6CTF | pdb_00006ctf

Crystal structure of GltPh fast mutant - R276S/M395R

PDB DOI: https://doi.org/10.2210/pdb6CTF/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2018-03-23 Released: 2018-10-10
Deposition Author(s): Boudker, O., Oh, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.05 Å
R-Value Free:
0.266 (Depositor), 0.268 (DCC)
R-Value Work:
0.222 (Depositor), 0.226 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Kinetic mechanism of coupled binding in sodium-aspartate symporter GltPh.

Oh, S., Boudker, O.

(2018) Elife 7

PubMed: 30255846 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.37291
Primary Citation Related Structures:
6CTF

PubMed Abstract:
Many secondary active membrane transporters pump substrates against concentration gradients by coupling their uptake to symport of sodium ions. Symport requires the substrate and ions to be always transported together. Cooperative binding of the solutes is a key mechanism contributing to coupled transport in the sodium and aspartate symporter from Pyrococcus horikoshii Glt _Ph. Here, we describe the kinetic mechanism of coupled binding for Glt _Ph in the inward facing state. The first of the three coupled sodium ions, binds weakly and slowly, enabling the protein to accept the rest of the ions and the substrate. The last ion binds tightly, but is in rapid equilibrium with solution. Its release is required for the complex disassembly. Thus, the first ion serves to 'open the door' for the substrate, the last ion 'locks the door' once the substrate is in, and one ion contributes to both events.

Organizational Affiliation

Department of Physiology & Biophysics, Weill Cornell Medicine, Cornell University, New York, United States.

Macromolecule Content

Total Structure Weight: 130.51 kDa
Atom Count: 9,171
Modeled Residue Count: 1,233
Deposited Residue Count: 1,233
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate transporter homolog	A, B, C	411	Pyrococcus horikoshii OT3	Mutation(s): 2 Gene Names: PH1295 Membrane Entity: Yes
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASP Query on ASP Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B], J [auth C]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.05 Å
R-Value Free: 0.266 (Depositor), 0.268 (DCC)
R-Value Work: 0.222 (Depositor), 0.226 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.475	α = 90
b = 196.42	β = 90
c = 194.328	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-10

Deposition Author(s):

Boudker, O.

Oh, S.

Funding Organization	Location	Grant Number
	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-10-10
Type: Initial release
Version 1.1: 2018-10-31
Changes: Data collection, Database references, Structure summary
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary