[English] 日本語
Yorodumi
- PDB-3q6m: Crystal Structure of Human MC-HSP90 in C2221 Space Group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q6m
TitleCrystal Structure of Human MC-HSP90 in C2221 Space Group
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / three domains / trimer of dimer / hexamer
Function / homology
Function and homology information


sperm plasma membrane / sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / Scavenging by Class F Receptors / positive regulation of protein polymerization / vRNP Assembly / UTP binding / dATP binding / telomerase holoenzyme complex assembly ...sperm plasma membrane / sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / Scavenging by Class F Receptors / positive regulation of protein polymerization / vRNP Assembly / UTP binding / dATP binding / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / mitochondrial transport / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / 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 / Uptake and function of diphtheria toxin / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / positive regulation of cell size / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / protein folding chaperone complex / HSF1-dependent transactivation / response to unfolded protein / regulation of protein-containing complex assembly / protein unfolding / Attenuation phase / enzyme-substrate adaptor activity / HSF1 activation / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / axonal growth cone / RHOBTB2 GTPase cycle / telomere maintenance via telomerase / positive regulation of lamellipodium assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / nitric oxide metabolic process / response to cold / skeletal muscle contraction / response to salt stress / positive regulation of defense response to virus by host / Signaling by ERBB2 / eNOS activation / positive regulation of telomere maintenance via telomerase / cardiac muscle cell apoptotic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / endocytic vesicle lumen / DNA polymerase binding / 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 / Recruitment of NuMA to mitotic centrosomes / lysosomal lumen / Anchoring of the basal body to the plasma membrane / ESR-mediated signaling / activation of innate immune response / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / nitric-oxide synthase regulator activity / ATP-dependent protein folding chaperone / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / neuron migration / cellular response to virus / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / positive regulation of protein import into nucleus / Signaling by ERBB2 KD Mutants / Regulation of actin dynamics for phagocytic cup formation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to estrogen / VEGFA-VEGFR2 Pathway / Regulation of necroptotic cell death / tau protein binding / histone deacetylase binding / Downregulation of ERBB2 signaling / positive regulation of nitric oxide biosynthetic process / Chaperone Mediated Autophagy / disordered domain specific binding / positive regulation of protein catabolic process / Aggrephagy
Similarity search - Function
Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 ...Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, C.C. / Lin, T.W. / Ko, T.P. / Wang, A.H.-J.
CitationJournal: Plos One / Year: 2011
Title: The hexameric structures of human heat shock protein 90
Authors: Lee, C.C. / Lin, T.W. / Ko, T.P. / Wang, A.H.-J.
History
DepositionJan 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,4036
Polymers157,1153
Non-polymers2883
Water2,396133
1
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
hetero molecules

A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,80612
Polymers314,2296
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)162.702, 304.553, 87.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Heat shock protein HSP 90-alpha / HSP90 / Heat shock 86 kDa / HSP 86 / HSP86 / Renal carcinoma antigen NY-REN-38


Mass: 52371.547 Da / Num. of mol.: 3
Fragment: Middle and C-terminal domain, UNP residues 293-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07900
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.5M ammonium sulfate, 0.1M Tris-sodium citrate, 0.1mM cis-dichloro(ethylenediamine)platinum (II), pH 5.4-5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
PH range: 5.4-5.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 43809 / Num. obs: 43634 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.5 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CGE

2cge


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 35.924 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.985 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25163 2185 5 %RANDOM
Rwork0.2086 ---
obs0.21094 41365 99.18 %-
all-41749 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---2.4 Å20 Å2
3---2.91 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9197 0 15 133 9345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.98212592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33251103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16124.923455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.599151895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2241554
X-RAY DIFFRACTIONr_chiral_restr0.1040.21392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5641.55568
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10929051
X-RAY DIFFRACTIONr_scbond_it1.47833805
X-RAY DIFFRACTIONr_scangle_it2.6454.53541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.003→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 139 -
Rwork0.261 2909 -
obs--95.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.3260.5494-2.4375100.5495.67670.16480.9210.2407-0.4142-0.1621-0.2853-0.321-0.0257-0.00270.0310.01020.05420.3560.00170.3251-15.084-39.835-4.187
223.16775.4715-8.38297.18411.60426.71080.6541-2.13930.78110.9372-0.76530.2337-0.22490.72480.11110.2883-0.1618-0.04310.4277-0.01710.5445-12.269-35.9727.668
35.15933.1607-2.05664.4504-2.1261.08890.4054-0.05720.52930.50990.0050.222-0.28460.0747-0.41040.2281-0.07920.11380.4714-0.16530.5403-44.844-51.81112.989
45.9518-1.51-2.21945.19240.68015.2518-0.0836-0.2864-0.05810.57550.16120.2360.36170.2685-0.07760.2712-0.0336-0.09720.36080.00940.2198-56.027-75.00127.422
59.3786-0.4757-0.05736.92471.17577.3289-0.2826-0.19240.6370.1678-0.0436-0.1147-0.04030.12790.32630.156-0.0344-0.01280.19370.08630.34662.213-65.74548.035
621.30613.7397-0.111813.43062.7465.3572-0.82681.5437-0.0262-0.87760.482-0.3054-0.30650.21460.34480.2061-0.02460.0190.42130.22580.31076.491-64.70236.124
76.41032.17453.35262.11531.32682.79270.0860.5818-0.4817-0.08960.1611-0.10470.06420.2588-0.24710.1552-0.00360.10.409-0.09880.4213-21.766-87.20431.042
88.357-3.97931.95536.94040.36214.30830.46971.0533-0.4549-0.6739-0.19390.44530.025-0.5865-0.27590.1976-0.0023-0.06380.6694-0.07540.2374-48.189-87.36117.041
910.76872.86081.046313.5197-0.94585.7409-0.2391-0.7859-0.48740.65580.3175-0.06680.24210.0432-0.07850.10260.1010.07130.23970.0540.4063-13.605-41.84148.786
103.6085-1.1441.685625.5556-3.83376.3676-0.17790.5778-0.7514-2.08590.2151-0.01950.44080.2462-0.03720.30360.05560.02790.2439-0.0640.4858-15.878-46.73637.222
111.2313-0.00550.230412.9539-1.66461.5243-0.13590.13450.0888-1.81380.31970.9352-0.154-0.0801-0.18380.5624-0.0284-0.09130.19030.09120.4477-20.175-10.43831.296
1212.78232.6852-0.56693.4851-0.46650.5569-0.71870.63950.8918-1.4590.70460.19530.4844-0.09880.01411.9844-0.01390.26580.4290.18010.3202-7.28711.48316.586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A294 - 349
2X-RAY DIFFRACTION2A359 - 395
3X-RAY DIFFRACTION3A405 - 615
4X-RAY DIFFRACTION4A630 - 697
5X-RAY DIFFRACTION5B294 - 349
6X-RAY DIFFRACTION6B359 - 395
7X-RAY DIFFRACTION7B405 - 615
8X-RAY DIFFRACTION8B630 - 699
9X-RAY DIFFRACTION9C294 - 349
10X-RAY DIFFRACTION10C360 - 395
11X-RAY DIFFRACTION11C406 - 614
12X-RAY DIFFRACTION12C630 - 697

+
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