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- PDB-2nc9: Apo solution structure of Hop TPR2A -

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Basic information

Entry
Database: PDB / ID: 2nc9
TitleApo solution structure of Hop TPR2A
ComponentsStress-induced-phosphoprotein 1
KeywordsCHAPERONE / heat-shock / Hsp90 / TPR
Function / homology
Function and homology information


dynein axonemal particle / cellular response to interleukin-7 / protein folding chaperone complex / RND1 GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Hsp90 protein binding / Golgi apparatus / protein-containing complex / RNA binding / nucleus / cytosol
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 / Tetratricopeptide repeat domain ...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 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Stress-induced-phosphoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsDarby, J.F. / Vidler, L.R. / Simpson, P.J. / Matthews, S.J. / Sharp, S.Y. / Pearl, L.H. / Hoelder, S. / Workman, P.
CitationJournal: Sci Rep / Year: 2020
Title: Solution structure of the Hop TPR2A domain and investigation of target druggability by NMR, biochemical and in silico approaches.
Authors: Darby, J.F. / Vidler, L.R. / Simpson, P.J. / Al-Lazikani, B. / Matthews, S.J. / Sharp, S.Y. / Pearl, L.H. / Hoelder, S. / Workman, P.
History
DepositionMar 23, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stress-induced-phosphoprotein 1


Theoretical massNumber of molelcules
Total (without water)15,5701
Polymers15,5701
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 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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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: 15569.569 Da / Num. of mol.: 1 / Fragment: residues 280-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: pTWO-E base on pET17-b vector / Gene: STIP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 (pLysS) / References: UniProt: P31948

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CO)CA
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D (H)CCH-TOCSY
1913D H(CCCO)NH-TOCSY
11013D (H)C(CCO)NH-TOCSY
11113D 1H-15N NOESY
11223D 1H-13C NOESY
11312D (HB)CB(CGCD)H-TOCSY
11412D 1H-13C HSQC aromatic
11512D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-13C; U-15N] protein, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-13C; U-15N] protein, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMentity-1[U-13C; U-15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
0.01 %sodium azide-51
1.5 mMentity-6[U-13C; U-15N]2
20 mMsodium phosphate-72
50 mMsodium chloride-82
1 mMDTT-92
0.01 %sodium azide-102
Sample conditionsIonic strength: 70 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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