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- PDB-4apo: AIP TPR domain in complex with human Tomm20 peptide -

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Basic information

Entry
Database: PDB / ID: 4apo
TitleAIP TPR domain in complex with human Tomm20 peptide
Components
  • AH RECEPTOR-INTERACTING PROTEIN
  • MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
KeywordsSIGNALING PROTEIN/PEPTIDE / SIGNALING PROTEIN-PEPTIDE COMPLEX / ARYL HYDROCARBON RECEPTOR
Function / homology
Function and homology information


GAF domain binding / tRNA import into mitochondrion / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / protein-transporting ATPase activity ...GAF domain binding / tRNA import into mitochondrion / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / protein-transporting ATPase activity / regulation of protein kinase A signaling / Mitochondrial protein import / protein targeting to mitochondrion / protein maturation by protein folding / protein insertion into mitochondrial outer membrane / aryl hydrocarbon receptor binding / sperm midpiece / PINK1-PRKN Mediated Mitophagy / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / xenobiotic metabolic process / peptidyl-prolyl cis-trans isomerase activity / cell periphery / unfolded protein binding / mitochondrial outer membrane / transcription coactivator activity / Ub-specific processing proteases / mitochondrion / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / AIP/AIPL1 / Tetratricopeptide repeat domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily ...Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / AIP/AIPL1 / Tetratricopeptide repeat domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
AH receptor-interacting protein / Mitochondrial import receptor subunit TOM20 homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsMorgan, R.M.L. / Roe, S.M. / Pearl, L.H. / Prodromou, C.
CitationJournal: Plos One / Year: 2012
Title: Structure of the Tpr Domain of Aip: Lack of Client Protein Interaction with the C-Terminal Alpha-7 Helix of the Tpr Domain of Aip is Sufficient for Pituitary Adenoma Predisposition.
Authors: Morgan, R.M. / Hernandez-Ramirez, L.C. / Trivellin, G. / Zhou, L. / Roe, S.M. / Korbonits, M. / Prodromou, C.
History
DepositionApr 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: AH RECEPTOR-INTERACTING PROTEIN
B: AH RECEPTOR-INTERACTING PROTEIN
D: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
E: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9436
Polymers39,3004
Non-polymers6432
Water8,611478
1
A: AH RECEPTOR-INTERACTING PROTEIN
E: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)19,6502
Polymers19,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-0.8 kcal/mol
Surface area8160 Å2
MethodPISA
2
B: AH RECEPTOR-INTERACTING PROTEIN
D: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2934
Polymers19,6502
Non-polymers6432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-5.8 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.200, 106.820, 68.470
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2117-

HOH

21A-2126-

HOH

31B-2098-

HOH

41B-2108-

HOH

51B-2233-

HOH

61D-2009-

HOH

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Components

#1: Protein AH RECEPTOR-INTERACTING PROTEIN / AIP / ARYL-HYDROCARBON RECEPTOR-INTERACTING PROTEIN / HBV X-ASSOCIATED PROTEIN 2 / XAP-2 / ...AIP / ARYL-HYDROCARBON RECEPTOR-INTERACTING PROTEIN / HBV X-ASSOCIATED PROTEIN 2 / XAP-2 / IMMUNOPHILIN HOMOLOG ARA9


Mass: 18973.553 Da / Num. of mol.: 2 / Fragment: TETRATRICOPEPTIDE REPEAT DOMAIN, RESIDUES 172-313 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTWO-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O00170
#2: Protein/peptide MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG / TOMM20 C-TERMINAL PEPTIDE / MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN / OUTER MITOCHONDRIAL ...TOMM20 C-TERMINAL PEPTIDE / MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN / OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20


Mass: 676.627 Da / Num. of mol.: 2 / Fragment: RESIDUES 140-145 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15388
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.04 Å3/Da / Density % sol: 39.88 % / Description: NONE
Crystal growDetails: PEG 3350, AMMONIUM SULFATE, BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 9, 2011 / Details: MIRRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→8.52 Å / Num. obs: 32055 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 24.09 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 8.7 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AIF

4aif


Resolution: 1.895→28.454 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 25.85 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2344 1455 5.1 %
Rwork0.1809 --
obs0.1836 28495 84.52 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.592 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 26.017 Å2
Baniso -1Baniso -2Baniso -3
1-3.3253 Å20 Å27.7211 Å2
2---1.3015 Å20 Å2
3----2.0238 Å2
Refinement stepCycle: LAST / Resolution: 1.895→28.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 42 478 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062578
X-RAY DIFFRACTIONf_angle_d0.9063492
X-RAY DIFFRACTIONf_dihedral_angle_d14.484985
X-RAY DIFFRACTIONf_chiral_restr0.068375
X-RAY DIFFRACTIONf_plane_restr0.003462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.895-1.96280.4868950.46151709X-RAY DIFFRACTION54
1.9628-2.04130.28361790.21983133X-RAY DIFFRACTION98
2.0413-2.13420.251240.1862465X-RAY DIFFRACTION77
2.1342-2.24670.25941840.21432699X-RAY DIFFRACTION95
2.2467-2.38740.29911320.20742596X-RAY DIFFRACTION95
2.3874-2.57160.24361440.17293155X-RAY DIFFRACTION98
2.5716-2.83020.21931400.16832635X-RAY DIFFRACTION82
2.8302-3.23920.21261760.16943112X-RAY DIFFRACTION98
3.2392-4.07910.21851290.15292491X-RAY DIFFRACTION77
4.0791-28.45740.2011520.1673045X-RAY DIFFRACTION94

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