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- PDB-4zcv: Structure of calcium-bound regulatory domain of the human ATP-Mg/... -

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Basic information

Entry
Database: PDB / ID: 4zcv
TitleStructure of calcium-bound regulatory domain of the human ATP-Mg/Pi carrier in the P212121 form
ComponentsCalcium-binding mitochondrial carrier protein SCaMC-1
KeywordsTRANSPORT PROTEIN / EF-hand / ATP-Mg/Pi / carrier / calcium
Function / homology
Function and homology information


ATP:phosphate antiporter activity / ADP:phosphate antiporter activity / ADP transport / adenine nucleotide transmembrane transporter activity / adenine nucleotide transport / mitochondrial ATP transmembrane transport / ATP transmembrane transporter activity / ATP transport / mitochondrial transport / cellular response to calcium ion ...ATP:phosphate antiporter activity / ADP:phosphate antiporter activity / ADP transport / adenine nucleotide transmembrane transporter activity / adenine nucleotide transport / mitochondrial ATP transmembrane transport / ATP transmembrane transporter activity / ATP transport / mitochondrial transport / cellular response to calcium ion / cellular response to oxidative stress / mitochondrial inner membrane / calcium ion binding / mitochondrion / membrane
Similarity search - Function
Graves disease carrier protein / Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif ...Graves disease carrier protein / Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial adenyl nucleotide antiporter SLC25A24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsHarborne, S.P.D. / Ruprecht, J.J. / Kunji, E.R.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Calcium-induced conformational changes in the regulatory domain of the human mitochondrial ATP-Mg/Pi carrier.
Authors: Harborne, S.P. / Ruprecht, J.J. / Kunji, E.R.
History
DepositionApr 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium-binding mitochondrial carrier protein SCaMC-1
B: Calcium-binding mitochondrial carrier protein SCaMC-1
C: Calcium-binding mitochondrial carrier protein SCaMC-1
D: Calcium-binding mitochondrial carrier protein SCaMC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,85326
Polymers75,4804
Non-polymers1,37422
Water79344
1
A: Calcium-binding mitochondrial carrier protein SCaMC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3708
Polymers18,8701
Non-polymers5017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calcium-binding mitochondrial carrier protein SCaMC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1786
Polymers18,8701
Non-polymers3085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Calcium-binding mitochondrial carrier protein SCaMC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2187
Polymers18,8701
Non-polymers3486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Calcium-binding mitochondrial carrier protein SCaMC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0865
Polymers18,8701
Non-polymers2164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.920, 77.010, 119.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Calcium-binding mitochondrial carrier protein SCaMC-1 / Mitochondrial ATP-Mg/Pi carrier protein 1 / Mitochondrial Ca(2+)-dependent solute carrier protein 1 ...Mitochondrial ATP-Mg/Pi carrier protein 1 / Mitochondrial Ca(2+)-dependent solute carrier protein 1 / Small calcium-binding mitochondrial carrier protein 1 / Solute carrier family 25 member 24


Mass: 18869.922 Da / Num. of mol.: 4 / Fragment: UNP residues 14-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC25A24, APC1, MCSC1, SCAMC1 / Plasmid: pNZ8048 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: Q6NUK1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.5 Å3/Da / Density % sol: 50.78 % / Description: Tetrahedral bi-pyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25-30% (w/v) PEG 8000, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.002 Å / Relative weight: 1
ReflectionResolution: 2.8→40.1 Å / Num. obs: 17779 / % possible obs: 99.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 52.38 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.064 / Net I/σ(I): 8.4 / Num. measured all: 57586 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.8-2.953.20.442.8828425500.7840.28399.7
8.85-40.12.80.04219.618026380.9710.03298.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å40.1 Å
Translation2.8 Å40.1 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4.1488refinement
iMOSFLM7.1.0data reduction
Aimless0.1.29data scaling
PHASER2.5.3phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5X

4n5x


Resolution: 2.8→40.098 Å / FOM work R set: 0.8129 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 902 5.09 %
Rwork0.211 16828 -
obs0.2133 17730 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.69 Å2 / Biso mean: 60.8 Å2 / Biso min: 16.81 Å2
Refinement stepCycle: final / Resolution: 2.8→40.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 61 44 4901
Biso mean--93.63 41.87 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114996
X-RAY DIFFRACTIONf_angle_d0.9276632
X-RAY DIFFRACTIONf_chiral_restr0.037731
X-RAY DIFFRACTIONf_plane_restr0.004858
X-RAY DIFFRACTIONf_dihedral_angle_d14.0361794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.97550.2961530.248827402893100
2.9755-3.20510.32861750.268927532928100
3.2051-3.52750.32151500.23692761291199
3.5275-4.03750.27081530.193827892942100
4.0375-5.08520.2141460.18142823296999
5.0852-40.10240.21911250.2092962308799
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)
14.29853.1533-5.87089.5295-0.57059.90480.4264-0.6229-0.78091.1608-0.168-1.56640.57591.0385-0.12060.6629-0.0923-0.10640.4727-0.10810.55968.2589-19.2456-30.1272
25.54273.68230.12366.5334-1.54425.0408-0.04450.60730.6172-0.4830.2970.7596-0.2092-1.1075-0.33030.3754-0.02050.06990.38410.07090.29730.3149-10.296-31.4829
33.97963.2368-1.62796.2809-4.68554.58370.2128-0.3799-0.25730.1644-0.525-0.65860.11810.34750.39290.4289-0.0583-0.0960.2947-0.0730.363410.7394-10.9606-21.3973
43.9827-1.58620.35288.89131.91716.59150.1701-1.9549-2.21321.5385-0.8984-0.16623.30132.92830.65020.93970.179-0.11871.03040.22370.87325.9766-29.1742-3.6257
58.08651.6562-3.07777.11654.9815.76510.152-0.9253-0.41641.4267-0.3742-0.87020.4433-0.8690.30610.9449-0.2801-0.25211.00730.10850.44921.6492-19.18353.5068
64.6025-1.49583.24577.7292-4.6194.04880.4672-0.3893-0.66791.2121-0.96830.00731.59450.62640.62981.2311-0.82130.11161.15530.1880.2236-6.7398-21.2657-4.2525
79.2475-1.37070.31618.97225.00082.92931.12820.3987-1.3025-0.8038-0.85691.15311.96810.18350.02421.28010.1244-0.50820.58640.28250.6503-3.4772-27.7847-11.9964
87.4281.3644-4.87264.3257-2.53595.91890.0671-0.2064-1.6195-0.7118-0.0456-0.2761.19010.03740.12170.6667-0.2189-0.22360.48630.00620.74563.9247-23.1815-15.4015
97.5925-3.7513-5.79557.25571.99139.12751.4701-0.82460.81910.0366-0.4562-0.8222-1.3190.6792-0.75420.7067-0.12-0.07610.44170.04980.30475.2282-13.0757-15.3448
103.7575-0.9236-0.87.52951.93855.22151.0109-0.89772.34161.2802-0.2930.2369-0.9424-0.3548-0.30031.1011-0.28350.2550.7019-0.19080.6532-1.327-10.8801-5.6259
118.9838-2.98020.11195.8775-0.47848.4182-0.3998-0.65581.0805-0.6001-0.17481.2452-0.4433-0.20680.31370.28270.0968-0.02420.476-0.11170.64211.394416.736-8.8087
128.2224-1.7666-5.85222.76760.68954.29270.1175-1.14681.35330.93370.3244-0.1605-1.1825-0.1087-0.58260.44750.05120.04370.5063-0.16130.430915.456820.38222.1671
136.2866-1.34762.63778.78444.49637.5845-0.0997-1.0839-0.16590.4803-0.0851-0.78990.0077-0.46950.19170.3112-0.1251-0.00070.52160.1190.355321.596710.79852.2962
143.1828-0.83862.23753.29091.75283.42020.19020.818-0.3321-0.86550.1224-0.62370.63810.4892-0.41750.2512-0.03160.02550.37170.02150.303322.44168.5455-9.4118
157.07844.7696-8.2966.4446-6.27729.4481-0.4645-0.0164-0.9603-0.6549-0.12890.02580.1493-0.64950.48310.3896-0.0983-0.10520.4883-0.01010.35338.7082.67020.6455
166.0920.39342.18738.8009-3.87183.719-0.3494-0.89670.08720.48730.55420.907-0.0569-1.4424-0.15470.36380.06160.13670.81240.08470.38692.69820.841321.6743
172.00048.0419.33296.24417.23258.4025-1.5779-0.66624.31941.5607-0.46562.7389-1.134-0.46641.75740.62410.3832-0.19361.2954-0.48271.5633-2.099111.530115.4718
182.63220.6628-4.20317.3549-1.25017.01350.002-0.7043-0.1940.06780.4635-0.2403-0.46970.4464-0.39450.2173-0.0377-0.05480.4874-0.01420.392810.41176.261113.069
197.37-2.525-0.93326.26790.796.5910.24290.77990.3134-0.70590.35360.4131-0.24160.1087-0.71490.5122-0.1713-0.00470.28710.0510.3933-2.6642-20.223-37.9556
207.03572.1698-2.95777.7435-0.46938.4445-0.0772-0.8962-0.2926-0.1363-0.0832-1.0559-0.56330.25490.11760.35830.0524-0.06520.31210.01350.31822.04-29.2506-32.7073
216.3019-0.2197-3.34324.9320.88273.8226-0.37750.1461-0.4809-0.1099-0.0193-0.30281.0165-0.1950.21240.53330.0356-0.00450.1742-0.02350.3695-7.6553-35.1716-35.4329
227.5797-1.0943-5.92584.77172.61867.58250.10660.65810.3822-0.197-0.13770.7416-0.9914-1.0204-0.11970.36030.1459-0.09550.3940.00730.348-16.1669-23.103-31.839
233.8276-0.8015-2.08559.1543-2.48616.58231.16030.12590.35520.0793-0.13892.9601-0.5687-0.82-0.09430.54450.30540.46380.5993-0.1650.806-26.2215-18.4169-13.1668
244.09162.06031.39284.45492.63883.7330.1668-1.0008-0.30151.3009-0.77310.81050.0362-0.19080.490.84-0.13630.30640.68550.05950.7259-24.8487-29.1803-7.2545
257.56071.97971.21078.9659-0.31168.28710.0541-0.80340.70910.4836-0.27810.1736-0.8786-0.07880.19120.4162-0.01110.08080.219-0.06710.4492-14.2036-18.9437-16.4336
263.07791.36992.57550.66391.11932.2212-0.1195-1.1872-0.51190.3057-0.4856-1.04062.2518-0.31070.38270.72370.0173-0.04280.48050.00910.5771-16.6578-31.0901-13.7455
276.6567-2.8503-1.11947.42392.22187.26090.36050.5669-0.008-0.5088-0.2238-0.4816-0.06570.2821-0.1180.19560.0372-0.02340.41930.13030.3447-3.572724.6146-2.2716
286.0334-0.53233.76414.6372.17777.2018-0.6784-0.42221.81660.53530.2101-1.5949-0.84911.16990.52510.4915-0.1068-0.1270.506-0.2470.93313.744834.0077.597
290.6850.91231.44051.52261.28034.4529-1.1818-0.41341.71240.48480.0322-0.9894-1.11091.46520.52960.10510.1064-0.54182.4155-0.95761.72515.164732.572623.6425
304.8279-3.35481.01446.5846-0.90344.4499-0.7948-1.447-0.00441.7211.8858-0.2225-0.05572.5207-1.00471.21950.3763-0.01281.6105-0.250.52315.857625.353929.0836
316.0643-5.76343.52475.6585-3.7462.9127-1.5067-2.6734-0.0640.85050.48-2.62240.46711.37130.90780.72590.36390.08841.7411-0.11531.01214.882121.242519.7707
323.219-0.38540.72782.15110.01351.7327-0.6368-0.5511.22750.40610.1808-0.89610.53850.46-0.3004-0.68690.44260.08451.2203-0.4270.63715.446726.719612.2509
338.3919-2.646-1.38796.0896-2.83086.07980.2514-0.7333-0.61820.0550.4310.76930.3011-0.9446-0.41330.7820.202-0.29561.1187-0.03670.4771-2.767724.894121.3511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 31 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 56 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 98 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 107 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 123 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 134 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 143 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 144 through 150 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 151 through 158 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 159 through 174 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 22 through 40 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 41 through 56 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 57 through 67 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 68 through 76 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 77 through 98 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 99 through 134 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 135 through 143 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 144 through 173 )B0
19X-RAY DIFFRACTION19chain 'C' and (resid 23 through 31 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 32 through 56 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 57 through 76 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 77 through 98 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 99 through 117 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 118 through 123 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 124 through 158 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 159 through 173 )C0
27X-RAY DIFFRACTION27chain 'D' and (resid 23 through 76 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 77 through 98 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 99 through 107 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 108 through 134 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 135 through 143 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 144 through 158 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 159 through 170 )D0

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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