9GKK | pdb_00009gkk

BetP heterotrimeric complex

PDB DOI: https://doi.org/10.2210/pdb9GKK/pdb
EM Map EMD-51422: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Corynebacterium glutamicum
Expression System: Escherichia coli DH5[alpha]
Mutation(s): Yes

Deposited: 2024-08-25 Released: 2025-09-10
Deposition Author(s): Urbansky, K., Fu, L., Madej, M.G., Ziegler, C.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9GKK

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

Literature

Structure of Glycine betaine transporter BetP heterotrimeric complex

Urbansky, K., Fu, L., Madej, M.G., Ziegler, C.

To be published.

Macromolecule Content

Total Structure Weight: 200.33 kDa
Atom Count: 11,878
Modeled Residue Count: 1,525
Deposited Residue Count: 1,809
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine betaine transporter BetP	A, B, C	603	Corynebacterium glutamicum	Mutation(s): 1 Gene Names: betP, Cgl0892, cg1016
UniProt
Find proteins for P54582 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore P54582 Go to UniProtKB: P54582
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54582
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PGT Query on PGT Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C]	J [auth B], M [auth C]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Interactions Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain J [auth B] Focus chain M [auth C]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
XKJ Query on XKJ Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain F [auth A] MOL2 format, chain O [auth C] MOL2 format, chain F [auth A] mmCIF format, chain O [auth C] mmCIF format, chain F [auth A]	F [auth A], O [auth C]	dodecyl beta-D-glucopyranoside C₁₈ H₃₆ O₆ PYIDGJJWBIBVIA-UYTYNIKBSA-N		Interactions Focus chain F [auth A] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain O [auth C]
BET Query on BET Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], N [auth C]	TRIMETHYL GLYCINE C₅ H₁₂ N O₂ KWIUHFFTVRNATP-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B], L [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2025-09-10
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.