9N2D | pdb_00009n2d

Cryo-EM structure of an extended F. johnsoniae BAM complex, composite map

PDB DOI: https://doi.org/10.2210/pdb9N2D/pdb
EM Map EMD-48835: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Flavobacterium johnsoniae UW101
Mutation(s): No

Deposited: 2025-01-28 Released: 2025-07-09
Deposition Author(s): Deme, J.C., Lea, S.M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 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

An extended BAM complex in the Bacteroidota

Liu, X., Orenday Tapia, L., Deme, J.C., Lea, S.M., Berks, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 312.24 kDa
Atom Count: 18,488
Modeled Residue Count: 2,284
Deposited Residue Count: 2,727
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bam D	A [auth F]	264	Flavobacterium johnsoniae UW101	Mutation(s): 0
UniProt
Find proteins for A5FE81 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FE81 Go to UniProtKB: A5FE81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5FE81
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bam A	B [auth A]	900	Flavobacterium johnsoniae UW101	Mutation(s): 0
UniProt
Find proteins for A5FJ90 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FJ90 Go to UniProtKB: A5FJ90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5FJ90
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bam H	C	517	Flavobacterium johnsoniae UW101	Mutation(s): 0
UniProt
Find proteins for A5FLQ8 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FLQ8 Go to UniProtKB: A5FLQ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5FLQ8
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Bam G	D [auth B]	409	Flavobacterium johnsoniae UW101	Mutation(s): 0
UniProt
Find proteins for A5FK27 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FK27 Go to UniProtKB: A5FK27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5FK27
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Bam M	E [auth D]	388	Flavobacterium johnsoniae UW101	Mutation(s): 0
UniProt
Find proteins for A5FNX9 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FNX9 Go to UniProtKB: A5FNX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5FNX9
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Bam P	F [auth E]	249	Flavobacterium johnsoniae UW101	Mutation(s): 0
UniProt
Find proteins for A5FJ21 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FJ21 Go to UniProtKB: A5FJ21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5FJ21
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Reference Sequence

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranuronic acid-(1-2)-[alpha-D-mannopyranose-(1-4)]beta-D-galactopyranose	G [auth J]	3		N/A	Interactions Focus chain G [auth J] Interactions & Density Focus chain G [auth J]

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranuronic acid-(1-2)-beta-D-galactopyranose	H [auth G]	2		N/A	Interactions Focus chain H [auth G] Interactions & Density Focus chain H [auth G]

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JSG Query on JSG Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid C₁₃₁ H₂₄₀ N₂ O₆₃ P₄ MVYTXVAKEAWEGM-SMTLFHDCSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
DGA Query on DGA Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	O [auth D] P [auth D] Q [auth D] R [auth D] S [auth D] O [auth D], P [auth D], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]