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- PDB-4aif: AIP TPR domain in complex with human Hsp90 peptide -

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Basic information

Entry
Database: PDB / ID: 4aif
TitleAIP TPR domain in complex with human Hsp90 peptide
Components
  • AH RECEPTOR-INTERACTING PROTEIN
  • HEAT SHOCK PROTEIN HSP 90-ALPHA
KeywordsSIGNALING PROTEIN/PEPTIDE / SIGNALING PROTEIN-PEPTIDE COMPLEX / ARYL HYDROCARBON RECEPTOR
Function / homology
Function and homology information


GAF domain binding / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / : / sperm plasma membrane / sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / Scavenging by Class F Receptors / positive regulation of protein polymerization ...GAF domain binding / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / : / sperm plasma membrane / sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / Scavenging by Class F Receptors / positive regulation of protein polymerization / vRNP Assembly / UTP binding / mitochondrial transport / dATP binding / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / Uptake and function of diphtheria toxin / positive regulation of cell size / dendritic growth cone / protein import into mitochondrial matrix / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / aryl hydrocarbon receptor binding / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / response to salt stress / protein folding chaperone complex / HSF1-dependent transactivation / response to unfolded protein / cardiac muscle cell apoptotic process / regulation of protein-containing complex assembly / Attenuation phase / HSF1 activation / enzyme-substrate adaptor activity / chaperone-mediated protein complex assembly / axonal growth cone / telomere maintenance via telomerase / neurofibrillary tangle assembly / positive regulation of lamellipodium assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / RHOBTB2 GTPase cycle / Dengue virus activates/modulates innate and adaptive immune responses / nitric oxide metabolic process / response to cold / protein unfolding / positive regulation of defense response to virus by host / skeletal muscle contraction / Signaling by ERBB2 / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of telomere maintenance via telomerase / endocytic vesicle lumen / DNA polymerase binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle contraction / Recruitment of mitotic centrosome proteins and complexes / lysosomal lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / activation of innate immune response / ESR-mediated signaling / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / protein tyrosine kinase binding / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / nitric-oxide synthase regulator activity / ATP-dependent protein folding chaperone / VEGFR2 mediated vascular permeability / brush border membrane / peptidyl-prolyl cis-trans isomerase activity / response to cocaine / cellular response to virus / protein maturation / positive regulation of protein import into nucleus / myelin sheath / neuron migration / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / protein refolding / Regulation of actin dynamics for phagocytic cup formation / response to estrogen
Similarity search - Function
: / AH receptor-interacting protein, N-terminal FKBP-type PPIase / AIP/AIPL1 / Tetratricopeptide repeat domain / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein ...: / AH receptor-interacting protein, N-terminal FKBP-type PPIase / AIP/AIPL1 / Tetratricopeptide repeat domain / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Mainly Alpha
Similarity search - Domain/homology
AH receptor-interacting protein / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 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
DepositionFeb 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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: HEAT SHOCK PROTEIN HSP 90-ALPHA
E: HEAT SHOCK PROTEIN HSP 90-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7275
Polymers34,6314
Non-polymers961
Water5,855325
1
A: AH RECEPTOR-INTERACTING PROTEIN
D: HEAT SHOCK PROTEIN HSP 90-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4123
Polymers17,3162
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-9.8 kcal/mol
Surface area8700 Å2
MethodPISA
2
B: AH RECEPTOR-INTERACTING PROTEIN
E: HEAT SHOCK PROTEIN HSP 90-ALPHA


Theoretical massNumber of molelcules
Total (without water)17,3162
Polymers17,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-3.8 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.820, 104.490, 69.270
Angle α, β, γ (deg.)90.00, 97.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2076-

HOH

21E-2010-

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: 16449.746 Da / Num. of mol.: 2 / Fragment: TETRATRICOPEPTIDE DOMAIN, RESIDUES 172-315 / 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 HEAT SHOCK PROTEIN HSP 90-ALPHA / HEAT SHOCK 86 KDA / HSP 86 / HSP86 / RENAL CARCINOMA ANTIGEN NY-REN-38


Mass: 865.929 Da / Num. of mol.: 2 / Fragment: C-TERMINAL PEPTIDE SRMEEVD, RESIDUES 726-732 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P07900
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 172 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 172 TO ALA

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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: 3.03 Å3/Da / Density % sol: 59.4 % / Description: NONE
Crystal growDetails: 1 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5, 1% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.01→40.41 Å / Num. obs: 29974 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 29.62 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.9
Reflection shellResolution: 2.01→8.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TPR HOMOLOGY MODEL

Resolution: 2.006→40.405 Å / SU ML: 0.29 / σ(F): 1.4 / Phase error: 22.72 / Stereochemistry target values: MLHL / Details: RESIDUES 172-176 AND 312-315 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.236 1519 5.1 %
Rwork0.1879 --
obs0.1903 29971 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.129 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 36.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.9602 Å20 Å21.099 Å2
2---0.1022 Å20 Å2
3----2.8579 Å2
Refinement stepCycle: LAST / Resolution: 2.006→40.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 5 325 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062461
X-RAY DIFFRACTIONf_angle_d0.963351
X-RAY DIFFRACTIONf_dihedral_angle_d13.17918
X-RAY DIFFRACTIONf_chiral_restr0.07372
X-RAY DIFFRACTIONf_plane_restr0.004437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0063-2.07110.35141420.28392559X-RAY DIFFRACTION99
2.0711-2.14510.28461530.24352545X-RAY DIFFRACTION99
2.1451-2.23090.25241350.21682601X-RAY DIFFRACTION99
2.2309-2.33250.26671270.20882571X-RAY DIFFRACTION100
2.3325-2.45540.28641570.2062593X-RAY DIFFRACTION100
2.4554-2.60920.22691320.20412566X-RAY DIFFRACTION100
2.6092-2.81070.27371290.19012599X-RAY DIFFRACTION100
2.8107-3.09340.23341270.18652612X-RAY DIFFRACTION100
3.0934-3.54080.2121430.1752607X-RAY DIFFRACTION100
3.5408-4.46010.19691310.15512599X-RAY DIFFRACTION99
4.4601-40.41340.22541430.18092600X-RAY DIFFRACTION98

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