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- PDB-6rs2: Structure of the Bateman module of human CNNM4. -

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Basic information

Entry
Database: PDB / ID: 6rs2
TitleStructure of the Bateman module of human CNNM4.
ComponentsMetal transporter CNNM4
KeywordsTRANSPORT PROTEIN / Cyclin M4 / ACDP4 / Magnesium / Transporter / Jalili syndrome / Magnesium absorption / Magnesium homeostasis / metal transport
Function / homology
Function and homology information


sodium ion transmembrane transporter activity / magnesium ion transport / magnesium ion homeostasis / magnesium ion transmembrane transporter activity / enamel mineralization / intracellular monoatomic cation homeostasis / visual perception / basolateral plasma membrane / protein-containing complex / plasma membrane
Similarity search - Function
Ancient conserved domain protein family / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain ...Ancient conserved domain protein family / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Roll / Alpha Beta
Similarity search - Domain/homology
Metal transporter CNNM4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.694 Å
AuthorsCorral-Rodriguez, M.A. / Stuiver, M. / Gomez-Garcia, I. / Oyenarte, I. / Gimenez, P. / Ereno-Orbea, J. / Diercks, T. / Muller, D. / Martinez-Cruz, L.A.
Funding support Spain, 5items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-77408-R Spain
Spanish Ministry of Economy and CompetitivenessBFU2013-47531-R Spain
Spanish Ministry of Economy and CompetitivenessCSD2008-00005 Spain
Spanish Ministry of Economy and CompetitivenessSEV-2016-0644 Spain
Spanish Ministry of Economy and CompetitivenessBES-2014-068464 Spain
Citation
Journal: Int J Mol Sci / Year: 2019
Title: Structural Insights into the Intracellular Region of the Human Magnesium Transport Mediator CNNM4.
Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Gonzalez-Recio, I. / Fernandez-Rodriguez, C. / Corral-Rodriguez, M.A. / Campos-Zarraga, I. / Simon, J. / Kostantin, E. / Hardy, S. / Diaz Quintana, A. ...Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Gonzalez-Recio, I. / Fernandez-Rodriguez, C. / Corral-Rodriguez, M.A. / Campos-Zarraga, I. / Simon, J. / Kostantin, E. / Hardy, S. / Diaz Quintana, A. / Zubillaga Lizeaga, M. / Merino, N. / Diercks, T. / Blanco, F.J. / Diaz Moreno, I. / Martinez-Chantar, M.L. / Tremblay, M.L. / Muller, D. / Siliqi, D. / Martinez-Cruz, L.A.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Structural Basis of the Oncogenic Interaction of Phosphatase PRL-1 with the Magnesium Transporter CNNM2.
Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Hardy, S. / Breiderhoff, T. / Stuiver, M. / Kostantin, E. / Diercks, T. / Pey, A.L. / Ereno-Orbea, J. / Martinez-Chantar, M.L. / Khalaf-Nazzal, R. / ...Authors: Gimenez-Mascarell, P. / Oyenarte, I. / Hardy, S. / Breiderhoff, T. / Stuiver, M. / Kostantin, E. / Diercks, T. / Pey, A.L. / Ereno-Orbea, J. / Martinez-Chantar, M.L. / Khalaf-Nazzal, R. / Claverie-Martin, F. / Muller, D. / Tremblay, M.L. / Martinez-Cruz, L.A.
#2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: Purification, crystallization and preliminary crystallographic analysis of the CBS-domain pair of cyclin M2 (CNNM2).
Authors: Gomez-Garcia, I. / Stuiver, M. / Ereno, J. / Oyenarte, I. / Corral-Rodriguez, M.A. / Muller, D. / Martinez-Cruz, L.A.
#3: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2011
Title: Purification, crystallization and preliminary crystallographic analysis of the CBS pair of the human metal transporter CNNM4.
Authors: Gomez Garcia, I. / Oyenarte, I. / Martinez-Cruz, L.A.
#4: Journal: Biochem. J. / Year: 2014
Title: Nucleotide binding triggers a conformational change of the CBS module of the magnesium transporter CNNM2 from a twisted towards a flat structure.
Authors: Corral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / de Opakua, A.I. / Blanco, F.J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / ...Authors: Corral-Rodriguez, M.A. / Stuiver, M. / Abascal-Palacios, G. / Diercks, T. / Oyenarte, I. / Ereno-Orbea, J. / de Opakua, A.I. / Blanco, F.J. / Encinar, J.A. / Spiwok, V. / Terashima, H. / Accardi, A. / Muller, D. / Martinez-Cruz, L.A.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionJul 15, 2020ID: 4IY3
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
B: Metal transporter CNNM4
C: Metal transporter CNNM4
D: Metal transporter CNNM4
A: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)70,5524
Polymers70,5524
Non-polymers00
Water00
1
B: Metal transporter CNNM4
C: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)35,2762
Polymers35,2762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-27 kcal/mol
Surface area15650 Å2
MethodPISA
2
D: Metal transporter CNNM4
A: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)35,2762
Polymers35,2762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-25 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.392, 141.363, 87.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Metal transporter CNNM4 / Ancient conserved domain-containing protein 4 / Cyclin-M4


Mass: 17638.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM4, ACDP4, KIAA1592 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6P4Q7

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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: 4.12 Å3/Da / Density % sol: 70.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 4 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.69→43.949 Å / Num. obs: 11864 / % possible obs: 98.7 % / Redundancy: 5.3 % / CC1/2: 0.99 / Rpim(I) all: 0.023 / Rrim(I) all: 0.052 / Rsym value: 0.047 / Net I/σ(I): 21
Reflection shellResolution: 3.69→3.76 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 11864 / CC1/2: 0.91 / Rpim(I) all: 0.209 / Rrim(I) all: 0.485 / Rsym value: 0.437 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KPB

3kpb


Resolution: 3.694→43.949 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.56
RfactorNum. reflection% reflection
Rfree0.2762 1178 9.96 %
Rwork0.2289 --
obs0.2337 11826 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.694→43.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 0 0 4559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044644
X-RAY DIFFRACTIONf_angle_d0.6836290
X-RAY DIFFRACTIONf_dihedral_angle_d12.1512822
X-RAY DIFFRACTIONf_chiral_restr0.046750
X-RAY DIFFRACTIONf_plane_restr0.005804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6942-3.86230.34611360.27631224X-RAY DIFFRACTION92
3.8623-4.06580.23941470.24211338X-RAY DIFFRACTION99
4.0658-4.32030.3241490.22411345X-RAY DIFFRACTION100
4.3203-4.65350.27611510.2151346X-RAY DIFFRACTION100
4.6535-5.12120.30511530.19951341X-RAY DIFFRACTION100
5.1212-5.86080.2871490.24021337X-RAY DIFFRACTION100
5.8608-7.37830.29681480.28051365X-RAY DIFFRACTION100
7.3783-43.95210.23021450.20711352X-RAY DIFFRACTION97

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