37BR | pdb_000037br

Bacillus subtilis GerAA(A318C):GerAB:GerAC(S56C) bound to D-alanine, in glyco-diosgenin

PDB DOI: https://doi.org/10.2210/pdb37BR/pdb
EM Map EMD-78055: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Bacillus subtilis subsp. subtilis str. 168
Mutation(s): Yes

Deposited: 2026-07-11 Released: 2026-09-30
Deposition Author(s): Cofsky, J.C., Kruse, A.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Helen Hay Whitney Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Bacterial spore nutrient receptors repurpose an ancient transporter as a germination trigger switch

Cofsky, J.C., Kruse, A.C.

To be published.

Macromolecule Content

Total Structure Weight: 695.98 kDa
Atom Count: 46,535
Modeled Residue Count: 5,645
Deposited Residue Count: 6,130
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spore germination protein A1	A, D [auth E], G [auth I], J [auth M], M [auth Q]	505	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 1 Gene Names: gerAA, gerA1, BSU33050
UniProt
Find proteins for P07868 (Bacillus subtilis (strain 168)) Explore P07868 Go to UniProtKB: P07868
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07868
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spore germination protein A2	B, E [auth F], H [auth J], K [auth N], N [auth R]	365	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: gerAB, gerA2, BSU33060
UniProt
Find proteins for P07869 (Bacillus subtilis (strain 168)) Explore P07869 Go to UniProtKB: P07869
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07869
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spore germination protein A3	C, F [auth G], I [auth K], L [auth O], O [auth S]	356	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 1 Gene Names: gerAC, gerA3, BSU33070
UniProt
Find proteins for P07870 (Bacillus subtilis (strain 168)) Explore P07870 Go to UniProtKB: P07870
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07870
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGA Query on DGA Download:Ideal Coordinates CCD File SDF format, chain W [auth G] SDF format, chain S [auth C] SDF format, chain IA [auth S] SDF format, chain EA [auth O] SDF format, chain AA [auth K] MOL2 format, chain W [auth G] MOL2 format, chain S [auth C] MOL2 format, chain IA [auth S] MOL2 format, chain EA [auth O] MOL2 format, chain AA [auth K] mmCIF format, chain W [auth G] mmCIF format, chain S [auth C] mmCIF format, chain IA [auth S] mmCIF format, chain EA [auth O] mmCIF format, chain AA [auth K]	AA [auth K], EA [auth O], IA [auth S], S [auth C], W [auth G]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain AA [auth K] Focus chain EA [auth O] Focus chain IA [auth S] Focus chain S [auth C] Focus chain W [auth G] Interactions & Density Focus chain AA [auth K] Focus chain EA [auth O] Focus chain IA [auth S] Focus chain S [auth C] Focus chain W [auth G]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain X [auth I] SDF format, chain T [auth E] SDF format, chain P [auth A] SDF format, chain FA [auth Q] SDF format, chain BA [auth M] MOL2 format, chain X [auth I] MOL2 format, chain T [auth E] MOL2 format, chain P [auth A] MOL2 format, chain FA [auth Q] MOL2 format, chain BA [auth M] mmCIF format, chain X [auth I] mmCIF format, chain T [auth E] mmCIF format, chain P [auth A] mmCIF format, chain FA [auth Q] mmCIF format, chain BA [auth M]	BA [auth M], FA [auth Q], P [auth A], T [auth E], X [auth I]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain BA [auth M] Focus chain FA [auth Q] Focus chain P [auth A] Focus chain T [auth E] Focus chain X [auth I] Interactions & Density Focus chain BA [auth M] Focus chain FA [auth Q] Focus chain P [auth A] Focus chain T [auth E] Focus chain X [auth I]
DAL (Subject of Investigation/LOI) Query on DAL Download:Ideal Coordinates CCD File SDF format, chain Z [auth J] SDF format, chain V [auth F] SDF format, chain R [auth B] SDF format, chain HA [auth R] SDF format, chain DA [auth N] MOL2 format, chain Z [auth J] MOL2 format, chain V [auth F] MOL2 format, chain R [auth B] MOL2 format, chain HA [auth R] MOL2 format, chain DA [auth N] mmCIF format, chain Z [auth J] mmCIF format, chain V [auth F] mmCIF format, chain R [auth B] mmCIF format, chain HA [auth R] mmCIF format, chain DA [auth N]	DA [auth N], HA [auth R], R [auth B], V [auth F], Z [auth J]	D-ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-UWTATZPHSA-N		Interactions Focus chain DA [auth N] Focus chain HA [auth R] Focus chain R [auth B] Focus chain V [auth F] Focus chain Z [auth J] Interactions & Density Focus chain DA [auth N] Focus chain HA [auth R] Focus chain R [auth B] Focus chain V [auth F] Focus chain Z [auth J]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Y [auth J] SDF format, chain U [auth F] SDF format, chain Q [auth B] SDF format, chain GA [auth R] SDF format, chain CA [auth N] MOL2 format, chain Y [auth J] MOL2 format, chain U [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain GA [auth R] MOL2 format, chain CA [auth N] mmCIF format, chain Y [auth J] mmCIF format, chain U [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain GA [auth R] mmCIF format, chain CA [auth N]	CA [auth N], GA [auth R], Q [auth B], U [auth F], Y [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth N] Focus chain GA [auth R] Focus chain Q [auth B] Focus chain U [auth F] Focus chain Y [auth J] Interactions & Density Focus chain CA [auth N] Focus chain GA [auth R] Focus chain Q [auth B] Focus chain U [auth F] Focus chain Y [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.1
MODEL REFINEMENT	Coot	1.3.1
RECONSTRUCTION	cryoSPARC	5.0.6

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-30

Deposition Author(s):

Cofsky, J.C.

Kruse, A.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R01AI164647
Helen Hay Whitney Foundation	United States	--