[English] 日本語
Yorodumi
- PDB-7s9i: Room-temperature Human Hsp90a-NTD bound to EC144 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s9i
TitleRoom-temperature Human Hsp90a-NTD bound to EC144
ComponentsHeat shock protein HSP 90-alpha
KeywordsChaperone / Hydrolase / heat shock / signaling
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / chaperone-mediated autophagy / sperm plasma membrane ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / chaperone-mediated autophagy / sperm plasma membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / 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 / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / enzyme-substrate adaptor activity / response to unfolded protein / skeletal muscle contraction / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / regulation of postsynaptic membrane neurotransmitter receptor levels / axonal growth cone / telomere maintenance via telomerase / positive regulation of lamellipodium assembly / nitric oxide metabolic process / eNOS activation / DNA polymerase binding / response to salt stress / positive regulation of defense response to virus by host / positive regulation of telomere maintenance via telomerase / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Signaling by ERBB2 / cardiac muscle cell apoptotic process / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / lysosomal lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / activation of innate immune response / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of interferon-beta production / protein tyrosine kinase binding / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / positive regulation of protein import into nucleus / Regulation of necroptotic cell death / VEGFA-VEGFR2 Pathway / response to estrogen / histone deacetylase binding / tau protein binding / Downregulation of ERBB2 signaling / neuron migration / Chaperone Mediated Autophagy / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Aggrephagy / MHC class II protein complex binding / positive regulation of protein catabolic process
Similarity search - Function
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 ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-7PP / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStachowski, T.R. / Vanarotti, M. / Fischer, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM142772-01 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Water Networks Repopulate Protein-Ligand Interfaces with Temperature.
Authors: Stachowski, T.R. / Vanarotti, M. / Seetharaman, J. / Lopez, K. / Fischer, M.
History
DepositionSep 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1542
Polymers26,7401
Non-polymers4141
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.315, 91.151, 99.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP 86 / HSP86 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS- ...Heat shock 86 kDa / HSP 86 / HSP86 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 26739.922 Da / Num. of mol.: 1
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)
References: UniProt: P07900, non-chaperonin molecular chaperone ATPase
#2: Chemical ChemComp-7PP / 5-{2-amino-4-chloro-7-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-methylpent-4-yn-2 -ol / EC44


Mass: 413.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Malic acid, pH 7

-
Data collection

DiffractionMean temperature: 278 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→36.81 Å / Num. obs: 30975 / % possible obs: 94.25 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.29 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.35
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.743 / Num. unique obs: 3036 / CC1/2: 0.395

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19rc5_4047refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YER

1yer


Resolution: 1.75→36.81 Å / SU ML: 0.2492 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1914 1944 6.5 %
Rwork0.1665 27945 -
obs0.1681 29889 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 29 92 1762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761906
X-RAY DIFFRACTIONf_angle_d1.11752605
X-RAY DIFFRACTIONf_chiral_restr0.0585289
X-RAY DIFFRACTIONf_plane_restr0.0091339
X-RAY DIFFRACTIONf_dihedral_angle_d8.7153275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.3351240.31751657X-RAY DIFFRACTION79.65
1.79-1.840.29681240.3031781X-RAY DIFFRACTION85.31
1.84-1.90.35791350.31911875X-RAY DIFFRACTION90.22
1.9-1.960.36391330.31221921X-RAY DIFFRACTION92.31
1.96-2.030.27791370.2411986X-RAY DIFFRACTION94.86
2.03-2.110.2191440.19012085X-RAY DIFFRACTION98.85
2.11-2.20.20421430.17112075X-RAY DIFFRACTION99.06
2.2-2.320.20581430.17892085X-RAY DIFFRACTION98.89
2.32-2.470.23781440.17332083X-RAY DIFFRACTION98.89
2.47-2.660.19451440.16792079X-RAY DIFFRACTION98.36
2.66-2.920.19991440.16922087X-RAY DIFFRACTION97.47
2.92-3.350.1811400.15832022X-RAY DIFFRACTION94.95
3.35-4.220.13511430.13062079X-RAY DIFFRACTION95.94
4.22-36.810.17631460.15322130X-RAY DIFFRACTION94.75
Refinement TLS params.Method: refined / Origin x: 33.061993215 Å / Origin y: 14.745990686 Å / Origin z: -20.297855447 Å
111213212223313233
T0.262925824135 Å20.0024722647851 Å20.0161003058234 Å2-0.222031132209 Å20.0241116050844 Å2--0.265339940911 Å2
L2.86601050199 °2-0.208496292085 °20.124953102939 °2-1.7612062897 °20.0671872812528 °2--2.45305346016 °2
S0.0157531993984 Å °-0.0673439182269 Å °0.0199671765582 Å °0.0299011869688 Å °-0.0296977026057 Å °0.0169009928185 Å °-0.0741206104314 Å °-0.0599384743833 Å °0.0197223781883 Å °
Refinement TLS groupSelection details: all

+
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