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

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Basic information

Entry
Database: PDB / ID: 4zcu
TitleStructure of calcium-bound regulatory domain of the human ATP-Mg/Pi carrier in the P2 form
ComponentsCalcium-binding mitochondrial carrier protein SCaMC-1
KeywordsTRANSPORT PROTEIN / EF-hand / ATP-Mg/Pi / carrier / calcium
Function / homology
Function and homology information


adenine nucleotide transmembrane transporter activity / adenine nucleotide transport / ATP:phosphate antiporter activity / ADP:phosphate antiporter activity / ADP transport / mitochondrial ATP transmembrane transport / ATP transmembrane transporter activity / ATP transport / mitochondrial transport / cellular response to calcium ion ...adenine nucleotide transmembrane transporter activity / adenine nucleotide transport / ATP:phosphate antiporter activity / ADP:phosphate antiporter activity / ADP 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: 2.1 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,32028
Polymers56,6103
Non-polymers1,71025
Water3,027168
1
A: Calcium-binding mitochondrial carrier protein SCaMC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,50310
Polymers18,8701
Non-polymers6339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium-binding mitochondrial carrier protein SCaMC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,50310
Polymers18,8701
Non-polymers6339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calcium-binding mitochondrial carrier protein SCaMC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3148
Polymers18,8701
Non-polymers4457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.080, 47.020, 93.240
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number3
Space group name H-MP121

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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.: 3 / 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.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.86 Å3/Da / Density % sol: 56.98 % / Description: Square-plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 29% (w/v) PEG 8000, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→39.393 Å / Num. obs: 36885 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.53 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.079 / Net I/σ(I): 7.3 / Num. measured all: 118930 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.163.20.9581.4984230500.5260.633100
8.91-39.3930.02225.515375120.9990.01596.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.35 Å39.39 Å
Translation6.86 Å39.39 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1488refinement
iMOSFLM7.1.0data reduction
Aimless0.2.14data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5X

4n5x


Resolution: 2.1→39.393 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 1867 5.06 %
Rwork0.2364 --
obs0.2383 36863 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 11 168 3926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013857
X-RAY DIFFRACTIONf_angle_d0.8295100
X-RAY DIFFRACTIONf_dihedral_angle_d14.4241403
X-RAY DIFFRACTIONf_chiral_restr0.031555
X-RAY DIFFRACTIONf_plane_restr0.003655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15680.33841430.32522677X-RAY DIFFRACTION100
2.1568-2.22030.34781440.33082696X-RAY DIFFRACTION100
2.2203-2.29190.35141430.31972669X-RAY DIFFRACTION100
2.2919-2.37380.3421490.28722677X-RAY DIFFRACTION100
2.3738-2.46890.34911220.29562708X-RAY DIFFRACTION100
2.4689-2.58120.34371470.28842641X-RAY DIFFRACTION100
2.5812-2.71730.32721400.27312699X-RAY DIFFRACTION100
2.7173-2.88750.2951480.25452675X-RAY DIFFRACTION100
2.8875-3.11030.32641270.25122711X-RAY DIFFRACTION100
3.1103-3.42320.2751570.23522673X-RAY DIFFRACTION100
3.4232-3.91810.22881470.19842708X-RAY DIFFRACTION99
3.9181-4.93490.22011560.17572701X-RAY DIFFRACTION99
4.9349-39.39970.22491440.20062761X-RAY DIFFRACTION98
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)
15.5904-2.6646-1.01437.5060.25663.28120.0836-0.54540.131-0.17630.45110.1410.0901-0.6757-0.44840.1846-0.0353-0.02070.3220.09020.1661-4.916528.731339.5317
22.3344.22411.06779.04863.10181.4342-0.28530.52630.1944-0.45220.23810.5303-0.5233-0.21510.01130.35250.1007-0.19430.2977-0.0330.3275-12.115221.579328.1307
38.981-4.7761.1342.5804-0.78934.9999-0.0613-0.3767-0.613-0.30410.06640.7210.2039-0.6279-0.0930.2136-0.01090.03460.2921-0.00360.3335-17.17490.182630.6314
47.2356-4.61614.74257.52062.29749.3087-0.3646-1.1551-0.35791.21820.0430.9860.0762-1.7460.30610.38010.08380.06350.5098-0.11760.427-20.307311.558436.8069
51.25250.8434-1.64952.0309-1.13653.7374-0.6049-0.2230.25890.21850.1353-0.95730.03530.09530.38490.35070.0829-0.11060.1735-0.09480.4082-6.48167.839434.19
62.0069-2.8595-2.66695.97931.62356.0774-0.2999-0.46570.6731-0.23010.497-1.841-0.29031.7622-0.34650.3443-0.0222-0.04710.9125-0.33670.78523.021919.44937.5654
73.8603-0.1297-1.10257.96970.37920.85650.13-0.69830.653-0.11820.3082-0.5346-0.0630.5639-0.40240.2149-0.00020.04110.2857-0.15240.323610.957423.439439.9395
81.7293.2877-0.48036.9983-1.76411.0612-0.21440.26-0.2209-0.47790.0541-0.55030.04960.26790.05010.35440.04610.27010.2845-0.00320.607823.931734.192527.7809
92.578-2.2246-0.86592.9805-1.45664.84280.1388-0.76080.478-0.31270.1784-0.6841-0.0840.3385-0.24010.33680.065-0.01030.3646-0.0870.373423.097653.320731.5924
100.3404-0.69920.07281.4354-0.17173.3347-0.2937-1.42792.76770.27760.0563-1.5607-0.77391.81670.13110.28820.04190.06291.0042-0.11570.962730.99244.531639.2771
110.2676-1.29060.02596.6712-0.37733.5788-0.6795-0.3374-0.65580.39390.12520.43950.35450.24550.40320.36590.11580.17380.230.18070.5518.558241.492434.3895
124.46030.80495.17333.6361-2.32489.0319-0.05730.64870.2163-0.44070.52060.71080.0824-1.9475-0.45910.5747-0.04210.10390.6870.1270.3839-3.4441-22.46335.8899
138.87571.21026.28239.59273.60736.13180.28870.7484-0.792-0.65040.0343-1.78160.4380.7574-0.3230.57040.01340.1370.2784-0.05480.75877.6212-27.63787.3253
142.1125-2.5942.62874.4191-4.3894.3602-0.19091.16740.7606-0.73950.1398-1.3221-0.67650.45740.09830.6293-0.11360.14260.40140.08340.54838.5048-15.49883.6554
155.68584.30261.52198.4232-3.90425.3535-0.00780.08480.84070.5796-0.2196-0.9044-1.32950.41080.17670.8945-0.190.37340.4829-0.21241.22628.5642-12.274614.5048
164.0121.04762.55854.8083-5.36899.66910.2976-0.8501-0.71591.2267-0.3514-0.7008-0.3069-0.35490.09790.8202-0.11470.02050.31730.09150.46796.5128-22.848519.2225
170.8599-1.2743-0.22077.6764-0.13631.2936-0.0491-0.0922-0.23990.6951-0.04450.99970.2848-0.52950.07020.6025-0.18970.38340.4089-0.15540.6128-9.5802-8.099513.0553
182.9902-0.0596-2.23782.879-1.71348.7429-0.41181.028-0.1639-0.16020.17850.049-0.0777-0.42740.28270.4916-0.14330.05870.3773-0.03870.3719-6.68710.826310.0433
190.9997-0.692-0.07643.01523.1054.4679-0.17050.5463-0.357-0.5333-0.17160.2195-0.0626-0.53190.50720.9487-0.34840.5550.2755-0.75730.6263-5.8228-4.56236.359
203.66512.4263-1.8168.7545-4.64115.7318-0.14280.0148-0.08760.1821-0.1658-1.4634-0.29820.31410.2940.6006-0.16270.21590.2429-0.16910.71641.95364.89513.3613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 151 )
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 174 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 31 )
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 76 )
8X-RAY DIFFRACTION8chain 'B' and (resid 77 through 107 )
9X-RAY DIFFRACTION9chain 'B' and (resid 108 through 133 )
10X-RAY DIFFRACTION10chain 'B' and (resid 134 through 143 )
11X-RAY DIFFRACTION11chain 'B' and (resid 144 through 174 )
12X-RAY DIFFRACTION12chain 'C' and (resid 22 through 31 )
13X-RAY DIFFRACTION13chain 'C' and (resid 32 through 40 )
14X-RAY DIFFRACTION14chain 'C' and (resid 41 through 56 )
15X-RAY DIFFRACTION15chain 'C' and (resid 57 through 67 )
16X-RAY DIFFRACTION16chain 'C' and (resid 68 through 76 )
17X-RAY DIFFRACTION17chain 'C' and (resid 77 through 107 )
18X-RAY DIFFRACTION18chain 'C' and (resid 108 through 134 )
19X-RAY DIFFRACTION19chain 'C' and (resid 135 through 158 )
20X-RAY DIFFRACTION20chain 'C' and (resid 159 through 174 )

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