9P1U | pdb_00009p1u

beta-barrel assembly machine from Escherichia coli in an late state of LptD assembly

PDB DOI: https://doi.org/10.2210/pdb9P1U/pdb
EM Map EMD-71134: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-06-10 Released: 2026-03-11
Deposition Author(s): Thomson, B.D., Marquez, M.D., Kahne, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structures of folding intermediates on BAM show diverse substrates fold by a uniform mechanism

Thomson, B.D., Marquez, M.D., Rawson, S., dos Santos, T.M.A., Harrison, S.C., Kahne, D.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.10.16.682720

Macromolecule Content

Total Structure Weight: 325.14 kDa
Atom Count: 15,852
Modeled Residue Count: 2,080
Deposited Residue Count: 2,924
Unique protein chains: 7

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamC	A [auth C]	344	Escherichia coli	Mutation(s): 0 Gene Names: bamC, dapX, nlpB, b2477, JW2462
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12)) Explore P0A903 Go to UniProtKB: P0A903
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A903
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamD	B [auth D]	245	Escherichia coli	Mutation(s): 0 Gene Names: bamD, yfiO, b2595, JW2577
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12)) Explore P0AC02 Go to UniProtKB: P0AC02
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AC02
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamE	C [auth E]	113	Escherichia coli	Mutation(s): 0 Gene Names: bamE, smpA, b2617, JW2598
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12)) Explore P0A937 Go to UniProtKB: P0A937
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A937
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly lipoprotein LptE	D [auth G]	193	Escherichia coli	Mutation(s): 0 Gene Names: lptE, rlpB, b0641, JW0636
UniProt
Find proteins for P0ADC1 (Escherichia coli (strain K12)) Explore P0ADC1 Go to UniProtKB: P0ADC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ADC1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly protein LptD	E [auth F]	819	Escherichia coli	Mutation(s): 1 Gene Names: lptD, imp, ostA, yabG, b0054, JW0053
UniProt
Find proteins for P31554 (Escherichia coli (strain K12)) Explore P31554 Go to UniProtKB: P31554
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31554
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamB	F [auth B]	392	Escherichia coli	Mutation(s): 0 Gene Names: bamB, yfgL, b2512, JW2496
UniProt
Find proteins for P77774 (Escherichia coli (strain K12)) Explore P77774 Go to UniProtKB: P77774
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P77774
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	G [auth A]	818	Escherichia coli	Mutation(s): 1 Gene Names: bamA, yaeT, yzzN, yzzY, b0177, JW0172
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12)) Explore P0A940 Go to UniProtKB: P0A940
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A940
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-11

Deposition Author(s):

Thomson, B.D.

Marquez, M.D.

Kahne, D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI081059
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI158028