[English] 日本語
Yorodumi
- PDB-5lum: Alpha-crystallin domain of human HSPB6 patched with its N-termina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lum
TitleAlpha-crystallin domain of human HSPB6 patched with its N-terminal peptide
Components(Heat shock protein beta-6) x 2
KeywordsProtein/Peptide / protein-peptide complex / IDRs / chaperone protein
Function / homology
Function and homology information


structural constituent of eye lens / chaperone-mediated protein folding / protein folding chaperone / positive regulation of angiogenesis / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / nuclear speck / negative regulation of apoptotic process ...structural constituent of eye lens / chaperone-mediated protein folding / protein folding chaperone / positive regulation of angiogenesis / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / nuclear speck / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / 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-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSluchanko, N.N. / Beelen, S. / Kulikova, A.A. / Weeks, S.D. / Antson, A.A. / Gusev, N.B. / Strelkov, S.V.
Funding support Russian Federation, Belgium, United Kingdom, 7items
OrganizationGrant numberCountry
RFBR14-04-00146, 16-04-00016 Russian Federation
FWOG069708N, G093615N and WO03315N Belgium
KULeuven grantOT13/097 Belgium
Wellcome Trust098230 United Kingdom
Biostruct-X283570 Belgium
European UnionFP7/2007-2013 Belgium
European Molecular Biology OrganizationASTF#637-2014 Belgium
CitationJournal: Structure / Year: 2017
Title: Structural Basis for the Interaction of a Human Small Heat Shock Protein with the 14-3-3 Universal Signaling Regulator.
Authors: Sluchanko, N.N. / Beelen, S. / Kulikova, A.A. / Weeks, S.D. / Antson, A.A. / Gusev, N.B. / Strelkov, S.V.
History
DepositionSep 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Heat shock protein beta-6
A: Heat shock protein beta-6
G: Heat shock protein beta-6
B: Heat shock protein beta-6
H: Heat shock protein beta-6
C: Heat shock protein beta-6
I: Heat shock protein beta-6
D: Heat shock protein beta-6
J: Heat shock protein beta-6
E: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,19814
Polymers47,81410
Non-polymers3844
Water25214
1
F: Heat shock protein beta-6
A: Heat shock protein beta-6
hetero molecules

F: Heat shock protein beta-6
A: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5108
Polymers19,1254
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4040 Å2
ΔGint-62 kcal/mol
Surface area9920 Å2
MethodPISA
2
G: Heat shock protein beta-6
B: Heat shock protein beta-6
H: Heat shock protein beta-6
C: Heat shock protein beta-6


Theoretical massNumber of molelcules
Total (without water)19,1254
Polymers19,1254
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-9 kcal/mol
Surface area9960 Å2
MethodPISA
3
I: Heat shock protein beta-6
D: Heat shock protein beta-6
J: Heat shock protein beta-6
E: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3186
Polymers19,1254
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-34 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.687, 105.687, 111.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein/peptide
Heat shock protein beta-6 / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 965.099 Da / Num. of mol.: 5 / Fragment: UNP Residues 2-10 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14558
#2: Protein
Heat shock protein beta-6 / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 8597.646 Da / Num. of mol.: 5 / Fragment: ACD domain, UNP Residues 72-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB6 / Production host: Escherichia coli (E. coli) / References: UniProt: O14558
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.77 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Tris-HCl (pH6.5),1.5M ammonium sulfate, 0.1M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.6→48 Å / Num. obs: 22684 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 99.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.22
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.6-2.672.6860.890.514199.9
2.67-2.741.9731.270.651100
2.74-2.821.3861.870.8231100
2.82-2.911.0762.440.87199.9
2.91-30.8213.290.918199.9
3-3.110.5394.690.9541100
3.11-3.230.3577.090.9841100
3.23-3.360.2679.980.99199.9
3.36-3.510.18914.080.9951100
3.51-3.680.13218.690.9971100
3.68-3.880.10223.470.9981100
3.88-4.110.08228.180.9981100
4.11-4.40.06136.940.9991100
4.4-4.750.04943.750.9991100
4.75-5.20.04743.760.999199.9
5.2-5.810.0538.850.9991100
5.81-6.710.04542.860.9991100
6.71-8.220.03652.911100
8.22-11.630.02964.7811100
11.630.02963.510.999198.7

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JUT

4jut


Resolution: 2.6→28.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.318 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.229
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1093 4.82 %RANDOM
Rwork0.207 ---
obs0.208 22661 100 %-
Displacement parametersBiso max: 219.72 Å2 / Biso mean: 100.11 Å2 / Biso min: 54.44 Å2
Baniso -1Baniso -2Baniso -3
1--7.571 Å20 Å20 Å2
2---7.571 Å20 Å2
3---15.142 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.6→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 20 14 3409
Biso mean--161.83 79.58 -
Num. residues----435
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1129SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes518HARMONIC5
X-RAY DIFFRACTIONt_it3500HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion426SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3450SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3500HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4778HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion19.24
LS refinement shellResolution: 2.6→2.73 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.28 134 4.53 %
Rwork0.256 2821 -
all-2955 -
obs--99.97 %
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)
11.36910.19520.61626.21570.0050.9857-0.04060.0359-0.2459-0.2458-0.0180.15350.1473-0.05350.0586-0.26510.01530.0683-0.41850.0106-0.486-64.498-10.710630.4044
25.9671-1.6738-3.24112.5954-0.06134.5946-0.04720.6127-0.4437-0.01780.02290.3349-0.2127-0.63420.0243-0.2560.060.0489-0.396-0.0417-0.3406-52.5288-17.813414.2212
35.2022-4.80891.59393.56570.20726.3314-0.4226-0.21350.74210.69650.4867-0.6436-0.16371.098-0.0641-0.22310.0613-0.084-0.2996-0.1258-0.4029-25.4755-24.512820.2014
45.8348-3.61780.53885.6337-0.24251.81520.56230.65470.225-1.5078-0.6240.5169-0.5561-0.78790.06170.08570.3321-0.1382-0.4134-0.0504-0.7455-61.83541.04040.1958
57.1913-4.9391-0.6016.67011.63437.30290.77330.49640.6884-0.9135-0.318-0.9708-1.529-0.065-0.4553-0.0998-0.02850.2848-0.5750.0982-0.5922-37.6429-4.8955-5.3087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* F|* }A72 - 149
2X-RAY DIFFRACTION1{ A|* F|* }F2 - 10
3X-RAY DIFFRACTION2{ B|* G|* }B72 - 149
4X-RAY DIFFRACTION2{ B|* G|* }G2 - 10
5X-RAY DIFFRACTION3{ C|* H|* }C72 - 149
6X-RAY DIFFRACTION3{ C|* H|* }H2 - 10
7X-RAY DIFFRACTION4{ D|* I|* }D72 - 149
8X-RAY DIFFRACTION4{ D|* I|* }I2 - 10
9X-RAY DIFFRACTION5{ E|* J|* }E72 - 149
10X-RAY DIFFRACTION5{ E|* J|* }J2 - 10

+
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