7OJG

CRYO-EM STRUCTURE OF UNDECAMERIC SLYB FROM ESCHERICHIA COLI K12

PDB DOI: https://doi.org/10.2210/pdb7OJG/pdb
EM Map EMD-12950: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli BW25113
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-14 Released: 2022-08-03
Deposition Author(s): Nguyen, V.S., Remaut, H.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 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: 210.48 kDa
Atom Count: 13,255
Modelled Residue Count: 1,518
Deposited Residue Count: 1,705
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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	155	Escherichia coli BW25113	Mutation(s): 0 Gene Names: slyB, SFxv_1871
UniProt
Find proteins for D2AGE2 (Shigella flexneri serotype X (strain 2002017)) Explore D2AGE2 Go to UniProtKB: D2AGE2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2AGE2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L8Z (Subject of Investigation/LOI) Query on L8Z Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain FB [auth H] SDF format, chain HA [auth D] SDF format, chain LB [auth I] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain RB [auth J] SDF format, chain TA [auth F] SDF format, chain V [auth B] SDF format, chain XB [auth K] SDF format, chain ZA [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain FB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain LB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain RB [auth J] MOL2 format, chain TA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain XB [auth K] MOL2 format, chain ZA [auth G]	BA [auth C] FB [auth H] HA [auth D] LB [auth I] N [auth A] BA [auth C], FB [auth H], HA [auth D], LB [auth I], N [auth A], NA [auth E], RB [auth J], TA [auth F], V [auth B], XB [auth K], ZA [auth G]	(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 C] Focus chain FB [auth H] Focus chain HA [auth D] Focus chain LB [auth I] Focus chain N [auth A] Focus chain NA [auth E] Focus chain RB [auth J] Focus chain TA [auth F] Focus chain V [auth B] Focus chain XB [auth K] Focus chain ZA [auth G] Interactions & Density Focus chain BA [auth C] Focus chain FB [auth H] Focus chain HA [auth D] Focus chain LB [auth I] Focus chain N [auth A] Focus chain NA [auth E] Focus chain RB [auth J] Focus chain TA [auth F] Focus chain V [auth B] Focus chain XB [auth K] Focus chain ZA [auth G]
LPP (Subject of Investigation/LOI) Query on LPP Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain CA [auth C] SDF format, chain GB [auth H] SDF format, chain IA [auth D] SDF format, chain MB [auth I] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain SB [auth J] SDF format, chain UA [auth F] SDF format, chain W [auth B] SDF format, chain YB [auth K] MOL2 format, chain AB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain GB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain MB [auth I] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain SB [auth J] MOL2 format, chain UA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain YB [auth K]	AB [auth G] CA [auth C] GB [auth H] IA [auth D] MB [auth I] AB [auth G], CA [auth C], GB [auth H], IA [auth D], MB [auth I], O [auth A], OA [auth E], SB [auth J], UA [auth F], W [auth B], YB [auth K]	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C₃₅ H₆₉ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-N		Interactions Focus chain AB [auth G] Focus chain CA [auth C] Focus chain GB [auth H] Focus chain IA [auth D] Focus chain MB [auth I] Focus chain O [auth A] Focus chain OA [auth E] Focus chain SB [auth J] Focus chain UA [auth F] Focus chain W [auth B] Focus chain YB [auth K] Interactions & Density Focus chain AB [auth G] Focus chain CA [auth C] Focus chain GB [auth H] Focus chain IA [auth D] Focus chain MB [auth I] Focus chain O [auth A] Focus chain OA [auth E] Focus chain SB [auth J] Focus chain UA [auth F] Focus chain W [auth B] Focus chain YB [auth K]
PLM (Subject of Investigation/LOI) Query on PLM Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth H] SDF format, chain CB [auth H] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain EB [auth H] SDF format, chain GA [auth D] SDF format, chain HB [auth I] SDF format, chain IB [auth I] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain KB [auth I] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain NB [auth J] SDF format, chain OB [auth J] SDF format, chain P [auth A] SDF format, chain PA [auth F] SDF format, chain Q [auth A] SDF format, chain QA [auth F] SDF format, chain QB [auth J] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain TB [auth K] SDF format, chain U [auth B] SDF format, chain UB [auth K] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain WB [auth K] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain YA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain HB [auth I] MOL2 format, chain IB [auth I] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain KB [auth I] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NB [auth J] MOL2 format, chain OB [auth J] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain QB [auth J] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain TB [auth K] MOL2 format, chain U [auth B] MOL2 format, chain UB [auth K] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain WB [auth K] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth G]	AA [auth C] BB [auth H] CB [auth H] DA [auth D] EA [auth D] AA [auth C], BB [auth H], CB [auth H], DA [auth D], EA [auth D], EB [auth H], GA [auth D], HB [auth I], IB [auth I], JA [auth E], KA [auth E], KB [auth I], L [auth A], MA [auth E], NB [auth J], OB [auth J], P [auth A], PA [auth F], Q [auth A], QA [auth F], QB [auth J], R [auth B], S [auth B], SA [auth F], TB [auth K], U [auth B], UB [auth K], VA [auth G], WA [auth G], WB [auth K], X [auth C], Y [auth C], YA [auth G]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BB [auth H] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain GA [auth D] Focus chain HB [auth I] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain KB [auth I] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NB [auth J] Focus chain OB [auth J] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain QB [auth J] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain TB [auth K] Focus chain U [auth B] Focus chain UB [auth K] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain WB [auth K] Focus chain X [auth C] Focus chain Y [auth C] Focus chain YA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth H] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain GA [auth D] Focus chain HB [auth I] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain KB [auth I] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NB [auth J] Focus chain OB [auth J] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain QB [auth J] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain TB [auth K] Focus chain U [auth B] Focus chain UB [auth K] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain WB [auth K] Focus chain X [auth C] Focus chain Y [auth C] Focus chain YA [auth G]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain DB [auth H] SDF format, chain FA [auth D] SDF format, chain JB [auth I] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain PB [auth J] SDF format, chain RA [auth F] SDF format, chain T [auth B] SDF format, chain VB [auth K] SDF format, chain XA [auth G] SDF format, chain Z [auth C] MOL2 format, chain DB [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain JB [auth I] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain PB [auth J] MOL2 format, chain RA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain VB [auth K] MOL2 format, chain XA [auth G] MOL2 format, chain Z [auth C]	DB [auth H] FA [auth D] JB [auth I] LA [auth E] M [auth A] DB [auth H], FA [auth D], JB [auth I], LA [auth E], M [auth A], PB [auth J], RA [auth F], T [auth B], VB [auth K], XA [auth G], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DB [auth H] Focus chain FA [auth D] Focus chain JB [auth I] Focus chain LA [auth E] Focus chain M [auth A] Focus chain PB [auth J] Focus chain RA [auth F] Focus chain T [auth B] Focus chain VB [auth K] Focus chain XA [auth G] Focus chain Z [auth C] Interactions & Density Focus chain DB [auth H] Focus chain FA [auth D] Focus chain JB [auth I] Focus chain LA [auth E] Focus chain M [auth A] Focus chain PB [auth J] Focus chain RA [auth F] Focus chain T [auth B] Focus chain VB [auth K] Focus chain XA [auth G] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 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

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-03

Deposition Author(s):

Nguyen, V.S.

Remaut, H.

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0G0818N
Research Foundation - Flanders (FWO)	Belgium	G0H5916N
Research Foundation - Flanders (FWO)	Belgium	FWOTM903
Research Foundation - Flanders (FWO)	Belgium	12ZM421N