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

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Basic information

Entry
Database: PDB / ID: 5jdf
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 1mM Ca2+
ComponentsUncharacterized membrane protein MJ0091
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: 2.65 Å
AuthorsLiao, J. / Jiang, Y.X. / Faraldo-Gomez, J.D.
Funding support United States, China, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)funding 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 Natural Science Foundation of China (NSFC)Project 31470817 China
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) 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
DepositionApr 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized membrane protein MJ0091
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,59315
Polymers32,2171
Non-polymers3,37614
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.801, 72.258, 95.803
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 Uncharacterized membrane protein MJ0091


Mass: 32217.379 Da / Num. of mol.: 1 / Mutation: L2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (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, 33 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H32
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 19 / 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: 54.02 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG400

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Data collection

DiffractionMean temperature: 100 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: 2.65→50 Å / Num. obs: 10595 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 63.91 Å2 / Rmerge(I) obs: 0.111 / Net I/av σ(I): 20.939 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.65-2.76.51100
2.7-2.746.91100
2.74-2.87.11100
2.8-2.857.31100
2.85-2.927.21100
2.92-2.987.311000.814
2.98-3.067.311000.718
3.06-3.147.211000.614
3.14-3.237.211000.478
3.23-3.347.211000.387
3.34-3.467.211000.346
3.46-3.67.211000.252
3.6-3.767.211000.195
3.76-3.967.111000.151
3.96-4.21711000.115
4.21-4.53711000.093
4.53-4.99711000.083
4.99-5.71711000.083
5.71-7.196.811000.065
7.19-506.2198.30.042

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Processing

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

3v5u


Resolution: 2.65→34.523 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.36
RfactorNum. reflection% reflection
Rfree0.281 1055 10 %
Rwork0.2244 --
obs0.2298 10548 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.09 Å2 / Biso mean: 72.3239 Å2 / Biso min: 39.06 Å2
Refinement stepCycle: final / Resolution: 2.65→34.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 133 19 2358
Biso mean--89.77 80.93 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042388
X-RAY DIFFRACTIONf_angle_d1.1433204
X-RAY DIFFRACTIONf_chiral_restr0.028390
X-RAY DIFFRACTIONf_plane_restr0.003374
X-RAY DIFFRACTIONf_dihedral_angle_d11.805869
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6381-2.75810.39291200.28191080120092
2.7581-2.90350.34261300.266111651295100
2.9035-3.08530.29651310.239511761307100
3.0853-3.32330.30411300.230511931323100
3.3233-3.65740.27081320.21411781310100
3.6574-4.18590.24341350.211512121347100
4.1859-5.27070.29841340.219512041338100
5.2707-34.52640.25941430.220712851428100

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