[English] 日本語
Yorodumi
- PDB-6rs2: Structure of the Bateman module of human CNNM4. -

+
Open data


ID or keywords:

Loading...

-
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 / enamel mineralization / intracellular monoatomic cation homeostasis / magnesium ion transmembrane transporter activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more