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- PDB-3us9: Crystal Structure of the NCX1 Intracellular Tandem Calcium Bindin... -

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Basic information

Entry
Database: PDB / ID: 3us9
TitleCrystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12)
ComponentsSodium/calcium exchanger 1
KeywordsMETAL BINDING PROTEIN / beta-sandwich / Calcium binding protein / intracellular
Function / homology
Function and homology information


Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Ion homeostasis / calcium:sodium antiporter activity / cell communication / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / ankyrin binding / positive regulation of the force of heart contraction ...Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Ion homeostasis / calcium:sodium antiporter activity / cell communication / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / ankyrin binding / positive regulation of the force of heart contraction / calcium ion import across plasma membrane / sodium ion transmembrane transport / positive regulation of bone mineralization / response to muscle stretch / calcium ion transmembrane transport / sarcolemma / postsynapse / calmodulin binding / axon / calcium ion binding / nucleoplasm / plasma membrane
Similarity search - Function
Sodium/calcium exchanger, isoform 1 / CalX-beta domain / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger membrane region ...Sodium/calcium exchanger, isoform 1 / CalX-beta domain / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger membrane region / Sodium/calcium exchanger protein / CalX-like domain superfamily / DnaJ domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sodium/calcium exchanger 1
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsGiladi, M. / Sasson, Y. / Hirsch, J.A. / Khananshvili, D.
CitationJournal: Plos One / Year: 2012
Title: A common Ca2+-driven interdomain module governs eukaryotic NCX regulation.
Authors: Giladi, M. / Sasson, Y. / Fang, X. / Hiller, R. / Buki, T. / Wang, Y.X. / Hirsch, J.A. / Khananshvili, D.
History
DepositionNov 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/calcium exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0994
Polymers32,9781
Non-polymers1203
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.670, 152.550, 79.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sodium/calcium exchanger 1 / Na(+)/Ca(2+)-exchange protein 1


Mass: 32978.445 Da / Num. of mol.: 1 / Fragment: CBD12 / Mutation: E454K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Tissue: brain / Gene: SLC8A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P23685
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsP23685 IS THE CARDIAC SPLICE VARIANT, INCLUDING EXONS ACDEF. THE SEQUENCE OF THIS PROTEIN IS ...P23685 IS THE CARDIAC SPLICE VARIANT, INCLUDING EXONS ACDEF. THE SEQUENCE OF THIS PROTEIN IS DERIVED FROM THE BRAIN SPLICE VARIANT, INCLUDING EXONS AD. THE RESIDUES 636-642 IN P23685 CORRESPOND TO EXON C, THE RESIDUES 649-676 IN P23685 CORRESPOND TO EXONS EF.

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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: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 7% PEG 8000, 0.2M Amonium Sulphate, 10% Sucrose, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2011
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 14002 / Num. obs: 14002 / % possible obs: 90 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.68-2.85116.4
2.85-3.07164.7
3.07-3.38198.8
3.38-3.87199.7
3.87-4.87199.7
4.87-43.02199.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QVM, 3GIN

2qvm

3gin


Resolution: 2.68→43.017 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.67 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 898 7.91 %RANDOM
Rwork0.2338 ---
all-11357 --
obs-11357 80.13 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.731 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 236.65 Å2 / Biso mean: 84.2688 Å2 / Biso min: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1-3.0742 Å2-0 Å2-0 Å2
2---2.1865 Å20 Å2
3----0.8877 Å2
Refinement stepCycle: LAST / Resolution: 2.68→43.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 3 12 1905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041917
X-RAY DIFFRACTIONf_angle_d0.8132588
X-RAY DIFFRACTIONf_chiral_restr0.055296
X-RAY DIFFRACTIONf_plane_restr0.002344
X-RAY DIFFRACTIONf_dihedral_angle_d14.092690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6803-2.84820.3485360.353434337916
2.8482-3.0680.32991190.29161397151665
3.068-3.37670.30891800.26942108228899
3.3767-3.8650.28131810.225521552336100
3.865-4.86840.24331890.189421832372100
4.8684-43.02260.26371930.23792273246699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07120.0713-0.00920.15940.12780.0990.19010.25160.1335-0.57470.34020.16360.8313-0.21280.22551.23390.27540.2485-0.062-0.17740.275650.1165-5.227825.9245
20.0301-0.00550.00780.0667-0.1070.13160.0007-0.00240.0889-0.22270.1031-0.00930.3836-0.03390.00250.6021-0.15110.1570.01620.2543-0.180942.05755.584728.4105
30.0422-0.05330.00840.1373-0.0023-0.0420.06280.00820.06580.07130.0277-0.10510.2350.19280.06090.39510.82480.3735-0.38030.06420.39956.6105-8.416929.3669
40.15150.0646-0.22270.0825-0.14810.4245-0.19120.3848-0.132-0.1108-0.14030.3170.2648-0.0767-0.27180.30960.15670.1420.3955-0.05240.307532.581922.477715.6878
50.19310.1043-0.09980.06790.06980.23110.15930.2539-0.19140.00950.10630.2237-0.278-0.31490.14760.29760.14530.00590.63680.13980.528120.879234.644912.1238
60.0145-0.0046-0.00810.0363-0.01670.02020.0439-0.0169-0.01750.19240.0914-0.0570.0586-0.03410.03880.2733-0.34110.29680.2347-0.0660.385345.300723.184536.478
7-0.0053-0.01520.01410.0365-0.02160.01830.14380.13250.0049-0.0776-0.4228-0.205-0.2337-0.0001-0.0363-0.1750.33310.15990.5508-0.00860.205727.371335.2815.838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 372:436)A372 - 436
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 437:453)A437 - 453
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 454:484)A454 - 484
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 485:542)A485 - 542
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 543:619)A543 - 619
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 620:632)A620 - 632
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 633:652)A633 - 652

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