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- PDB-9qqu: Crystal structure of an engineered TPR domain in complex with the... -

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Basic information

Entry
Database: PDB / ID: 9qqu
TitleCrystal structure of an engineered TPR domain in complex with the HSP90 peptide MEEVD
Components
  • Heat shock protein HSP 90-alpha
  • Stress-induced-phosphoprotein 1
KeywordsCHAPERONE / Engineered protein / Complex / Tetratricopeptide repeat domain / Hsp90 protein binding
Function / homology
Function and homology information


dynein axonemal particle / cellular response to interleukin-7 / RND1 GTPase cycle / sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding ...dynein axonemal particle / cellular response to interleukin-7 / RND1 GTPase cycle / sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / dATP binding / sperm plasma membrane / chaperone-mediated autophagy / mitochondrial transport / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / 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 / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / protein folding chaperone complex / response to unfolded protein / regulation of protein-containing complex assembly / Attenuation phase / enzyme-substrate adaptor activity / HSF1 activation / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / axonal growth cone / RHOBTB2 GTPase cycle / telomere maintenance via telomerase / regulation of postsynaptic membrane neurotransmitter receptor levels / nitric oxide metabolic process / positive regulation of lamellipodium assembly / skeletal muscle contraction / positive regulation of defense response to virus by host / Signaling by ERBB2 / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of telomere maintenance via telomerase / response to salt stress / cardiac muscle cell apoptotic process / endocytic vesicle lumen / DNA polymerase binding / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / lysosomal lumen / Anchoring of the basal body to the plasma membrane / ESR-mediated signaling / activation of innate immune response / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / protein tyrosine kinase binding / response to cold / Constitutive Signaling by Overexpressed ERBB2 / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Hsp90 protein binding / Signaling by ERBB2 ECD mutants / cellular response to virus / positive regulation of protein import into nucleus / Signaling by ERBB2 KD Mutants / Regulation of actin dynamics for phagocytic cup formation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to estrogen / VEGFA-VEGFR2 Pathway / Regulation of necroptotic cell death / tau protein binding / neuron migration / histone deacetylase binding / Downregulation of ERBB2 signaling / Chaperone Mediated Autophagy
Similarity search - Function
STI1/HOP, DP domain / STI1/HOP, DP domain / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site ...STI1/HOP, DP domain / STI1/HOP, DP domain / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha / Stress-induced-phosphoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsPinotis, N. / Bell, R. / Williams, M.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)101004806European Union
CitationJournal: To Be Published
Title: Engineering a robust protein-protein interaction motif
Authors: Bell, R. / Pinotsis, N. / Driva, D. / Daviter, T. / Garza-Garcia, A. / Williams, M.A.
History
DepositionApr 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stress-induced-phosphoprotein 1
B: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7204
Polymers18,5282
Non-polymers1922
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-20 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.692, 67.692, 56.212
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-101-

SO4

21B-101-

SO4

31A-335-

HOH

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Components

#1: Protein Stress-induced-phosphoprotein 1 / STI1 / Hsc70/Hsp90-organizing protein / Hop / Renal carcinoma antigen NY-REN-11 / Transformation- ...STI1 / Hsc70/Hsp90-organizing protein / Hop / Renal carcinoma antigen NY-REN-11 / Transformation-sensitive protein IEF SSP 3521


Mass: 17880.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31948
#2: Protein/peptide Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP 86 / HSP86 / Heat shock protein family C member 1 / Lipopolysaccharide- ...Heat shock 86 kDa / HSP 86 / HSP86 / Heat shock protein family C member 1 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 647.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Acetylated methionine / Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: synthetic construct (others)
References: UniProt: P07900, non-chaperonin molecular chaperone ATPase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 29 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium Acetate, pH 5.0 2.0 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.13→57 Å / Num. obs: 8617 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 37.76 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.294 / Net I/σ(I): 7.1
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 695 / CC1/2: 0.501 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDS20230630data reduction
Aimless0.7.7data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→40.57 Å / SU ML: 0.2924 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.3079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2561 431 5.02 %
Rwork0.1976 8161 -
obs0.2004 8592 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.83 Å2
Refinement stepCycle: LAST / Resolution: 2.13→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 10 39 1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241226
X-RAY DIFFRACTIONf_angle_d0.46531639
X-RAY DIFFRACTIONf_chiral_restr0.035166
X-RAY DIFFRACTIONf_plane_restr0.0033213
X-RAY DIFFRACTIONf_dihedral_angle_d9.5407168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.440.33111710.26572644X-RAY DIFFRACTION99.68
2.44-3.070.28221220.22572716X-RAY DIFFRACTION99.93
3.08-40.570.22751380.17272801X-RAY DIFFRACTION99.56
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)
12.211761723050.560287361046-0.3986599476651.38465995380.1606401995721.44332940340.00350561278345-0.001420714513180.172610671486-0.00443058781198-0.0456526236731-0.05569224378-0.1736782344070.1226795303860.02522698244920.3222962247330.000380924607632-0.0139133637680.2741254037870.02173359623610.27043743271-25.16-5.698-4.985
24.417568212951.356243783731.671352313060.7086711445131.028092183421.50300869903-0.109647675730.03886182040030.364640964547-0.771582246999-0.210851969180.07487632799-0.564021933966-0.1693786597210.1794698248450.551055532841-0.04244161673920.1166161511070.398842956139-0.03613716889440.393457802058-25.396-2.3062.104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:150 )A12 - 150
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:6 )B1 - 6

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