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- PDB-4p60: Structure of the N-terminal domain of the human mitochondrial asp... -

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Basic information

Entry
Database: PDB / ID: 4p60
TitleStructure of the N-terminal domain of the human mitochondrial aspartate/glutamate carrier Aralar in the apo state
ComponentsCalcium-binding mitochondrial carrier protein Aralar1
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


3-sulfino-L-alanine: proton, glutamate antiporter activity / aspartate:glutamate, proton antiporter activity / acidic amino acid transmembrane transporter activity / malate-aspartate shuttle / aspartate family amino acid metabolic process / L-glutamate transmembrane transport / L-glutamate transmembrane transporter activity / aspartate transmembrane transport / Aspartate and asparagine metabolism / L-aspartate transmembrane transporter activity ...3-sulfino-L-alanine: proton, glutamate antiporter activity / aspartate:glutamate, proton antiporter activity / acidic amino acid transmembrane transporter activity / malate-aspartate shuttle / aspartate family amino acid metabolic process / L-glutamate transmembrane transport / L-glutamate transmembrane transporter activity / aspartate transmembrane transport / Aspartate and asparagine metabolism / L-aspartate transmembrane transporter activity / Mitochondrial protein import / Gluconeogenesis / gluconeogenesis / response to calcium ion / mitochondrial inner membrane / calcium ion binding / mitochondrion / identical protein binding / membrane
Similarity search - Function
Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / 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
Similarity search - Domain/homology
Electrogenic aspartate/glutamate antiporter SLC25A12, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsThangaratnarajah, C. / Ruprecht, J.J. / Kunji, E.R.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Mitochondrial European Educational TrainingGA n317433
CitationJournal: Nat Commun / Year: 2014
Title: Calcium-induced conformational changes of the regulatory domain of human mitochondrial aspartate/glutamate carriers.
Authors: Thangaratnarajah, C. / Ruprecht, J.J. / Kunji, E.R.
History
DepositionMar 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Dec 20, 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

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Assembly

Deposited unit
A: Calcium-binding mitochondrial carrier protein Aralar1
B: Calcium-binding mitochondrial carrier protein Aralar1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6263
Polymers71,6032
Non-polymers231
Water37821
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-35 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.520, 103.520, 185.559
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Calcium-binding mitochondrial carrier protein Aralar1 / Mitochondrial aspartate glutamate carrier 1 / Solute carrier family 25 member 12


Mass: 35801.316 Da / Num. of mol.: 2 / Fragment: Residues 2-311
Source method: isolated from a genetically manipulated source
Details: N-terminal domain of Aralar, apo-state / Source: (gene. exp.) Homo sapiens (human) / Gene: SLC25A12, ARALAR1 / Plasmid: pNZ8048
Production host: Lactococcus lactis subsp. cremoris NZ9000 (lactic acid bacteria)
Strain (production host): NZ9000 / References: UniProt: O75746
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.01 Å3/Da / Density % sol: 38.7 % / Description: Hexagonal block
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3M sodium acetate, 0.1M Tris, 8% PEG 20000, 8% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→29.503 Å / Num. obs: 23734 / % possible obs: 99.7 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 19
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.242 / Mean I/σ(I) obs: 1.7 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P5X

4p5x


Resolution: 2.4→29.5 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 1213 5.12 %Random selection
Rwork0.2452 ---
obs0.2477 23682 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 1 21 4102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034173
X-RAY DIFFRACTIONf_angle_d0.655656
X-RAY DIFFRACTIONf_dihedral_angle_d11.2041465
X-RAY DIFFRACTIONf_chiral_restr0.026637
X-RAY DIFFRACTIONf_plane_restr0.003735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3996-2.49570.3821220.3532414X-RAY DIFFRACTION98
2.4957-2.60920.35921440.31272432X-RAY DIFFRACTION100
2.6092-2.74670.34781360.29542437X-RAY DIFFRACTION100
2.7467-2.91860.33811450.29672442X-RAY DIFFRACTION100
2.9186-3.14370.33961480.29242464X-RAY DIFFRACTION100
3.1437-3.45960.32491390.25862471X-RAY DIFFRACTION100
3.4596-3.95920.28881180.2282523X-RAY DIFFRACTION100
3.9592-4.98430.25571340.20632547X-RAY DIFFRACTION100
4.9843-29.50570.27071270.23262739X-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)
11.60961.999-1.31212.3157-1.55971.14780.1034-3.04230.20412.4723-0.4317-0.1919-0.97551.8430.30991.20040.34990.10471.60620.79721.083636.014918.658683.3708
24.7660.5697-0.3515.4982-2.436.2984-0.3683-0.66650.12360.20410.4190.08370.23650.66180.00460.7470.2277-0.1230.88950.03070.645428.327431.720178.5682
34.47570.4357-0.52842.61270.08167.0749-0.0986-1.0350.55161.00190.2376-0.664-1.08860.13670.02430.83110.1431-0.18640.6879-0.10030.533922.847143.628174.5968
43.5347-1.34831.18792.4153-2.90866.6002-1.2088-0.9451-0.8321-0.16920.8230.74690.0741-0.044-0.0430.57480.1589-0.24650.6551-00.317418.721436.043169.9633
57.36642.91560.08066.8866-2.67333.8696-0.13640.0765-0.37370.43860.0031-0.2437-0.03650.45610.13040.33780.0785-0.00830.3137-0.0340.379215.306228.261655.5101
66.31470.84331.68387.8377-3.68697.1673-0.0508-0.6684-1.14910.4531-0.08510.51770.6-0.32360.00180.52010.0497-0.02910.32720.01250.56175.902816.454356.3334
77.3602-0.92612.90257.23180.92958.18170.1993-1.0017-1.16480.9176-0.1370.4290.9685-0.7139-0.05920.6356-0.06880.06640.52080.03870.6508-22.991135.32862.2393
84.0842-1.09310.52654.34812.42032.2215-0.225-0.23970.28540.25370.2092-0.1356-0.2026-0.1284-0.04570.64050.1591-0.19080.43090.0170.4915-0.117842.865961.9409
95.94531.99250.17385.5096-0.03811.6211-0.3245-1.7818-0.52410.3944-0.09770.3952-0.2018-0.67720.30710.91550.3682-0.11341.33110.12880.54443.06935.523982.7918
106.7146-2.30263.69023.41150.71133.5163-0.0725-1.0504-0.96870.13840.2972-0.04341.0411-0.2564-0.230.94130.28560.02851.52850.53140.94071.837823.96981.342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 121 )
3X-RAY DIFFRACTION3chain 'A' and (resid 122 through 146 )
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 169 )
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 239 )
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 295 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 169 )
9X-RAY DIFFRACTION9chain 'B' and (resid 170 through 238 )
10X-RAY DIFFRACTION10chain 'B' and (resid 239 through 308 )

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