7M1T | pdb_00007m1t

Crystal structure of an archaeal CNNM, MtCorB, with C-terminal deletion in complex with Mg2+-ATP

PDB DOI: https://doi.org/10.2210/pdb7M1T/pdb
Entry: 7M1T supersedes: 7LJ7

Classification: MEMBRANE PROTEIN
Organism(s): Methanoculleus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2021-03-15 Released: 2021-06-16
Deposition Author(s): Chen, Y.S., Kozlov, G., Gehring, K.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free:
0.267 (Depositor), 0.267 (DCC)
R-Value Work:
0.226 (Depositor), 0.228 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an archaeal CorB magnesium transporter.

Chen, Y.S., Kozlov, G., Moeller, B.E., Rohaim, A., Fakih, R., Roux, B., Burke, J.E., Gehring, K.

(2021) Nat Commun 12: 4028-4028

PubMed: 34188059 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-24282-7
Primary Citation Related Structures:
7M1T, 7M1U, 7MSU

PubMed Abstract:
CNNM/CorB proteins are a broadly conserved family of integral membrane proteins with close to 90,000 protein sequences known. They are associated with Mg ²⁺ transport but it is not known if they mediate transport themselves or regulate other transporters. Here, we determine the crystal structure of an archaeal CorB protein in two conformations (apo and Mg ²⁺-ATP bound). The transmembrane DUF21 domain exists in an inward-facing conformation with a Mg ²⁺ ion coordinated by a conserved π-helix. In the absence of Mg ²⁺-ATP, the CBS-pair domain adopts an elongated dimeric configuration with previously unobserved domain-domain contacts. Hydrogen-deuterium exchange mass spectrometry, analytical ultracentrifugation, and molecular dynamics experiments support a role of the structural rearrangements in mediating Mg ²⁺-ATP sensing. Lastly, we use an in vitro, liposome-based assay to demonstrate direct Mg ²⁺ transport by CorB proteins. These structural and functional insights provide a framework for understanding function of CNNMs in Mg ²⁺ transport and associated diseases.

Organizational Affiliation

Department of Biochemistry & Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.

Macromolecule Content

Total Structure Weight: 79.18 kDa
Atom Count: 5,085
Modeled Residue Count: 637
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin, contains CBS domains	A, B	326	Methanoculleus thermophilus	Mutation(s): 0 Gene Names: SAMN04488571_101329 Membrane Entity: Yes
UniProt
Find proteins for A0A1G8XA46 (Methanoculleus thermophilus) Explore A0A1G8XA46 Go to UniProtKB: A0A1G8XA46
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1G8XA46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain T [auth B] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B]	J [auth A], T [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain T [auth B] Interactions & Density Focus chain J [auth A] Focus chain T [auth B]
UMQ Query on UMQ Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain D [auth A]	D [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free: 0.267 (Depositor), 0.267 (DCC)
R-Value Work: 0.226 (Depositor), 0.228 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.05	α = 90
b = 118.676	β = 90
c = 177.305	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-16

Deposition Author(s):

Chen, Y.S.

Kozlov, G.

Gehring, K.

This entry supersedes: 7LJ7

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2020-07195

Revision History (Full details and data files)

Version 1.0: 2021-06-16
Type: Initial release
Version 1.1: 2021-07-07
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description