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- PDB-4p5x: Structure of the N-terminal domain of the human mitochondrial asp... -

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Basic information

Entry
Database: PDB / ID: 4p5x
TitleStructure of the N-terminal domain of the human mitochondrial aspartate/glutamate carrier Aralar in the calcium-bound state
ComponentsCalcium-binding mitochondrial carrier protein Aralar1
Keywordscalcium binding protein / regulatory-domain / EF hand / mitochondrial carrier
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: 2.261 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 / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
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 / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8412
Polymers35,8011
Non-polymers401
Water41423
1
A: Calcium-binding mitochondrial carrier protein Aralar1
hetero molecules

A: Calcium-binding mitochondrial carrier protein Aralar1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6834
Polymers71,6032
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3750 Å2
ΔGint-49 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.450, 54.450, 168.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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.: 1 / Fragment: Residues 6-311
Source method: isolated from a genetically manipulated source
Details: N-terminal domain of Aralar / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 38.9 % / Description: Hexagonal block
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M MIB, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.898 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.898 Å / Relative weight: 1
ReflectionResolution: 2.26→28.033 Å / Num. obs: 14197 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 21.3
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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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: 4P5W

4p5w


Resolution: 2.261→28.03 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 710 5 %Random selection
Rwork0.2312 ---
obs0.2334 14196 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.1 Å2
Refinement stepCycle: LAST / Resolution: 2.261→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 1 23 2141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052169
X-RAY DIFFRACTIONf_angle_d0.5432948
X-RAY DIFFRACTIONf_dihedral_angle_d10.47768
X-RAY DIFFRACTIONf_chiral_restr0.021327
X-RAY DIFFRACTIONf_plane_restr0.003381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2613-2.43580.32161510.27442613X-RAY DIFFRACTION100
2.4358-2.68070.27121390.26132650X-RAY DIFFRACTION100
2.6807-3.06820.3171400.25672679X-RAY DIFFRACTION100
3.0682-3.8640.28611430.2452694X-RAY DIFFRACTION100
3.864-28.03550.25291370.21032850X-RAY DIFFRACTION99
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)
17.8359-2.65420.49558.38383.65326.0681-0.30110.1539-1.1250.1778-0.08760.88470.1266-0.86840.21160.38830.084-0.02470.7215-0.01550.5855-18.1835-7.32331.3394
24.01771.12810.03883.08651.47887.93830.3921-0.01440.12980.0217-0.24020.5485-0.4651-1.0094-0.15560.39480.1463-0.04910.5290.02020.5513-17.122213.193321.3447
32.3557-1.31040.75924.0283-0.05483.19880.9955-0.0562-1.51620.62610.06480.23471.9952-0.3513-0.61321.5376-0.12-0.53510.44620.02480.9972-10.4017-4.324737.875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 294 )

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