5A1S | pdb_00005a1s

Crystal structure of the sodium-dependent citrate symporter SeCitS form Salmonella enterica.

PDB DOI: https://doi.org/10.2210/pdb5A1S/pdb

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

Deposited: 2015-05-05 Released: 2016-02-17
Deposition Author(s): Woehlert, D., Groetzinger, M.J., Kuhlbrandt, W., Yildiz, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.246 (Depositor), 0.247 (DCC)
R-Value Work:
0.208 (Depositor), 0.212 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanism of Na(+)-dependent citrate transport from the structure of an asymmetrical CitS dimer.

Wohlert, D., Grotzinger, M.J., Kuhlbrandt, W., Yildiz, O.

(2015) Elife 4: e09375-e09375

PubMed: 26636752 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.09375
Primary Citation Related Structures:
5A1S

PubMed Abstract:
The common human pathogen Salmonella enterica takes up citrate as a nutrient via the sodium symporter SeCitS. Uniquely, our 2.5 Å x-ray structure of the SeCitS dimer shows three different conformations of the active protomer. One protomer is in the outside-facing state. Two are in different inside-facing states. All three states resolve the substrates in their respective binding environments. Together with comprehensive functional studies on reconstituted proteoliposomes, the structures explain the transport mechanism in detail. Our results indicate a six-step process, with a rigid-body 31° rotation of a helix bundle that translocates the bound substrates by 16 Å across the membrane. Similar transport mechanisms may apply to a wide variety of related and unrelated secondary transporters, including important drug targets.

Organizational Affiliation

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 195.95 kDa
Atom Count: 13,270
Modeled Residue Count: 1,721
Deposited Residue Count: 1,792
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CITRATE-SODIUM SYMPORTER	A, B, C, D	448	Salmonella enterica	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain N [auth A] SDF format, chain H [auth A] SDF format, chain DA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain N [auth A] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain N [auth A] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth D]	DA [auth D], H [auth A], N [auth A], U [auth C], V [auth C]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain N [auth A] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain N [auth A] Focus chain U [auth C] Focus chain V [auth C]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain CA [auth D]	CA [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Interactions & Density Focus chain CA [auth D]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain G [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain G [auth A]	G [auth A] K [auth A] L [auth A] P [auth B] Q [auth B] G [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], T [auth C], Y [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain Y [auth D]
UND Query on UND Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain I [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain I [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain I [auth A]	I [auth A], Z [auth D]	UNDECANE C₁₁ H₂₄ RSJKGSCJYJTIGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D], BA [auth D], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] O [auth B] R [auth C] S [auth C] E [auth A], F [auth A], O [auth B], R [auth C], S [auth C], W [auth D], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246 (Depositor), 0.247 (DCC)
R-Value Work: 0.208 (Depositor), 0.212 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.382	α = 90.44
b = 89.935	β = 113.79
c = 91.843	γ = 99.55

Software Package:

Software Name	Purpose
PARROT	model building
Aimless	data scaling
SHELXD	phasing
CRANK2	phasing
PARROT	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-17
Type: Initial release
Version 1.1: 2017-03-22
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Structure summary