[English] 日本語
Yorodumi
- PDB-3q9q: HspB1 fragment second crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q9q
TitleHspB1 fragment second crystal form
ComponentsHeat shock protein beta-1Heat shock response
KeywordsCHAPERONE / Alpha-crystallin domain / Charcot-Marie-Tooth disease / neuronopathy / Ig-like fold / Stress response / intra-cellular chaperones / nucleus
Function / homology
Function and homology information


anterograde axonal protein transport / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cornified envelope / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / protein kinase C inhibitor activity / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus ...anterograde axonal protein transport / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cornified envelope / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / protein kinase C inhibitor activity / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / chaperone-mediated protein folding / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein folding chaperone / axon cytoplasm / proteasome complex / protein kinase C binding / ubiquitin binding / positive regulation of interleukin-1 beta production / regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / regulation of protein phosphorylation / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / response to virus / spindle / platelet aggregation / Z disc / VEGFA-VEGFR2 Pathway / positive regulation of angiogenesis / unfolded protein binding / positive regulation of tumor necrosis factor production / response to heat / protein refolding / RNA polymerase II-specific DNA-binding transcription factor binding / Extra-nuclear estrogen signaling / cytoskeleton / intracellular signal transduction / focal adhesion / negative regulation of apoptotic process / protein kinase binding / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Heat shock protein beta-1, ACD domain / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat shock protein beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBaranova, E.V. / Beelen, S. / Gusev, N.B. / Strelkov, S.V.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Three-Dimensional Structure of alpha-Crystallin Domain Dimers of Human Small Heat Shock Proteins HSPB1 and HSPB6
Authors: Baranova, E.V. / Weeks, S.D. / Beelen, S. / Bukach, O.V. / Gusev, N.B. / Strelkov, S.V.
History
DepositionJan 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock protein beta-1
B: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)18,5792
Polymers18,5792
Non-polymers00
Water1,04558
1
A: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)9,2891
Polymers9,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)9,2891
Polymers9,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.455, 74.455, 119.971
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLYSLYSchain A and (resseq 94:114 or resseq 116:126 or resseq 133:170 )AA94 - 1148 - 28
12GLYGLYALAALAchain A and (resseq 94:114 or resseq 116:126 or resseq 133:170 )AA116 - 12630 - 40
13TYRTYRPROPROchain A and (resseq 94:114 or resseq 116:126 or resseq 133:170 )AA133 - 17047 - 84
21ARGARGLYSLYSchain B and (resseq 94:114 or resseq 116:126 or resseq 133:170 )BB94 - 1148 - 28
22GLYGLYALAALAchain B and (resseq 94:114 or resseq 116:126 or resseq 133:170 )BB116 - 12630 - 40
23TYRTYRPROPROchain B and (resseq 94:114 or resseq 116:126 or resseq 133:170 )BB133 - 17047 - 84

-
Components

#1: Protein Heat shock protein beta-1 / Heat shock response / HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / ...HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / HSP 27 / Stress-responsive protein 27 / SRP27


Mass: 9289.354 Da / Num. of mol.: 2 / Fragment: residues 90-171 / Mutation: E125A, E126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB1 / Plasmid: pPEP-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: P04792
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.2M ammonium sulfate, 0.2M di-ammonium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2008
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.2→43.9 Å / Num. all: 13766 / Num. obs: 10572 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rsym value: 0.072 / Net I/σ(I): 15.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.76 / % possible all: 90

-
Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q9P

3q9p


Resolution: 2.2→39.99 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.02 / σ(F): 1.35 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3125 791 7.48 %random
Rwork0.2808 ---
obs0.2831 10572 99.91 %-
all-13766 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.6 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 161.04 Å2 / Biso mean: 66.6043 Å2 / Biso min: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.5561 Å20 Å20 Å2
2---0.5561 Å2-0 Å2
3---1.1122 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 0 58 1201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051184
X-RAY DIFFRACTIONf_angle_d1.0181618
X-RAY DIFFRACTIONf_chiral_restr0.081189
X-RAY DIFFRACTIONf_plane_restr0.006207
X-RAY DIFFRACTIONf_dihedral_angle_d17.612437
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A529X-RAY DIFFRACTIONPOSITIONAL0.049
12B529X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2001-2.33790.34691340.310115571691
2.3379-2.51840.30961300.293915871717
2.5184-2.77180.37441300.295915971727
2.7718-3.17280.33641290.286316031732
3.1728-3.99680.25611230.265816561779
3.9968-39.99690.3151450.273517811926
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)
11.8172-1.07230.08441.49290.0941.4639-0.05130.07-0.0145-0.0255-0.04990.0585-0.0713-0.01390.09210.198-0.0589-0.01840.2220.03790.228422.57016.676814.7839
21.72-2.38651.037-0.314-0.82353.40080.47240.1459-0.4618-0.4661-0.3891-0.0265-1.28310.7991-0.12561.1362-0.3424-0.03140.4138-0.06770.390411.557719.905744.7233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA89 - 94
2X-RAY DIFFRACTION2chain BB94 - 1

+
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