7OJF | pdb_00007ojf

CRYO-EM STRUCTURE OF SLYB13-BAMA FROM ESCHERICHIA COLI.

PDB DOI: https://doi.org/10.2210/pdb7OJF/pdb
EM Map EMD-12949: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli BW25113
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2021-05-14 Released: 2022-07-27
Deposition Author(s): Nguyen, V.S., Remaut, H.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains

Janssens, A., Nguyen, V.S., Cecil, A.J., Van der Verren, S.E., Timmerman, E., Deghelt, M., Pak, A.J., Collet, J.F., Impens, F., Remaut, H.

(2023) Nature

DOI: https://doi.org/10.1038/s41586-023-06925-5

Macromolecule Content

Total Structure Weight: 332.07 kDa
Atom Count: 19,318
Modeled Residue Count: 2,319
Deposited Residue Count: 2,825
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane lipoprotein slyB	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	155	Escherichia coli BW25113	Mutation(s): 0 Gene Names: slyB, SFxv_1871

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	N	810	Escherichia coli BW25113	Mutation(s): 0 Gene Names: bamA Membrane Entity: Yes
UniProt
Find proteins for C3TPJ2 (Escherichia coli) Explore C3TPJ2 Go to UniProtKB: C3TPJ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3TPJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L8Z Query on L8Z Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CB [auth K] SDF format, chain FA [auth E] SDF format, chain GB [auth L] SDF format, chain LB [auth M] SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain UA [auth I] SDF format, chain X [auth C] SDF format, chain YA [auth J] SDF format, chain QA [auth H] SDF format, chain MA [auth G] SDF format, chain IA [auth F] MOL2 format, chain BA [auth D] MOL2 format, chain CB [auth K] MOL2 format, chain FA [auth E] MOL2 format, chain GB [auth L] MOL2 format, chain LB [auth M] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth I] MOL2 format, chain X [auth C] MOL2 format, chain YA [auth J] MOL2 format, chain QA [auth H] MOL2 format, chain MA [auth G] MOL2 format, chain IA [auth F] mmCIF format, chain BA [auth D] mmCIF format, chain CB [auth K] mmCIF format, chain FA [auth E] mmCIF format, chain GB [auth L] mmCIF format, chain LB [auth M] mmCIF format, chain P [auth A] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth I] mmCIF format, chain X [auth C] mmCIF format, chain YA [auth J] mmCIF format, chain QA [auth H] mmCIF format, chain MA [auth G] mmCIF format, chain IA [auth F]	BA [auth D] CB [auth K] FA [auth E] GB [auth L] IA [auth F] BA [auth D], CB [auth K], FA [auth E], GB [auth L], IA [auth F], LB [auth M], MA [auth G], P [auth A], QA [auth H], T [auth B], UA [auth I], X [auth C], YA [auth J]	(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(~{E},3~{R})-3-dodecanoyloxytetradec-5-enoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(~{E},3~{R})-3-oxidanyltetradec-11-enoyl]amino]-4-[(~{E},3~{R})-3-oxidanyltetradec-5-enoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(~{E},3~{R})-3-tetradecanoyloxytetradec-7-enoyl]oxy-oxan-2-yl]methoxy]-4,5-bis(oxidanyl)oxane-2-carboxylic acid C₁₀₂ H₁₈₂ N₂ O₃₂ P₂ NOEIKEOYYQLMFH-XTQPGWFYSA-N		Interactions Focus chain BA [auth D] Focus chain CB [auth K] Focus chain FA [auth E] Focus chain GB [auth L] Focus chain IA [auth F] Focus chain LB [auth M] Focus chain MA [auth G] Focus chain P [auth A] Focus chain QA [auth H] Focus chain T [auth B] Focus chain UA [auth I] Focus chain X [auth C] Focus chain YA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain CB [auth K] Focus chain FA [auth E] Focus chain GB [auth L] Focus chain IA [auth F] Focus chain LB [auth M] Focus chain MA [auth G] Focus chain P [auth A] Focus chain QA [auth H] Focus chain T [auth B] Focus chain UA [auth I] Focus chain X [auth C] Focus chain YA [auth J]
LPP Query on LPP Download:Ideal Coordinates CCD File SDF format, chain DB [auth K] SDF format, chain HB [auth L] SDF format, chain JA [auth F] SDF format, chain MB [auth M] SDF format, chain NA [auth G] SDF format, chain Q [auth A] SDF format, chain RA [auth H] SDF format, chain U [auth B] SDF format, chain VA [auth I] SDF format, chain Y [auth C] SDF format, chain ZA [auth J] SDF format, chain CA [auth D] MOL2 format, chain DB [auth K] MOL2 format, chain HB [auth L] MOL2 format, chain JA [auth F] MOL2 format, chain MB [auth M] MOL2 format, chain NA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth I] MOL2 format, chain Y [auth C] MOL2 format, chain ZA [auth J] MOL2 format, chain CA [auth D] mmCIF format, chain DB [auth K] mmCIF format, chain HB [auth L] mmCIF format, chain JA [auth F] mmCIF format, chain MB [auth M] mmCIF format, chain NA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth I] mmCIF format, chain Y [auth C] mmCIF format, chain ZA [auth J] mmCIF format, chain CA [auth D]	CA [auth D] DB [auth K] HB [auth L] JA [auth F] MB [auth M] CA [auth D], DB [auth K], HB [auth L], JA [auth F], MB [auth M], NA [auth G], Q [auth A], RA [auth H], U [auth B], VA [auth I], Y [auth C], ZA [auth J]	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C₃₅ H₆₉ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-N		Interactions Focus chain CA [auth D] Focus chain DB [auth K] Focus chain HB [auth L] Focus chain JA [auth F] Focus chain MB [auth M] Focus chain NA [auth G] Focus chain Q [auth A] Focus chain RA [auth H] Focus chain U [auth B] Focus chain VA [auth I] Focus chain Y [auth C] Focus chain ZA [auth J] Interactions & Density Focus chain CA [auth D] Focus chain DB [auth K] Focus chain HB [auth L] Focus chain JA [auth F] Focus chain MB [auth M] Focus chain NA [auth G] Focus chain Q [auth A] Focus chain RA [auth H] Focus chain U [auth B] Focus chain VA [auth I] Focus chain Y [auth C] Focus chain ZA [auth J]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain FB [auth L] SDF format, chain HA [auth F] SDF format, chain JB [auth M] SDF format, chain LA [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth H] SDF format, chain S [auth B] SDF format, chain TA [auth I] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain WA [auth J] SDF format, chain BB [auth K] MOL2 format, chain EA [auth E] MOL2 format, chain FB [auth L] MOL2 format, chain HA [auth F] MOL2 format, chain JB [auth M] MOL2 format, chain LA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth I] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain WA [auth J] MOL2 format, chain BB [auth K] mmCIF format, chain EA [auth E] mmCIF format, chain FB [auth L] mmCIF format, chain HA [auth F] mmCIF format, chain JB [auth M] mmCIF format, chain LA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth I] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain WA [auth J] mmCIF format, chain BB [auth K]	BB [auth K] EA [auth E] FB [auth L] HA [auth F] JB [auth M] BB [auth K], EA [auth E], FB [auth L], HA [auth F], JB [auth M], LA [auth G], O [auth A], OA [auth H], S [auth B], TA [auth I], V [auth C], WA [auth J], Z [auth D]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain BB [auth K] Focus chain EA [auth E] Focus chain FB [auth L] Focus chain HA [auth F] Focus chain JB [auth M] Focus chain LA [auth G] Focus chain O [auth A] Focus chain OA [auth H] Focus chain S [auth B] Focus chain TA [auth I] Focus chain V [auth C] Focus chain WA [auth J] Focus chain Z [auth D] Interactions & Density Focus chain BB [auth K] Focus chain EA [auth E] Focus chain FB [auth L] Focus chain HA [auth F] Focus chain JB [auth M] Focus chain LA [auth G] Focus chain O [auth A] Focus chain OA [auth H] Focus chain S [auth B] Focus chain TA [auth I] Focus chain V [auth C] Focus chain WA [auth J] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth D] SDF format, chain EB [auth K] SDF format, chain GA [auth E] SDF format, chain IB [auth M] SDF format, chain KA [auth F] SDF format, chain KB [auth M] SDF format, chain PA [auth H] SDF format, chain R [auth A] SDF format, chain SA [auth H] SDF format, chain W [auth C] SDF format, chain XA [auth J] SDF format, chain AB [auth J] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EB [auth K] MOL2 format, chain GA [auth E] MOL2 format, chain IB [auth M] MOL2 format, chain KA [auth F] MOL2 format, chain KB [auth M] MOL2 format, chain PA [auth H] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain XA [auth J] MOL2 format, chain AB [auth J] mmCIF format, chain AA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EB [auth K] mmCIF format, chain GA [auth E] mmCIF format, chain IB [auth M] mmCIF format, chain KA [auth F] mmCIF format, chain KB [auth M] mmCIF format, chain PA [auth H] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain XA [auth J] mmCIF format, chain AB [auth J]	AA [auth D] AB [auth J] DA [auth D] EB [auth K] GA [auth E] AA [auth D], AB [auth J], DA [auth D], EB [auth K], GA [auth E], IB [auth M], KA [auth F], KB [auth M], PA [auth H], R [auth A], SA [auth H], W [auth C], XA [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth J] Focus chain DA [auth D] Focus chain EB [auth K] Focus chain GA [auth E] Focus chain IB [auth M] Focus chain KA [auth F] Focus chain KB [auth M] Focus chain PA [auth H] Focus chain R [auth A] Focus chain SA [auth H] Focus chain W [auth C] Focus chain XA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth J] Focus chain DA [auth D] Focus chain EB [auth K] Focus chain GA [auth E] Focus chain IB [auth M] Focus chain KA [auth F] Focus chain KB [auth M] Focus chain PA [auth H] Focus chain R [auth A] Focus chain SA [auth H] Focus chain W [auth C] Focus chain XA [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Nguyen, V.S.

Remaut, H.

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references
Version 1.2: 2024-11-20
Changes: Structure summary
Version 1.3: 2025-07-02
Changes: Structure summary
Version 1.4: 2025-09-10
Changes: Data collection, Data processing, Experimental preparation