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- PDB-4k1c: VCX1 Calcium/Proton Exchanger -

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Basic information

Entry
Database: PDB / ID: 4k1c
TitleVCX1 Calcium/Proton Exchanger
ComponentsVacuolar calcium ion transporter
KeywordsMEMBRANE PROTEIN/METAL TRANSPORT / Structural Genomics / PSI-Biology / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Membrane Protein CAX NCX NCKX / Calcium transport / Vacuole / TRANSPORT PROTEIN / MEMBRANE PROTEIN-METAL TRANSPORT complex
Function / homology
Function and homology information


calcium:proton antiporter activity / potassium:proton antiporter activity / fungal-type vacuole / fungal-type vacuole membrane / calcium ion transmembrane transport / transmembrane transport / intracellular calcium ion homeostasis / calcium ion transport / metal ion binding
Similarity search - Function
Calcium/proton exchanger / Calcium/proton exchanger CAX-like / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein
Similarity search - Domain/homology
IODIDE ION / : / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Vacuolar calcium ion transporter
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWaight, A.B. / Pedersen, B.P. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Nature / Year: 2013
Title: Structural basis for alternating access of a eukaryotic calcium/proton exchanger.
Authors: Waight, A.B. / Pedersen, B.P. / Schlessinger, A. / Bonomi, M. / Chau, B.H. / Roe-Zurz, Z. / Risenmay, A.J. / Sali, A. / Stroud, R.M.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar calcium ion transporter
B: Vacuolar calcium ion transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,31131
Polymers91,2502
Non-polymers4,06129
Water1,13563
1
A: Vacuolar calcium ion transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,86022
Polymers45,6251
Non-polymers3,23521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar calcium ion transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4519
Polymers45,6251
Non-polymers8268
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Vacuolar calcium ion transporter
hetero molecules

A: Vacuolar calcium ion transporter
hetero molecules

A: Vacuolar calcium ion transporter
hetero molecules

B: Vacuolar calcium ion transporter
hetero molecules

B: Vacuolar calcium ion transporter
hetero molecules

B: Vacuolar calcium ion transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,93393
Polymers273,7516
Non-polymers12,18287
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation7_544x+1/3,y-1/3,z-1/31
crystal symmetry operation8_544-y+1/3,x-y-1/3,z-1/31
crystal symmetry operation9_544-x+y+1/3,-x-1/3,z-1/31
Buried area33370 Å2
ΔGint-592 kcal/mol
Surface area77990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.110, 130.110, 156.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Vacuolar calcium ion transporter / High copy number undoes manganese protein 1 / Manganese resistance 1 protein / Vacuolar Ca(2+)/H(+) exchanger


Mass: 45625.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VCX1, HUM1, MNR1, YDL128W / Plasmid: 2 MICRON / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q99385

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Non-polymers , 5 types, 92 molecules

#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.04 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.5498 Å
DetectorDate: Jun 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 44747 / Num. obs: 44539 / % possible obs: 99.5 % / Observed criterion σ(I): -3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→53.019 Å / SU ML: 0.34 / σ(F): 1.99 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 1407 3.21 %
Rwork0.2007 --
obs0.2015 43768 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→53.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 173 63 5933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016009
X-RAY DIFFRACTIONf_angle_d0.6478178
X-RAY DIFFRACTIONf_dihedral_angle_d12.1572119
X-RAY DIFFRACTIONf_chiral_restr0.043998
X-RAY DIFFRACTIONf_plane_restr0.003968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.38230.37931480.32024260X-RAY DIFFRACTION100
2.3823-2.47760.35991290.30684239X-RAY DIFFRACTION99
2.4776-2.59040.32361360.27294231X-RAY DIFFRACTION100
2.5904-2.7270.2791450.25274211X-RAY DIFFRACTION100
2.727-2.89780.29851480.2324249X-RAY DIFFRACTION100
2.8978-3.12150.26811380.21424225X-RAY DIFFRACTION99
3.1215-3.43560.24221330.20274243X-RAY DIFFRACTION100
3.4356-3.93260.22071370.18484254X-RAY DIFFRACTION100
3.9326-4.95410.21151410.18014215X-RAY DIFFRACTION99
4.9541-53.03280.17881520.18224234X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.26060.1437-0.19020.0959-0.05540.222-0.07490.43470.5676-0.54430.29471.23520.0801-0.733101.1730.0608-0.03170.71310.13130.699935.9965-2.4179-40.2778
22.32710.26290.6312.88480.74710.3790.072-0.14090.0739-0.3614-0.1226-0.2708-0.16580.3629-0.00640.26340.04820.02650.18290.00320.28639.5986-10.0065-24.682
30.6167-0.1575-0.08230.7675-0.61651.2630.1974-0.2270.2198-0.565-0.1469-0.29580.74760.77530.0140.31870.05980.04010.1590.04920.408353.2516-8.8834-24.0356
40.45550.3624-0.12740.4017-0.21360.2007-0.11350.0438-0.03850.00870.1773-0.05190.0244-0.02410.00120.19360.00940.01960.1841-0.00720.184951.366-27.1655-30.1767
52.54470.4587-0.42633.73690.44720.48510.1185-0.2551-0.01060.30770.0966-0.04080.0562-0.06790.00710.1243-0.0116-0.01760.1638-0.04230.155967.6741-19.696-20.6861
62.12990.61030.41910.0752-0.0035-0.0339-0.64930.29171.7852-0.42440.06410.1579-0.1272-0.061-0.04210.3964-0.0156-0.07930.51920.13980.461153.169-16.0866-44.9837
70.0885-0.02240.0510.0277-0.11410.3689-0.49430.08240.122-0.10660.0376-0.67410.118-1.00140.00241.25560.04230.09260.6396-0.15241.047442.4275-4.4935-44.349
80.9026-0.05330.13180.65920.51230.4574-0.2481-0.23140.18370.151-0.46-0.6808-0.0129-0.3639-0.05870.25420.05510.07140.23370.02080.390842.7653-7.2197-19.5742
90.92610.2567-0.11831.16240.08340.18460.0544-0.0620.0060.0325-0.04390.0031-0.11750.010400.2060.03270.04460.18610.01090.186552.6225-25.8774-24.33
100.0062-0.00820.02110.0147-0.01830.0267-0.6514-0.60120.7740.29620.3756-0.0178-0.6882-0.21300.65450.2202-0.10360.6325-0.03440.579150.4087-29.61-4.2846
110.23490.0240.11830.58950.280.14110.1271-0.3893-1.23731.5978-0.03470.09050.61120.08720.01421.07260.09370.28440.77390.05980.93129.1587-45.6016-9.594
122.5432-0.0527-0.39092.6078-1.26610.6123-0.19270.0695-0.32070.41340.12570.10260.5799-0.0741-0.00020.530.14080.01320.3282-0.09110.44256.5025-37.6119-23.3745
130.6181-0.0814-0.06790.27-0.27780.33950.2762-0.13730.61690.21840.3457-1.0055-0.82970.54010.13460.41290.0484-0.14520.3667-0.12540.458116.0928-26.811-23.3636
140.89210.31830.40610.57940.7020.3920.1695-0.12570.0288-0.0166-0.0627-0.0596-0.19850.2985-0.08340.16240.0166-0.01890.2584-0.06310.2225-1.1917-18.6115-19.5785
150.55110.5409-0.29380.5543-0.19060.01060.4181-0.25750.32740.3627-0.115-0.1573-0.12130.33760.02210.19180.02040.03610.21980.01090.22787.8134-7.8807-16.4303
161.44270.88410.13884.2217-1.64140.81930.05751.56290.1674-1.08330.405-0.27420.68080.40650.12760.13220.11180.18660.61730.02410.169810.4748-2.3981-40.8669
171.7842-0.14481.11461.16220.61816.5377-0.51030.33080.1422-0.161-0.19890.1679-0.646-0.2904-1.15180.04870.04910.08870.1775-0.08260.188920.2457-11.2445-22.2884
183.36950.506-0.68220.0994-0.08020.6089-0.04980.1651-1.7293-0.11180.1122-0.43780.12650.27720.06910.4406-0.12140.04170.45170.03620.56968.531-24.5946-2.2241
194.2748-1.4157-1.22532.04120.49180.3713-0.3896-0.0701-0.32610.40220.1513-0.05160.53640.151-0.0130.48320.01960.01310.2486-0.06660.39037.4138-32.7475-25.5354
201.1818-0.1635-0.33640.06510.1448-0.134-0.00910.0678-0.0536-0.04020.0229-0.07690.03710.222800.25160.0157-0.01090.2723-0.04340.20072.1942-15.2168-22.3849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 22:39)
2X-RAY DIFFRACTION2(chain A and resid 40:93)
3X-RAY DIFFRACTION3(chain A and resid 94:114)
4X-RAY DIFFRACTION4(chain A and resid 115:161)
5X-RAY DIFFRACTION5(chain A and resid 162:220)
6X-RAY DIFFRACTION6(chain A and resid 221:241)
7X-RAY DIFFRACTION7(chain A and resid 242:251)
8X-RAY DIFFRACTION8(chain A and resid 252:279)
9X-RAY DIFFRACTION9(chain A and resid 280:397)
10X-RAY DIFFRACTION10(chain A and resid 398:401)
11X-RAY DIFFRACTION11(chain B and resid 22:41)
12X-RAY DIFFRACTION12(chain B and resid 42:92)
13X-RAY DIFFRACTION13(chain B and resid 93:115)
14X-RAY DIFFRACTION14(chain B and resid 116:153)
15X-RAY DIFFRACTION15(chain B and resid 154:178)
16X-RAY DIFFRACTION16(chain B and resid 179:194)
17X-RAY DIFFRACTION17(chain B and resid 195:222)
18X-RAY DIFFRACTION18(chain B and resid 223:242)
19X-RAY DIFFRACTION19(chain B and resid 243:302)
20X-RAY DIFFRACTION20(chain B and resid 303:400)

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