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

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Basic information

Entry
Database: PDB / ID: 5hya
TitleStructural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchangerNCX_Mj soaked with 150 mM Na+ and nominal 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 / 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
ACETATE ION / 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: 1.897 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 the 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
DepositionFeb 1, 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

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Assembly

Deposited unit
A: sodium,calcium exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,60924
Polymers32,3311
Non-polymers4,27823
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-2 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.490, 72.879, 96.206
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
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, 123 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H32
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 54.16 %
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: Jun 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.897→50 Å / Num. obs: 27960 / % possible obs: 98.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 25.06 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.482 / Net I/av σ(I): 32.893 / Net I/σ(I): 9.6 / Num. measured all: 261239
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
1.9-1.938.913531.2997.8
1.93-1.97913791.25897.90.871
1.97-2.01913741.26399.20.653
2.01-2.05913441.27798.20.573
2.05-2.099.113701.29298.10.481
2.09-2.149.113881.24898.90.384
2.14-2.199.113561.23899.10.329
2.19-2.259.213951.29798.80.278
2.25-2.329.313651.32798.80.232
2.32-2.399.313921.35298.90.195
2.39-2.489.413831.38299.10.186
2.48-2.589.613961.35699.30.154
2.58-2.79.713891.36399.10.125
2.7-2.849.814041.40199.20.112
2.84-3.029.814191.42999.60.093
3.02-3.259.914071.58299.40.078
3.25-3.589.714261.87799.60.063
3.58-4.099.614272.13599.60.047
4.09-5.169.414672.09399.70.039
5.16-508.815261.9797.60.039

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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: 1.897→37.673 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 2000 7.17 %
Rwork0.1789 25906 -
obs0.1809 27906 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.08 Å2 / Biso mean: 28.5066 Å2 / Biso min: 11.03 Å2
Refinement stepCycle: final / Resolution: 1.897→37.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 261 100 2579
Biso mean--45.75 38.49 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062510
X-RAY DIFFRACTIONf_angle_d0.9663321
X-RAY DIFFRACTIONf_chiral_restr0.038388
X-RAY DIFFRACTIONf_plane_restr0.005379
X-RAY DIFFRACTIONf_dihedral_angle_d15.196948
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 (%)
1.8973-1.94470.25991370.22841772190996
1.9447-1.99730.24881390.20261813195298
1.9973-2.05610.2321410.19151808194998
2.0561-2.12240.22271400.17331816195699
2.1224-2.19830.20031410.16661827196899
2.1983-2.28630.21561410.15751820196199
2.2863-2.39030.20861410.15381838197999
2.3903-2.51630.19221440.16471864200899
2.5163-2.67390.20351410.15161828196999
2.6739-2.88030.21651430.16741852199599
2.8803-3.170.22861450.17111880202599
3.17-3.62840.21271460.1818932039100
3.6284-4.57020.17791470.171219092056100
4.5702-37.68010.20521540.21221986214098

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