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- PDB-6mn6: Crystal structure of the cytosolic domain of human CNNM3 -

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Basic information

Entry
Database: PDB / ID: 6mn6
TitleCrystal structure of the cytosolic domain of human CNNM3
ComponentsMetal transporter CNNM3
KeywordsMETAL TRANSPORT / CNNM3 / Mg2+ transporter / cystathionine-beta-synthase domain / cyclic nucleotide-binding homology domain / open conformation / MEMBRANE PROTEIN
Function / homology
Function and homology information


magnesium ion homeostasis / intracellular manganese ion homeostasis / transmembrane transporter activity / monoatomic ion transport / membrane / plasma membrane / cytoplasm
Similarity search - Function
Ancient conserved domain protein family / Ion transporter-like, CBS domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. ...Ancient conserved domain protein family / Ion transporter-like, CBS domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Metal transporter CNNM3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å
AuthorsChen, Y.S. / Yang, M. / Gehring, K.
CitationJournal: Structure / Year: 2020
Title: Mg2+-ATP Sensing in CNNM, a Putative Magnesium Transporter.
Authors: Chen, Y.S. / Kozlov, G. / Fakih, R. / Yang, M. / Zhang, Z. / Kovrigin, E.L. / Gehring, K.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal transporter CNNM3
B: Metal transporter CNNM3


Theoretical massNumber of molelcules
Total (without water)82,9422
Polymers82,9422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-44 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.063, 128.063, 111.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Metal transporter CNNM3 / Ancient conserved domain-containing protein 3 / Cyclin-M3


Mass: 41470.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM3, ACDP3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NE01

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5; 0.5 M succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6235 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6235 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 12603 / % possible obs: 100 % / Redundancy: 11.9 % / Rsym value: 0.148 / Net I/σ(I): 12.2
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 90 / CC1/2: 0.203 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K23, 6DFD

5k23

6dfd


Resolution: 3.36→49.75 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.263 -5 %
Rwork0.217 --
obs-12603 65.72 %
Refinement stepCycle: LAST / Resolution: 3.36→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 0 0 4551

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