9VDC | pdb_00009vdc

Cryo-EM structure of the aspartate:alanine antiporter AspT WT

PDB DOI: https://doi.org/10.2210/pdb9VDC/pdb
EM Map EMD-64982: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Tetragenococcus halophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-06-08 Released: 2025-08-06
Deposition Author(s): Nanatani, K., Kanno, R., Kawabata, T., Watanabe, S., Hidaka, M., Yamanaka, T., Toda, K., Fujiki, T., Kunii, K., Miyamoto, A., Chiba, F., Ogasawara, S., Murata, T., Humbel, B.M., Inaba, K., Mitsuoka, K., Guan, L., Abe, K., Yamamoto, M., Koshiba, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

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

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure and molecular mechanism of the aspartate:alanine antiporter AspT from Tetragenococcus halophilus

Nanatani, K., Kanno, R., Kawabata, T., Watanabe, S., Hidaka, M., Yamanaka, T., Toda, K., Fujiki, T., Kunii, K., Miyamoto, A., Chiba, F., Ogasawara, S., Murata, T., Humbel, B.M., Inaba, K., Mitsuoka, K., Guan, L., Abe, K., Yamamoto, M., Koshiba, S.

To be published.

Macromolecule Content

Total Structure Weight: 116.43 kDa
Atom Count: 8,097
Modeled Residue Count: 1,089
Deposited Residue Count: 1,098
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate/alanine antiporter	A, B	549	Tetragenococcus halophilus	Mutation(s): 0 Gene Names: aspT
UniProt
Find proteins for Q8L3K8 (Tetragenococcus halophilus) Explore Q8L3K8 Go to UniProtKB: Q8L3K8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8L3K8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASP (Subject of Investigation/LOI) Query on ASP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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	1.21.1_5286:
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16K07653
Japan Society for the Promotion of Science (JSPS)	Japan	20K05779
Japan Society for the Promotion of Science (JSPS)	Japan	23K05004
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121019
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121038