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- PDB-2n5x: C-terminal domain of Cdc37 cochaperone -

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Basic information

Entry
Database: PDB / ID: 2n5x
TitleC-terminal domain of Cdc37 cochaperone
ComponentsHsp90 co-chaperone Cdc37
KeywordsCHAPERONE / cdc37 / Hsp90 / kinase / co-chaperone
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 / post-transcriptional regulation of gene expression / 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 ...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 / post-transcriptional regulation of gene expression / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of type I interferon-mediated signaling pathway / protein targeting / RHOBTB2 GTPase cycle / Signaling by ERBB2 / heat shock protein binding / Constitutive Signaling by Overexpressed ERBB2 / Signaling by ERBB2 TMD/JMD mutants / Hsp90 protein binding / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Downregulation of ERBB2 signaling / kinase binding / unfolded protein binding / protein folding / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / protein-folding chaperone binding / scaffold protein binding / protein stabilization / protein kinase binding / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #250 / 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 ...Helix Hairpins - #250 / 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 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKeramisanou, D. / Dudhat, A. / Pare, M.
CitationJournal: J.Biomol.Nmr / Year: 2015
Title: The C-terminal domain of human Cdc37 studied by solution NMR.
Authors: Zhang, Z. / Keramisanou, D. / Dudhat, A. / Pare, M. / Gelis, I.
History
DepositionAug 2, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hsp90 co-chaperone Cdc37


Theoretical massNumber of molelcules
Total (without water)10,1971
Polymers10,1971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hsp90 co-chaperone Cdc37 / Hsp90 chaperone protein kinase-targeting subunit / p50Cdc37 / Hsp90 co-chaperone Cdc37 / N- ...Hsp90 chaperone protein kinase-targeting subunit / p50Cdc37 / Hsp90 co-chaperone Cdc37 / N-terminally processed


Mass: 10197.366 Da / Num. of mol.: 1 / Fragment: C-terminal domain of Cdc37, UNP residues 288-378
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CO)CA
1313D HN(CA)CB
1413D CBCA(CO)NH
1522D 1H-15N HSQC
1612D 1H-13C HSQC
1732D 1H-13C HSQC aliphatic
1813D H(CCO)NH
1913D C(CO)NH
11023D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11212D 1H-13C HSQC aromatic
11322D 1H-15N HSQC
11413D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-0.5 mM [U-100% 13C; U-100% 15N] Cdc37, 100 mM sodium chloride, 50 mM HEPES, 7 % [U-100% 2H] D2O, 93 % H2O, 2 mM DTT, 93% H2O/7% D2O93% H2O/7% D2O
20.3-0.5 mM [U-100% 15N] Cdc37, 100 mM sodium chloride, 50 mM HEPES, 7 % [U-2H] D2O, 93 % H2O, 2 mM DTT, 93% H2O/7% D2O93% H2O/7% D2O
30.3-0.5 mM [U-10% 13C; U-100% 15N] Cdc37, 100 mM sodium chloride, 5 mM HEPES, 7 % [U-2H] D2O, 93 % H2O, 2 mM DTT, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCdc37-1[U-100% 13C; U-100% 15N]0.3-0.51
100 mMsodium chloride-21
50 mMHEPES-31
7 %D2O-4[U-100% 2H]1
93 %H2O-51
2 mMDTT-61
mMCdc37-7[U-100% 15N]0.3-0.52
100 mMsodium chloride-82
50 mMHEPES-92
7 %D2O-10[U-2H]2
93 %H2O-112
2 mMDTT-122
mMCdc37-13[U-10% 13C; U-100% 15N]0.3-0.53
100 mMsodium chloride-143
5 mMHEPES-153
7 %D2O-16[U-2H]3
93 %H2O-173
2 mMDTT-183
Sample conditionsIonic strength: 100 / pH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian VNMRSVarianVNMRS6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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