[English] 日本語
Yorodumi
- PDB-4cgv: First TPR of Spaghetti (RPAP3) bound to HSP90 peptide SRMEEVD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cgv
TitleFirst TPR of Spaghetti (RPAP3) bound to HSP90 peptide SRMEEVD
Components
  • HEAT SHOCK PROTEIN HSP 90-ALPHAHeat shock response
  • RNA POLYMERASE II-ASSOCIATED PROTEIN 3
KeywordsCHAPERONE / R2TP / TAH1 / PIH1
Function / homology
Function and homology information


R2TP complex / RPAP3/R2TP/prefoldin-like complex / 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 ...R2TP complex / RPAP3/R2TP/prefoldin-like complex / 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 / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / 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 / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / positive regulation of cell size / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / protein unfolding / chaperone-mediated protein complex assembly / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / axonal growth cone / 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 / positive regulation of cardiac muscle contraction / Recruitment of mitotic centrosome proteins and complexes / cardiac muscle cell apoptotic process / positive regulation of telomerase activity / Signaling by ERBB2 / positive regulation of defense response to virus by host / endocytic vesicle lumen / response to salt stress / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / response to cold / positive regulation of interferon-beta production / nitric-oxide synthase regulator activity / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / 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 / 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 / VEGFA-VEGFR2 Pathway / histone deacetylase binding / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / Regulation of PLK1 Activity at G2/M Transition
Similarity search - Function
RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain ...RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Mainly Alpha
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha / RNA polymerase II-associated protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsRoe, S.M. / Pal, M.
CitationJournal: Structure / Year: 2014
Title: Structural Basis for Phosphorylation-Dependent Recruitment of Tel2 to Hsp90 by Pih1.
Authors: Pal, M. / Morgan, M. / Phelps, S.E. / Roe, S.M. / Parry-Morris, S. / Downs, J.A. / Polier, S. / Pearl, L.H. / Prodromou, C.
History
DepositionNov 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
B: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
C: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
D: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
E: HEAT SHOCK PROTEIN HSP 90-ALPHA
F: HEAT SHOCK PROTEIN HSP 90-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9177
Polymers63,8256
Non-polymers921
Water1,44180
1
B: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
F: HEAT SHOCK PROTEIN HSP 90-ALPHA


Theoretical massNumber of molelcules
Total (without water)16,3892
Polymers16,3892
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-1.7 kcal/mol
Surface area6820 Å2
MethodPISA
2
A: RNA POLYMERASE II-ASSOCIATED PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)15,5231
Polymers15,5231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
E: HEAT SHOCK PROTEIN HSP 90-ALPHA


Theoretical massNumber of molelcules
Total (without water)16,3892
Polymers16,3892
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA POLYMERASE II-ASSOCIATED PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6152
Polymers15,5231
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.050, 59.120, 65.860
Angle α, β, γ (deg.)63.42, 67.50, 82.43
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 128:251 )
211CHAIN D AND (RESSEQ 128:251 )
112CHAIN B AND (RESSEQ 128:251 )
212CHAIN C AND (RESSEQ 128:251 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.96454, 0.263937, 0.000842), (0.263937, 0.96454, -0.000358), (-0.000907, -0.000123, -1)8.41701, -1.06655, 2.72084
2given(-0.964958, 0.262404, 0.00071), (0.262405, 0.964954, 0.002638), (7.0E-6, 0.002732, -0.999996)8.41165, -1.10225, 2.7077

-
Components

#1: Protein
RNA POLYMERASE II-ASSOCIATED PROTEIN 3 / SPAGHETTI


Mass: 15523.374 Da / Num. of mol.: 4 / Fragment: FIRST TPR, RESIDUES 120-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9H6T3
#2: Protein/peptide HEAT SHOCK PROTEIN HSP 90-ALPHA / Heat shock response / HEAT SHOCK 86 KDA / HSP 86 / HSP86 / RENAL CARCINOMA ANTIGEN NY-REN-38 / HSP90


Mass: 865.929 Da / Num. of mol.: 2 / Fragment: C-TERMINAL PEPTIDE, RESIDUES 726-732 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P07900
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.3 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.54→54.83 Å / Num. obs: 20092 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.1
Reflection shellResolution: 2.54→2.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 2.54→54.832 Å / SU ML: 0.34 / σ(F): 0.12 / Phase error: 32.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1991 5.1 %
Rwork0.2403 --
obs0.2416 19592 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→54.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 6 80 4009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053990
X-RAY DIFFRACTIONf_angle_d0.7515391
X-RAY DIFFRACTIONf_dihedral_angle_d13.5091462
X-RAY DIFFRACTIONf_chiral_restr0.042590
X-RAY DIFFRACTIONf_plane_restr0.003717
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A927X-RAY DIFFRACTIONPOSITIONAL
12D927X-RAY DIFFRACTIONPOSITIONAL0.065
21B941X-RAY DIFFRACTIONPOSITIONAL
22C941X-RAY DIFFRACTIONPOSITIONAL0.025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5401-2.60360.39321130.33182337X-RAY DIFFRACTION81
2.6036-2.6740.3514900.30182402X-RAY DIFFRACTION82
2.674-2.75270.35031500.29712460X-RAY DIFFRACTION85
2.7527-2.84150.34561420.292500X-RAY DIFFRACTION88
2.8415-2.94310.37561240.29272518X-RAY DIFFRACTION86
2.9431-3.06090.32181680.28462726X-RAY DIFFRACTION95
3.0609-3.20020.2851540.26312776X-RAY DIFFRACTION96
3.2002-3.36890.30521700.24342758X-RAY DIFFRACTION97
3.3689-3.57990.26451560.24022782X-RAY DIFFRACTION96
3.5799-3.85630.23821300.22142778X-RAY DIFFRACTION94
3.8563-4.24420.22121540.2092726X-RAY DIFFRACTION94
4.2442-4.8580.1971360.20032734X-RAY DIFFRACTION94
4.858-6.11930.2871560.24172806X-RAY DIFFRACTION97
6.1193-54.84430.19981480.20962740X-RAY DIFFRACTION94

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more