Y], M [auth Z]	779	Escherichia coli	Mutation(s): 0 Gene Names: bcsB, A8C65_00280, AC789_1c39010, ACU57_05345, AM464_10380, BHS81_21120, BK292_24560, BON72_13325, BON75_10020, BON76_21165... bcsB, A8C65_00280, AC789_1c39010, ACU57_05345, AM464_10380, BHS81_21120, BK292_24560, BON72_13325, BON75_10020, BON76_21165, BON94_21155, BZL31_14275, C5P01_24165, C9162_26260, CI641_010915, CWS33_18410, D3O91_11715, D9I18_15765, DQF57_09480, E0J34_09745, E0K84_22715, E2127_16410, E2128_18000, E2129_18135, E2134_17800, E5P22_13645, ELV08_08610, F1E03_18495, F1E19_10130, FRV13_18850
UniProt
Find proteins for A0A061KLG7 (Escherichia coli) Explore A0A061KLG7 Go to UniProtKB: A0A061KLG7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A061KLG7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic di-GMP binding protein BcsE	C [auth E], H [auth U]	536	Escherichia coli	Mutation(s): 0 Gene Names: bcsE, yhjS, b3536, JW3504
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulose biosynthesis protein BcsF	D [auth F], G [auth S]	63	Escherichia coli	Mutation(s): 0 Gene Names: bcsF, Z4953, ECs4417
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein	E [auth Q], J [auth W]	250	Escherichia coli	Mutation(s): 0 Gene Names: bcsQ, yhjQ, A8C65_00290, ACU57_05335, BMT91_17060, BON75_10030, BvCmsHHP019_01723, BvCmsSINP011_05061, C2U48_15650, D3O91_11725... bcsQ, yhjQ, A8C65_00290, ACU57_05335, BMT91_17060, BON75_10030, BvCmsHHP019_01723, BvCmsSINP011_05061, C2U48_15650, D3O91_11725, D9H68_14440, D9I18_15755, D9I97_13990, DAH34_22885, DAH37_19450, E2127_16420, E2128_18010, E2129_18145, E2134_17810, EAI42_04085, EC1094V2_71, NCTC10429_00778, NCTC11022_03734, NCTC9058_01652
UniProt
Find proteins for A0A0B1KWQ0 (Escherichia coli) Explore A0A0B1KWQ0 Go to UniProtKB: A0A0B1KWQ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0B1KWQ0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein YhjR	F [auth R], I [auth V]	77	Escherichia coli	Mutation(s): 0 Gene Names: yhjR, b3535, JW3503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulose biosynthesis protein BcsG	N [auth G], O [auth D]	536	Escherichia coli	Mutation(s): 0 Gene Names: bcsG, yhjU, b3538, JW3506
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2E (Subject of Investigation/LOI) Query on C2E Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain S [auth E] SDF format, chain V [auth U] SDF format, chain W [auth U] SDF format, chain P [auth A] SDF format, chain R [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth E] MOL2 format, chain V [auth U] MOL2 format, chain W [auth U] MOL2 format, chain P [auth A] MOL2 format, chain R [auth E]	P [auth A] Q [auth A] R [auth E] S [auth E] V [auth U] P [auth A], Q [auth A], R [auth E], S [auth E], V [auth U], W [auth U]	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C₂₀ H₂₄ N₁₀ O₁₄ P₂ PKFDLKSEZWEFGL-MHARETSRSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth E] Focus chain S [auth E] Focus chain V [auth U] Focus chain W [auth U] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth E] Focus chain S [auth E] Focus chain V [auth U] Focus chain W [auth U]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain T [auth Q] SDF format, chain X [auth W] MOL2 format, chain T [auth Q] MOL2 format, chain X [auth W]	T [auth Q], X [auth W]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain T [auth Q] Focus chain X [auth W] Interactions & Density Focus chain T [auth Q] Focus chain X [auth W]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain U [auth Q] SDF format, chain Y [auth W] MOL2 format, chain U [auth Q] MOL2 format, chain Y [auth W]	U [auth Q], Y [auth W]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain U [auth Q] Focus chain Y [auth W] Interactions & Density Focus chain U [auth Q] Focus chain Y [auth W]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Anso, I.

Krasteva, P.V.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	757507

Revision History (Full details and data files)

Version 1.0: 2024-10-16
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

9FNN

Cryo-EM structure of the c-di-GMP-saturated 'crown'less Bcs macrocomplex for cellulose secretion in E. coli

Structural basis for synthase activation and cellulose modification in the E. coli Type II Bcs secretion system.

Entity ID: 1

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

Entity Groups

Sequence Annotations

Expand

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 6

Entity Groups

Sequence Annotations

Expand

Entity ID: 7

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)