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

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Basic information

Entry
Database: PDB / ID: 5jdh
TitleStructural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 10 mM Na+ and 10mM 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 / 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 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / Uncharacterized membrane protein MJ0091
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 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)funding for Jose D. Faraldo-Gomez 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized membrane protein MJ0091
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,39623
Polymers32,1601
Non-polymers4,23622
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.883, 72.218, 96.099
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: 32160.326 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 , 9 types, 79 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 212.415 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H32
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
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: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18126 / % possible obs: 99.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 38.67 Å2 / Rmerge(I) obs: 0.103 / Net I/av σ(I): 22.448 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.2-2.247.11100
2.24-2.287.21100
2.28-2.327.211000.991
2.32-2.377.211000.833
2.37-2.427.311000.732
2.42-2.487.311000.687
2.48-2.547.211000.549
2.54-2.617.311000.449
2.61-2.697.211000.374
2.69-2.777.211000.327
2.77-2.877.311000.286
2.87-2.997.211000.239
2.99-3.127.211000.192
3.12-3.297.211000.148
3.29-3.497.211000.104
3.49-3.767.111000.074
3.76-4.14711000.065
4.14-4.746.3196.30.055
4.74-5.976.911000.044
5.97-506.4198.80.028

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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: 2.203→31.208 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2369 1447 8 %
Rwork0.1928 --
obs0.1962 18080 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.57 Å2 / Biso mean: 46.875 Å2 / Biso min: 21.13 Å2
Refinement stepCycle: final / Resolution: 2.203→31.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 169 57 2458
Biso mean--68.56 55.34 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042482
X-RAY DIFFRACTIONf_angle_d0.653319
X-RAY DIFFRACTIONf_chiral_restr0.024395
X-RAY DIFFRACTIONf_plane_restr0.003386
X-RAY DIFFRACTIONf_dihedral_angle_d10.879922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2028-2.28150.29121390.25071601174097
2.2815-2.37280.26931430.219916441787100
2.3728-2.48070.24171420.204816291771100
2.4807-2.61150.24111430.18716461789100
2.6115-2.7750.22771450.172716691814100
2.775-2.98910.22531420.176616341776100
2.9891-3.28960.21571450.177816691814100
3.2896-3.76490.22121460.188816821828100
3.7649-4.74070.2241460.17811667181398
4.7407-31.21120.25621560.210717921948100

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