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- PDB-6n7e: Crystal structure of the cytosolic domain of human CNNM2 in compl... -

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Basic information

Entry
Database: PDB / ID: 6n7e
TitleCrystal structure of the cytosolic domain of human CNNM2 in complex with AMP-PNP and Mg2+
ComponentsMetal transporter CNNM2,Metal transporter CNNM2
KeywordsMETAL TRANSPORT / CNNM2 / Mg2+ transporter / cystathionine-beta-synthase domain / cyclic nucleotide-binding homology domain / ATP-bound / closed conformation / MEMBRANE PROTEIN
Function / homology
Function and homology information


magnesium ion homeostasis / magnesium ion transmembrane transporter activity / basolateral plasma membrane / glutamatergic synapse / ATP binding / 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 / CBS-domain / CBS domain superfamily / CBS domain ...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 / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / RmlC-like jelly roll fold / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Metal transporter CNNM2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsChen, Y.S. / 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
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Mar 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 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metal transporter CNNM2,Metal transporter CNNM2
B: Metal transporter CNNM2,Metal transporter CNNM2
C: Metal transporter CNNM2,Metal transporter CNNM2
D: Metal transporter CNNM2,Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,43016
Polymers163,2114
Non-polymers2,21912
Water724
1
A: Metal transporter CNNM2,Metal transporter CNNM2
D: Metal transporter CNNM2,Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7158
Polymers81,6052
Non-polymers1,1106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-73 kcal/mol
Surface area31110 Å2
MethodPISA
2
B: Metal transporter CNNM2,Metal transporter CNNM2
C: Metal transporter CNNM2,Metal transporter CNNM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7158
Polymers81,6052
Non-polymers1,1106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-70 kcal/mol
Surface area31080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)290.582, 111.139, 103.519
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Metal transporter CNNM2,Metal transporter CNNM2 / Ancient conserved domain-containing protein 2 / Cyclin-M2


Mass: 40802.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM2, ACDP2 / Plasmid: pET-29a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9H8M5
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 5.03 Å3/Da / Density % sol: 75.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 0.5 M magnesium formate, 5 mM AMP-PNP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 36991 / % possible obs: 99.8 % / Redundancy: 3.4 % / Net I/σ(I): 17.6
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 683 / CC1/2: 0.148 / % 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: 4P1O, 6DJ3

4p1o

6dj3


Resolution: 3.5→48.76 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.282 -5 %0.241
Rwork0.282 ---
obs-36990 90.02 %-
Refinement stepCycle: LAST / Resolution: 3.5→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9279 0 132 4 9415

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