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- PDB-2nca: Structural Model for the N-terminal Domain of Human Cdc37 -

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Basic information

Entry
Database: PDB / ID: 2nca
TitleStructural Model for the N-terminal Domain of Human Cdc37
ComponentsHsp90 co-chaperone Cdc37
KeywordsCHAPERONE / cochaperone
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 / regulation of cyclin-dependent protein serine/threonine kinase activity / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib ...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 / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 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 / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsZhang, Z. / Keramisanou, D. / Gelis, I.
CitationJournal: Mol.Cell / Year: 2016
Title: Molecular Mechanism of Protein Kinase Recognition and Sorting by the Hsp90 Kinome-Specific Cochaperone Cdc37.
Authors: Keramisanou, D. / Aboalroub, A. / Zhang, Z. / Liu, W. / Marshall, D. / Diviney, A. / Larsen, R.W. / Landgraf, R. / Gelis, I.
History
DepositionMar 23, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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)15,4071
Polymers15,4071
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)20 / 100target function
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: 15407.263 Da / Num. of mol.: 1 / Fragment: N-terminal Domain residues 1-120
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): BL21DE3 / References: UniProt: Q16543

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: N-terminal Domain of Human Cdc37
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HMQC
1333D HNCA
1433D HN(CO)CA
1533D HN(CA)CB
1633D CBCA(CO)NH
1733D HNCO
1833D HCACO
1933D H(CCO)NH
11033D (H)CCH-TOCSY
11133D C(CO)NH
11213D 1H-15N NOESY
11333D 1H-13C NOESY
1142HMQC-NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] N-Cdc37, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM U-2H; VILMA methyl 1H/13C N-Cdc37, 100% D2O100% D2O
30.5 mM [U-100% 13C; U-100% 15N] N-Cdc37, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMN-Cdc37-1[U-100% 15N]1
0.5 mMN-Cdc37-2U-2H; VILMA methyl 1H/13C2
0.5 mMN-Cdc37-3[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System6001
Varian Uniform NMR SystemVarianUniform NMR System8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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