9I6D | pdb_00009i6d

Glutamate transporter homologue GltPh mutant P206R in Complex with L-Aspartate and Sodium Ions in Salipro

PDB DOI: https://doi.org/10.2210/pdb9I6D/pdb
EM Map EMD-52653: EMDB EMDataResource

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

Deposited: 2025-01-29 Released: 2026-02-18
Deposition Author(s): Horn, G., Overa, C., Fu, L., Urbansky, K., Madej, M.G., Ziegler, C.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.34 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

CryoEM Structure of Glutamate transporter homologue GltPh mutant P206R in complex with L-Aspartate and Sodium ions in Salipro

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

To be published.

Macromolecule Content

Total Structure Weight: 140.48 kDa
Atom Count: 9,387
Modeled Residue Count: 1,224
Deposited Residue Count: 1,275
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate transporter homolog	A, B, C	425	Pyrococcus horikoshii	Mutation(s): 1 Gene Names: PH1295
UniProt
Find proteins for O59010 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59010 Go to UniProtKB: O59010
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O59010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D3D (Subject of Investigation/LOI) Query on D3D Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth C] SDF format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth B]	J [auth A], Q [auth B], R [auth C]	(19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-UCZVXENKSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth C] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth C]
PG8 (Subject of Investigation/LOI) Query on PG8 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain U [auth C] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain U [auth C]	F [auth A], M [auth B], U [auth C]	1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL) C₂₂ H₄₂ O₁₀ P BQEXNLVNNRZNEI-WOJBJXKFSA-M		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain U [auth C]
PGM (Subject of Investigation/LOI) Query on PGM Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain V [auth C] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C] mmCIF format, chain G [auth A]	G [auth A], N [auth B], V [auth C]	1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)] C₂₂ H₄₄ O₉ P BVJSKAUUFXBDOB-SFTDATJTSA-M		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain V [auth C]
ASP (Subject of Investigation/LOI) Query on ASP Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain S [auth C] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain S [auth C] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B], S [auth C]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain S [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain O [auth B] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A]	H [auth A] I [auth A] O [auth B] P [auth B] W [auth C] H [auth A], I [auth A], O [auth B], P [auth B], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain T [auth C] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth C] mmCIF format, chain E [auth A]	E [auth A], L [auth B], T [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.34 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	REFMAC	5

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	2518

Revision History (Full details and data files)

Version 1.0: 2026-02-18
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.