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

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Basic information

Entry
Database: PDB / ID: 5hxh
TitleStructural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with zero Na+ and 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
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: 2.804 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 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 / 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
B: sodium,calcium exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,65414
Polymers64,0582
Non-polymers2,59612
Water70339
1
A: sodium,calcium exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9456
Polymers32,0291
Non-polymers9165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-11 kcal/mol
Surface area13680 Å2
MethodPISA
2
B: sodium,calcium exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7108
Polymers32,0291
Non-polymers1,6807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.177, 46.827, 96.963
Angle α, β, γ (deg.)90.000, 106.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein sodium,calcium exchanger


Mass: 32029.131 Da / Num. of mol.: 2 / Fragment: UNP residues 2-300 / 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, 51 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H32
#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.: 39 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
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: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 21489 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.85 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.045 / Rrim(I) all: 0.11 / Χ2: 0.93 / Net I/av σ(I): 17.721 / Net I/σ(I): 7.4 / Num. measured all: 124985
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.855.78960.5610.5580.72299.9
2.85-2.96.38690.6530.4670.756100
2.9-2.966.78540.7350.3910.7381000.943
2.96-3.0278640.7740.3620.8051000.8970.969
3.02-3.087.28840.8270.2940.8371000.7390.797
3.08-3.157.38900.8760.2520.8691000.6320.681
3.15-3.237.38480.9230.2030.8941000.5140.554
3.23-3.327.38950.9580.1460.891000.3690.397
3.32-3.427.38520.9660.1260.9151000.320.344
3.42-3.537.38920.9770.0960.9661000.2440.263
3.53-3.657.38540.9840.0791.071000.1990.214
3.65-3.87.38960.990.0611.0561000.1560.167
3.8-3.977.48710.9930.0471.04999.90.1180.127
3.97-4.187.38900.9950.0381.0881000.0960.103
4.18-4.447.18750.9970.031.0481000.0750.081
4.44-4.796.98900.9960.0291.1899.70.0720.077
4.79-5.277.38940.9970.031.0671000.0750.081
5.27-6.037.38930.9970.030.9361000.0750.08
6.03-7.597.39030.9980.0220.8411000.0570.061
7.59-506.99340.9980.0180.78198.60.0440.048

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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: 2.804→34.962 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 2153 10.02 %
Rwork0.2033 19336 -
obs0.2093 17644 63.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.95 Å2 / Biso mean: 43.2353 Å2 / Biso min: 9.36 Å2
Refinement stepCycle: final / Resolution: 2.804→34.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 123 39 4544
Biso mean--54.44 33.17 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034608
X-RAY DIFFRACTIONf_angle_d0.7056228
X-RAY DIFFRACTIONf_chiral_restr0.022770
X-RAY DIFFRACTIONf_plane_restr0.003736
X-RAY DIFFRACTIONf_dihedral_angle_d12.0111637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8038-2.8690.2859170.28621471647
2.869-2.94070.2768620.297656662827
2.9407-3.02010.337970.281587096743
3.0201-3.1090.29811140.27181035114950
3.109-3.20920.3231140.26351017113151
3.2092-3.32390.28581200.2661089120952
3.3239-3.45680.3051190.26771058117752
3.4568-3.6140.2591200.24631073119353
3.614-3.80430.28651310.22291177130858
3.8043-4.04230.26261680.18871480164872
4.0423-4.35390.25481940.18111783197788
4.3539-4.79110.25542170.1771952216995
4.7911-5.48210.27362220.193419992221100
5.4821-6.89810.33452330.215320672300100
6.8981-34.96420.17972250.15492023224899

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