7A0X

Structure of dimeric sodium proton antiporter NhaA, at pH 6.0, crystallized with chimeric Fab antibodies

PDB DOI: https://doi.org/10.2210/pdb7A0X/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, Gallus gallus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2020-08-11 Released: 2022-02-23
Deposition Author(s): Fippel, A., Lentes, C.J., Mir, S.H., Wirth, C., Hunte, C.
Funding Organization(s): German Research Foundation (DFG), European Communitys Seventh Framework Programme

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.241
R-Value Work: 0.205
R-Value Observed: 0.206

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Molecular determinants for substrate uptake in electrogenic sodium/proton antiporters

Fippel, A., Mir, S.H., Wirth, C., Gross, N.M., Lentes, C.J., Bialas, E., Frank, F., Ulbrich, M.H., Andrade, S.L.A., Kulik, A., Hunte, C.

To be published.

Macromolecule Content

Total Structure Weight: 189.86 kDa
Atom Count: 12,318
Modelled Residue Count: 1,592
Deposited Residue Count: 1,736
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)/H(+) antiporter NhaA	A, B	406	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: nhaA, STM0039 Membrane Entity: Yes
UniProt
Find proteins for Q8ZRZ3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZRZ3 Go to UniProtKB: Q8ZRZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZRZ3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain	C, E	252	Gallus gallus, Homo sapiens This entity is chimeric	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain	D, F	210	Gallus gallus, Homo sapiens This entity is chimeric	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 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]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
3PH Query on 3PH Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B]	H [auth A], K [auth B], L [auth B]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain O [auth B]	J [auth A], O [auth B], R [auth E], S [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Focus chain R [auth E] Focus chain S [auth E] Interactions & Density Focus chain J [auth A] Focus chain O [auth B] Focus chain R [auth E] Focus chain S [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B]	I [auth A], N [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain U [auth F] MOL2 format, chain U [auth F]	U [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain U [auth F] Interactions & Density Focus chain U [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth F] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth F]	P [auth C], Q [auth C], T [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth F] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.241
R-Value Work: 0.205
R-Value Observed: 0.206
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.01	α = 90
b = 91.713	β = 109.798
c = 139.997	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
STARANISO	data scaling
XDS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-02-23

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	BIOSS - EXC-294
German Research Foundation (DFG)	Germany	CIBSS - EXC-2189 - Project ID 390939984
German Research Foundation (DFG)	Germany	CRC - 1381 - Project ID ID 403222702
German Research Foundation (DFG)	Germany	CRC - 746
European Communitys Seventh Framework Programme	European Union	EDICT - HEALTH-F4-2007-201924

Revision History (Full details and data files)

Version 1.0: 2022-02-23
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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Help and Resources

7A0X

Structure of dimeric sodium proton antiporter NhaA, at pH 6.0, crystallized with chimeric Fab antibodies

Molecular determinants for substrate uptake in electrogenic sodium/proton antiporters

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)