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- PDB-6g52: CRYSTAL STRUCTURE OF THE CNMP BINDING DOMAIN OF THE MAGNESIUM TRA... -

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Basic information

Entry
Database: PDB / ID: 6g52
TitleCRYSTAL STRUCTURE OF THE CNMP BINDING DOMAIN OF THE MAGNESIUM TRANSPORTER CNNM4
ComponentsMetal transporter CNNM4
KeywordsMETAL TRANSPORT / CYCLIN M4 / ACDP4 / MAGNESIUM / TRANSPORTER / JALILI SYNDROME / MAGNESIUM ABSORPTION / MAGNESIUM HOMEOSTASIS
Function / homology
Function and homology information


sodium ion transmembrane transporter activity / magnesium ion transport / magnesium ion homeostasis / enamel mineralization / intracellular monoatomic cation homeostasis / magnesium ion transmembrane transporter activity / visual perception / basolateral plasma membrane / protein-containing complex / plasma membrane
Similarity search - Function
Metal transporter CNNM4-like, immunoglobulin-like 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 superfamily / CBS domain / CBS domain / CBS domain profile. ...Metal transporter CNNM4-like, immunoglobulin-like 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 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
Similarity search - Domain/homology
Metal transporter CNNM4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.691 Å
AuthorsGimenez, P. / Oyenarte, I. / Hardy, S. / Zubillaga, M. / Merino, N. / Blanco, F.J. / Siliqi, D. / Tremblay, M. / Muller, D. / Martinez-Cruz, L.A.
Funding support Spain, 5items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2013-47531-R Spain
Spanish Ministry of Economy and CompetitivenessBFU2016-77408-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
DepositionMar 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_seq_map_depositor_info
Item: _audit_author.name / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Dec 25, 2019Group: 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
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
I: Metal transporter CNNM4
B: Metal transporter CNNM4
C: Metal transporter CNNM4
D: Metal transporter CNNM4
E: Metal transporter CNNM4
F: Metal transporter CNNM4
G: Metal transporter CNNM4
H: Metal transporter CNNM4
A: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)192,6699
Polymers192,6699
Non-polymers00
Water00
1
C: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
A: Metal transporter CNNM4


Theoretical massNumber of molelcules
Total (without water)21,4081
Polymers21,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.738, 116.738, 243.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 21407.645 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM4, ACDP4, KIAA1592 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6P4Q7
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.5 M Sodium Formate, 5 % PEG 3350, 0.1 M TRIS pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.69→243.96 Å / Num. obs: 21343 / % possible obs: 99.7 % / Redundancy: 19.4 % / Biso Wilson estimate: 41.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.042 / Rrim(I) all: 0.184 / Χ2: 1.464 / Net I/σ(I): 13.9 / Num. measured all: 413360
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.69-3.9110.0271.3771.463800649163630.7791.45198
3.91-4.1810.5830.6493.1664136606060600.9530.682100
4.18-4.5210.7180.3136.5860320562856280.9910.328100
4.52-4.9510.1860.1959.7352731517751770.9950.205100
4.95-5.5310.4760.18911.7749551473047300.9930.199100
5.53-6.3810.6060.17813.3443814413141310.9930.187100
6.38-7.8110.3580.11519.5336283350335030.9970.121100
7.81-11.0110.410.06333.2728044269426940.9980.066100
11.01-63.2869.690.06136.8614681151815150.9980.06499.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.691→63.286 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0.18 / Phase error: 28.99 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3026 1989 9.62 %
Rwork0.2844 18687 -
obs0.2861 20676 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 253.07 Å2 / Biso mean: 100.772 Å2 / Biso min: 39.8 Å2
Refinement stepCycle: final / Resolution: 3.691→63.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9252 0 0 0 9252
Num. residues----1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039445
X-RAY DIFFRACTIONf_angle_d0.74812837
X-RAY DIFFRACTIONf_chiral_restr0.0531474
X-RAY DIFFRACTIONf_plane_restr0.0041635
X-RAY DIFFRACTIONf_dihedral_angle_d16.8285568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.691-3.78330.41991180.40411091120981
3.7833-3.88550.38681360.35161299143595
3.8855-3.99990.39231350.32431263139894
3.9999-4.12890.29641350.30611297143296
4.1289-4.27650.32291420.29221332147497
4.2765-4.44770.29711380.28211333147199
4.4477-4.650.23751430.24511347149098
4.65-4.89510.29681480.25641348149699
4.8951-5.20170.32331440.28251347149199
5.2017-5.60310.26211490.288813761525100
5.6031-6.16650.30511500.3131366151699
6.1665-7.05780.34291450.301813851530100
7.0578-8.88820.21711500.241314201570100
8.8882-63.29520.24511560.21081483163999

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