[English] 日本語
Yorodumi
- PDB-4aif: AIP TPR domain in complex with human Hsp90 peptide -

+
Open data


ID or keywords:

Loading...

-
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-ALPHAHeat shock response
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 / regulation of protein kinase A signaling / protein targeting to mitochondrion / protein maturation by protein folding / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding ...GAF domain binding / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / regulation of protein kinase A signaling / protein targeting to mitochondrion / protein maturation by protein folding / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / 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 / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / aryl hydrocarbon receptor binding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / skeletal muscle contraction / protein unfolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / DNA polymerase binding / positive regulation of lamellipodium assembly / axonal growth cone / eNOS activation / endocytic vesicle lumen / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle contraction / positive regulation of defense response to virus by host / Signaling by ERBB2 / Recruitment of mitotic centrosome proteins and complexes / cardiac muscle cell apoptotic process / response to salt stress / positive regulation of telomerase activity / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of interferon-beta production / activation of innate immune response / xenobiotic metabolic process / response to cold / nitric-oxide synthase regulator activity / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / AURKA Activation by TPX2 / response to cocaine / VEGFR2 mediated vascular permeability / peptidyl-prolyl cis-trans isomerase activity / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / cellular response to virus / VEGFA-VEGFR2 Pathway / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus
Similarity search - Function
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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain ...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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 response / 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 / Sulfate


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more