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

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Basic information

Entry
Database: PDB / ID: 5hxs
TitleStructural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 10mM Sr2+
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 / A middle domain of Talin 1 / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special ...NCX, central ion-binding region / NCX, peripheral helical region / Sodium/potassium/calcium exchanger / A middle domain of Talin 1 / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PENTADECANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / STRONTIUM ION / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Uncharacterized membrane protein MJ0091
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.789 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 Institutefor 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 HealthDivision of Intramural 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 31, 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 / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
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)34,56913
Polymers32,0291
Non-polymers2,53912
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-42 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.516, 72.353, 96.000
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: 32029.131 Da / Num. of mol.: 1 / Fragment: UNP residues 1-300 / 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 , 5 types, 22 molecules

#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C15H32
#4: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
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: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.789→50 Å / Num. obs: 8927 / % possible obs: 98.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134 / Χ2: 1.604 / Net I/av σ(I): 19.01 / Net I/σ(I): 8.3 / Num. measured all: 57652
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.855.40.883960.6740.3990.971.14190.4
2.85-2.95.50.8064350.6610.3580.8851.20796.5
2.9-2.9660.8144040.7480.3510.8891.13596.4
2.96-3.026.10.6694500.8940.2850.7291.23699.6
3.02-3.086.50.5664270.8660.2320.6131.24598.8
3.08-3.156.50.5734310.9350.2360.621.30198.6
3.15-3.236.60.4894440.9150.2020.531.414100
3.23-3.326.60.394480.9430.1590.4221.45598.9
3.32-3.426.60.344340.9590.140.3691.484100
3.42-3.536.60.2824470.960.1170.3061.58599.1
3.53-3.656.70.214340.9790.0870.2271.83199.8
3.65-3.86.70.1614520.9880.0660.1741.92999.3
3.8-3.976.80.154370.9910.0620.1631.86699.8
3.97-4.186.70.1184570.990.050.1291.802100
4.18-4.446.90.0994480.9920.0410.1071.864100
4.44-4.796.80.0934510.9940.0380.11.808100
4.79-5.276.90.094610.9920.0370.0981.825100
5.27-6.036.80.0874680.9930.0360.0951.781100
6.03-7.596.70.0594690.9980.0240.0641.916100
7.59-5060.0455140.9990.020.0491.76798.1

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Processing

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

3v5u


Resolution: 2.789→39.998 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 893 10 %
Rwork0.2233 8034 -
obs0.2285 8907 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.95 Å2 / Biso mean: 62.1679 Å2 / Biso min: 30.28 Å2
Refinement stepCycle: final / Resolution: 2.789→39.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 112 10 2346
Biso mean--74.43 59.22 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042374
X-RAY DIFFRACTIONf_angle_d0.8873188
X-RAY DIFFRACTIONf_chiral_restr0.028389
X-RAY DIFFRACTIONf_plane_restr0.004376
X-RAY DIFFRACTIONf_dihedral_angle_d10.918863
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 (%)
2.7891-2.96380.33341380.25481240137894
2.9638-3.19250.28991460.24481315146199
3.1925-3.51360.32621490.237213391488100
3.5136-4.02160.29261490.215513441493100
4.0216-5.06520.24631520.208413591511100
5.0652-40.00250.25351590.2231437159699

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