7A0W

Structure of dimeric sodium proton antiporter NhaA, at pH 8.5, crystallized with chimeric Fab antibodies

• PDB DOI: https://doi.org/10.2210/pdb7A0W/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., Gross, N.M., Mir, S.H., Wirth, C., Hunte, C.
• Funding Organization(s): German Research Foundation (DFG), European Communitys Seventh Framework Programme

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.235 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Starting Models: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B2C1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 189.38 kDa 
• Atom Count: 12,332 
• Modelled Residue Count: 1,593 
• Deposited Residue Count: 1,736 
• Unique protein chains: 3

Macromolecules

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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	G [auth A]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PH	H [auth A], K [auth B], L [auth B], M [auth B]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C39 H77 O8 P YFWHNAWEOZTIPI-DIPNUNPCSA-N
PG4	J [auth A], O [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	I [auth A], N [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	P [auth C], Q [auth C], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.235 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.788	α = 90
b = 92.163	β = 109.885
c = 139.105	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

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Fippel, A., Gross, N.M., Mir, S.H., Wirth, C., Hunte, C.

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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 403222702
German Research Foundation (DFG)	Germany	CRC - 746
European Communitys Seventh Framework Programme	European Union	EDICT - HEALTH-F4-2007-201924

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary