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- PDB-5hxc: Structural mechanisms of extracellular ion exchange and induced b... -

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Basic information

Entry
Database: PDB / ID: 5hxc
TitleStructural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 20 mM Na+ and zero Ca2+
Componentssodium,calcium exchanger
KeywordsMEMBRANE PROTEIN / Na+/Ca2+ exchange / Calcium signalling / membrane transporter / induced conformational change
Function / homology
Function and homology information


calcium, potassium:sodium antiporter activity / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / plasma membrane
Similarity search - Function
NCX, central ion-binding region / NCX, peripheral helical region / Sodium/potassium/calcium exchanger / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / A middle domain of Talin 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special ...NCX, central ion-binding region / NCX, peripheral helical region / Sodium/potassium/calcium exchanger / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / A middle domain of Talin 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MYC / PENTADECANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Uncharacterized membrane protein MJ0091
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsLiao, J. / Jiang, Y.X. / Faraldo-Gomez, J.D.
Funding support China, United States, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaProject 31470817 China
Howard Hughes Medical Institutefund for Youxing Jiang United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079179 United States
Welch FoundationGrant I-1578 United States
National Institutes of HealthIntramural Research of National Heart, Lung and Blood Institute United States
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger
Authors: Liao, J. / Marinelli, F. / Lee, C. / Huang, Y. / Faraldo-Gomez, J.D. / Jiang, Y.
#1: Journal: Science / Year: 2012
Title: Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger.
Authors: Liao, J. / Li, H. / Zeng, W. / Sauer, D.B. / Belmares, R. / Jiang, Y.
History
DepositionJan 30, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Derived calculations / Structure summary
Category: entity / pdbx_audit_support ...entity / pdbx_audit_support / pdbx_struct_oper_list / struct
Item: _entity.pdbx_description / _pdbx_audit_support.funding_organization ..._entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct.pdbx_descriptor
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sodium,calcium exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,89221
Polymers32,3311
Non-polymers4,56020
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.754, 72.560, 95.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein sodium,calcium exchanger


Mass: 32331.480 Da / Num. of mol.: 1 / Mutation: L2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0091 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57556

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Non-polymers , 7 types, 88 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN


Mass: 318.235 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C15H10O8
#6: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H32
#7: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / Details: PEG 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20791 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 32.78 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.046 / Rrim(I) all: 0.113 / Χ2: 1.375 / Net I/av σ(I): 20.574 / Net I/σ(I): 7.2 / Num. measured all: 147318
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.1-2.14710120.6020.4461.17299.8
2.14-2.187.110240.7420.4041.131100
2.18-2.22710010.7620.3571.24399.90.8910.961
2.22-2.26710470.8130.2911.2641000.7220.78
2.26-2.317.110060.8150.271.411000.670.723
2.31-2.37710290.8740.2191.2881000.5440.587
2.37-2.427.110130.9150.1911.291000.4790.517
2.42-2.497.110270.9140.1911.3211000.4780.516
2.49-2.567.110230.9360.1541.4971000.3840.414
2.56-2.657.210270.9520.1211.3891000.3050.329
2.65-2.747.210440.9680.1081.4131000.2720.293
2.74-2.857.210190.980.0931.4151000.2350.254
2.85-2.987.210300.9880.0731.341000.1840.198
2.98-3.147.210470.9890.0591.351000.1480.16
3.14-3.337.210480.9940.0471.4021000.1190.128
3.33-3.597.210380.9960.0351.5421000.0880.095
3.59-3.957.210540.9970.0251.7431000.0640.069
3.95-4.527.110710.9980.0181.6121000.0450.048
4.52-5.7710800.9990.0171.4081000.0430.047
5.7-506.5115110.0121.23799.10.0280.03

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V5U

3v5u


Resolution: 2.101→37.718 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 1998 9.63 %
Rwork0.1857 18741 -
obs0.19 20739 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.4 Å2 / Biso mean: 36.4059 Å2 / Biso min: 16.28 Å2
Refinement stepCycle: final / Resolution: 2.101→37.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 166 68 2478
Biso mean--54.86 46.9 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082564
X-RAY DIFFRACTIONf_angle_d1.2693431
X-RAY DIFFRACTIONf_chiral_restr0.037409
X-RAY DIFFRACTIONf_plane_restr0.005400
X-RAY DIFFRACTIONf_dihedral_angle_d10.397941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.101-2.15350.29661310.25071231136292
2.1535-2.21180.29421400.232613041444100
2.2118-2.27680.25641430.208813351478100
2.2768-2.35030.28041410.185713221463100
2.3503-2.43430.24681390.17913111450100
2.4343-2.53170.2151420.16813321474100
2.5317-2.64690.20551420.154613381480100
2.6469-2.78640.22441440.161913421486100
2.7864-2.9610.20851400.16513221462100
2.961-3.18950.19831450.165413541499100
3.1895-3.51020.21361440.181713521496100
3.5102-4.01770.22671460.17513691515100
4.0177-5.05990.22071470.182613711518100
5.0599-37.7240.24741540.218714581612100

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