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- PDB-2k5b: Human CDC37-HSP90 docking model based on NMR -

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Basic information

Entry
Database: PDB / ID: 2k5b
TitleHuman CDC37-HSP90 docking model based on NMR
Components
  • Heat shock protein HSP 90-alpha
  • Hsp90 co-chaperone Cdc37
KeywordsCHAPERONE / CDC37 / HSP90 / protein-protein interaction / heat shock protein / P50 / Alternative splicing / ATP-binding / Cytoplasm / Nucleotide-binding / Phosphoprotein / Stress response / Polymorphism
Function / homology
Function and homology information


regulation of type II interferon-mediated signaling pathway / HSP90-CDC37 chaperone complex / positive regulation of mitophagy in response to mitochondrial depolarization / protein kinase regulator activity / protein folding chaperone complex / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding ...regulation of type II interferon-mediated signaling pathway / HSP90-CDC37 chaperone complex / positive regulation of mitophagy in response to mitochondrial depolarization / protein kinase regulator activity / protein folding chaperone complex / 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 / post-transcriptional regulation of gene expression / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / regulation of cyclin-dependent protein serine/threonine kinase activity / Respiratory syncytial virus genome replication / 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 / Assembly and release of respiratory syncytial virus (RSV) virions / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / regulation of type I interferon-mediated signaling pathway / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / protein unfolding / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / protein targeting / RHOBTB2 GTPase cycle / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / : / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of defense response to virus by host / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Recruitment of NuMA to mitotic centrosomes / response to salt stress / Anchoring of the basal body to the plasma membrane / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / lysosomal lumen / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Hsp90 protein binding / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / Downregulation of ERBB2 signaling / kinase binding
Similarity search - Function
Cdc37, Hsp90 binding domain / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 ...Cdc37, Hsp90 binding domain / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 / Cdc37, N-terminal domain / Cdc37 N terminal kinase binding / 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 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha / Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsStructure of the human CDC37-HSP90 complex based on NMR using CSPs, RDCs and docking with HADDOCK
AuthorsSreeramulu, S. / Jonker, H.R.A. / Lancaster, C.R. / Richter, C. / Langer, T. / Schwalbe, H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The human Cdc37.Hsp90 complex studied by heteronuclear NMR spectroscopy
Authors: Sreeramulu, S. / Jonker, H.R.A. / Langer, T. / Richter, C. / Lancaster, C.R. / Schwalbe, H.
History
DepositionJun 26, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
B: Hsp90 co-chaperone Cdc37


Theoretical massNumber of molelcules
Total (without water)39,0572
Polymers39,0572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the best HADDOCK scoring
RepresentativeModel #1best haddock score

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Components

#1: Protein Heat shock protein HSP 90-alpha / HSP 86 / Renal carcinoma antigen NY-REN-38


Mass: 23535.592 Da / Num. of mol.: 1 / Fragment: residues 14-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07900
#2: Protein Hsp90 co-chaperone Cdc37 / Hsp90 chaperone protein kinase-targeting subunit / p50Cdc37


Mass: 15521.082 Da / Num. of mol.: 1 / Fragment: residues 148-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC37, CDC37A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16543
Sequence detailsTHIS RESIDUE IS UNP DATABASE P07900 REF.1(CAA33259)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the human CDC37-HSP90 complex based on NMR using CSPs, RDCs and docking with HADDOCK
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D 1H-15N NOESY
1333D 1H-15N NOESY
141IPAP(1H,15N)HSQC
151IPAP(1H,15N)HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM [U-100% 15N] human HSP90, 0.8mM [U-100% 15N] human CDC37, 50mM HEPES, 100mM sodium chloride, 1mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.8mM [U-100% 15N, U-100% 2H] human HSP90, 0.8mM human CDC37, 50mM HEPES, 100mM sodium chloride, 1mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.8mM human HSP90, 0.8mM [U-100% 15N, U-100% 2H] human CDC37, 50mM HEPES, 100mM sodium chloride, 1mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMhuman HSP90[U-100% 15N]1
0.8 mMhuman CDC37[U-100% 15N]1
50 mMHEPES1
100 mMsodium chloride1
1 mMDTT1
0.8 mMhuman HSP90[U-100% 15N, U-100% 2H]2
0.8 mMhuman CDC372
50 mMHEPES2
100 mMsodium chloride2
1 mMDTT2
0.8 mMhuman HSP903
0.8 mMhuman CDC37[U-100% 15N, U-100% 2H]3
50 mMHEPES3
100 mMsodium chloride3
1 mMDTT3
Sample conditionsIonic strength: 100 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
CARA1.8.3Keller and Wuthrichdata analysis
CARA1.8.3Keller and Wuthrichpeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
HADDOCK2A. Bonvin & C. Dominguezgeometry optimization
HADDOCK2Dominguez, Boelens and Bonvinrefinement
HADDOCK2A. Bonvin & C. Dominguezstructure solution
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structure was calculated using HADDOCK Details can be found in the jrnl citation above
NMR representativeSelection criteria: best haddock score
NMR ensembleConformer selection criteria: structures with the best HADDOCK scoring
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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