[English] 日本語
Yorodumi
- PDB-8rha: HSPB7ACD C131S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rha
TitleHSPB7ACD C131S
ComponentsHeat shock protein beta-7
KeywordsCHAPERONE / apo chaperone
Function / homology
Function and homology information


filamin binding / aggresome / regulation of heart contraction / response to unfolded protein / Cajal body / actin cytoskeleton / heart development / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Heat shock protein beta-7, ACD domain / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Heat shock protein beta-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWang, Z. / Benesch, J. / Allison, T.M. / McDonough, M.A. / Song, H. / Bolla, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Filamin C dimerisation is regulated by HSPB7.
Authors: Wang, Z. / Cao, G. / Collier, M.P. / Qiu, X. / Broadway-Stringer, S. / Saman, D. / Ng, J.Z.Y. / Sen, N. / Azad, A.J. / Hooper, C. / Zimmermann, J. / McDonough, M.A. / Brem, J. / Rabe, P. / ...Authors: Wang, Z. / Cao, G. / Collier, M.P. / Qiu, X. / Broadway-Stringer, S. / Saman, D. / Ng, J.Z.Y. / Sen, N. / Azad, A.J. / Hooper, C. / Zimmermann, J. / McDonough, M.A. / Brem, J. / Rabe, P. / Song, H. / Alderson, T.R. / Schofield, C.J. / Bolla, J.R. / Djinovic-Carugo, K. / Furst, D.O. / Warscheid, B. / Degiacomi, M.T. / Allison, T.M. / Hochberg, G.K.A. / Robinson, C.V. / Gehmlich, K. / Benesch, J.L.P.
History
DepositionDec 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock protein beta-7
B: Heat shock protein beta-7
C: Heat shock protein beta-7


Theoretical massNumber of molelcules
Total (without water)28,5133
Polymers28,5133
Non-polymers00
Water1086
1
A: Heat shock protein beta-7


Theoretical massNumber of molelcules
Total (without water)9,5041
Polymers9,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein beta-7


Theoretical massNumber of molelcules
Total (without water)9,5041
Polymers9,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heat shock protein beta-7


Theoretical massNumber of molelcules
Total (without water)9,5041
Polymers9,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.858, 57.858, 167.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Heat shock protein beta-7 / HspB7 / Cardiovascular heat shock protein / cvHsp


Mass: 9504.431 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB7, CVHSP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UBY9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium formate dihydrate 20% w/v polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 5, 2019
RadiationMonochromator: synchrontron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.18→55.78 Å / Num. obs: 15713 / % possible obs: 100 % / Redundancy: 25.4 % / CC1/2: 1 / Rmerge(I) obs: 0.138 / Net I/σ(I): 14.5
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 25.1 % / Rmerge(I) obs: 1.418 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 764 / CC1/2: 0.957 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→54.74 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 17.409 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27961 773 4.9 %RANDOM
Rwork0.25341 ---
obs0.25475 14850 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.524 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å20 Å2
2--3.73 Å20 Å2
3----7.47 Å2
Refinement stepCycle: 1 / Resolution: 2.18→54.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 6 1806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121838
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161690
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.8332502
X-RAY DIFFRACTIONr_angle_other_deg0.5121.7893894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3915230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.828518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20910299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
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_it1.5763.517923
X-RAY DIFFRACTIONr_mcbond_other1.5753.518923
X-RAY DIFFRACTIONr_mcangle_it2.5746.2981149
X-RAY DIFFRACTIONr_mcangle_other2.5756.31150
X-RAY DIFFRACTIONr_scbond_it2.243.861915
X-RAY DIFFRACTIONr_scbond_other2.2383.863916
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6736.9271353
X-RAY DIFFRACTIONr_long_range_B_refined5.18134.511832
X-RAY DIFFRACTIONr_long_range_B_other5.17934.531833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.18→2.236 Å
RfactorNum. reflection% reflection
Rfree0.427 59 -
Rwork0.339 1064 -
obs--99.03 %
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)
14.0752-0.4427-0.48814.21570.87095.16350.0740.0063-0.0018-0.2679-0.1013-0.13040.2890.20230.02730.21330.0098-0.02120.0159-0.01110.15458.70723.2064.488
23.58180.36880.55649.3573-0.48753.95620.06620.2034-0.0542-0.0536-0.13430.8287-0.2162-0.35880.06810.04410.0054-0.05430.1265-0.05660.2304-3.99223.411-7.927
35.711.3872-0.95413.3302-0.58149.4080.0421-0.08060.3914-0.1988-0.00810.2393-0.5556-0.0981-0.0340.0949-0.01430.00170.0424-0.02610.14942.90831.59618.136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|10-85 }
2X-RAY DIFFRACTION2{ B|6-85 }
3X-RAY DIFFRACTION3{ C|10-84 }

+
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