2IUB

Crystal structure of a divalent metal ion transporter CorA at 2.9 A resolution.

PDB DOI: https://doi.org/10.2210/pdb2IUB/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2006-06-01 Released: 2006-08-03
Deposition Author(s): Eshaghi, S., Niegowski, D., Kohl, A., Martinez Molina, D., Lesley, S.A., Nordlund, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.291 (Depositor), 0.290 (DCC)
R-Value Work:
0.260 (Depositor), 0.260 (DCC)
R-Value Observed:
0.262 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Divalent Metal Ion Transporter Cora at 2.9 Angstrom Resolution.

Eshaghi, S., Niegowski, D., Kohl, A., Martinez Molina, D., Lesley, S.A., Nordlund, P.

(2006) Science 313: 354

PubMed: 16857941 Search on PubMed
DOI: https://doi.org/10.1126/science.1127121
Primary Citation of Related Structures:
2IUB

PubMed Abstract:
CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone-shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg2+ and Co2+. The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.

Organizational Affiliation

Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden. Said.Eshaghi@ki.se

Macromolecule Content

Total Structure Weight: 430.36 kDa
Atom Count: 27,580
Modelled Residue Count: 3,353
Deposited Residue Count: 3,630
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIVALENT CATION TRANSPORT-RELATED PROTEIN	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	363	Thermotoga maritima	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9WZ31 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZ31 Go to UniProtKB: Q9WZ31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WZ31
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain AA [auth F] SDF format, chain EA [auth G] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	AA [auth F] DA [auth G] EA [auth G] K [auth A] N [auth B] AA [auth F], DA [auth G], EA [auth G], K [auth A], N [auth B], R [auth D], S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain S [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain JA [auth J] SDF format, chain M [auth A] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain HA [auth G] SDF format, chain IA [auth H] SDF format, chain KA [auth J] SDF format, chain L [auth A] SDF format, chain LA [auth J] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain JA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain KA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain JA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain KA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F]	BA [auth F] CA [auth F] FA [auth G] GA [auth G] HA [auth G] BA [auth F], CA [auth F], FA [auth G], GA [auth G], HA [auth G], IA [auth H], JA [auth J], KA [auth J], L [auth A], LA [auth J], M [auth A], O [auth B], P [auth C], Q [auth C], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth H] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain L [auth A] Focus chain LA [auth J] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth H] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain L [auth A] Focus chain LA [auth J] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.291 (Depositor), 0.290 (DCC)
R-Value Work: 0.260 (Depositor), 0.260 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.23	α = 90
b = 151.46	β = 98.88
c = 143.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-08-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-03
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description