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- PDB-6f2r: A heterotetramer of human HspB2 and HspB3 -

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Basic information

Entry
Database: PDB / ID: 6f2r
TitleA heterotetramer of human HspB2 and HspB3
Components
  • (Heat shock protein beta- ...) x 2
  • (HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock ...) x 2
  • (Unknown peptide from HspB2 or ...) x 5
KeywordsCHAPERONE / sHSP / crystallin
Function / homology
Function and homology information


structural constituent of eye lens / response to unfolded protein / enzyme activator activity / nuclear speck / nucleus / cytoplasm / cytosol
Similarity search - Function
Heat shock protein beta-3 / 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 ...Heat shock protein beta-3 / 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-3 / Heat shock protein beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsClark, A.R. / Cole, A.R. / Boelens, W.C. / Keep, N.H. / Slingsby, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0801846 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2018
Title: Terminal Regions Confer Plasticity to the Tetrameric Assembly of Human HspB2 and HspB3.
Authors: Clark, A.R. / Vree Egberts, W. / Kondrat, F.D.L. / Hilton, G.R. / Ray, N.J. / Cole, A.R. / Carver, J.A. / Benesch, J.L.P. / Keep, N.H. / Boelens, W.C. / Slingsby, C.
History
DepositionNov 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct.title
Revision 1.2Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
C: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
D: Heat shock protein beta-2
E: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
T: Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-2
G: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
I: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
V: Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-2
K: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
M: Unknown peptide from HspB2 or HspB3
N: Unknown peptide from HspB2 or HspB3
O: Unknown peptide from HspB2 or HspB3
Q: Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-2
F: Heat shock protein beta-2
J: Heat shock protein beta-2
1: Unknown peptide from HspB2 or HspB3
2: Unknown peptide from HspB2 or HspB3
3: Unknown peptide from HspB2 or HspB3
W: Unknown peptide from HspB2 or HspB3
X: Unknown peptide from HspB2 or HspB3
Y: Unknown peptide from HspB2 or HspB3


Theoretical massNumber of molelcules
Total (without water)256,61421
Polymers256,61421
Non-polymers00
Water00
1
A: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
C: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
D: Heat shock protein beta-2
M: Unknown peptide from HspB2 or HspB3
Q: Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-2
1: Unknown peptide from HspB2 or HspB3
W: Unknown peptide from HspB2 or HspB3


Theoretical massNumber of molelcules
Total (without water)85,7377
Polymers85,7377
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
T: Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-2
G: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
N: Unknown peptide from HspB2 or HspB3
F: Heat shock protein beta-2
2: Unknown peptide from HspB2 or HspB3
Y: Unknown peptide from HspB2 or HspB3


Theoretical massNumber of molelcules
Total (without water)85,4817
Polymers85,4817
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
V: Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-2
K: HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2
O: Unknown peptide from HspB2 or HspB3
J: Heat shock protein beta-2
3: Unknown peptide from HspB2 or HspB3
X: Unknown peptide from HspB2 or HspB3


Theoretical massNumber of molelcules
Total (without water)85,3967
Polymers85,3967
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.139, 177.139, 126.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock ... , 2 types, 6 molecules AEICGK

#1: Protein HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2 / HspB2 / DMPK-binding protein / MKBP


Mass: 22896.740 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16082
#2: Protein HspB2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2,Heat shock protein beta-2 / HspB2 / DMPK-binding protein / MKBP


Mass: 22045.689 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16082

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Heat shock protein beta- ... , 2 types, 6 molecules DFJTVQ

#3: Protein Heat shock protein beta-2 / HspB2 / DMPK-binding protein / MKBP


Mass: 20258.480 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB2 / Production host: Homo sapiens (human) / References: UniProt: Q16082
#4: Protein Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-3,Heat shock protein beta-2 / HspB3 / Heat shock 17 kDa protein / HSP 17 / Protein 3 / HspB3 / Heat shock 17 kDa protein / HSP 17 ...HspB3 / Heat shock 17 kDa protein / HSP 17 / Protein 3 / HspB3 / Heat shock 17 kDa protein / HSP 17 / Protein 3 / HspB3 / Heat shock 17 kDa protein / HSP 17 / Protein 3 / HspB3 / Heat shock 17 kDa protein / HSP 17 / Protein 3 / HspB2 / DMPK-binding protein / MKBP


Mass: 18183.744 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB3, HSP27, HSPL27, HSPB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12988

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Unknown peptide from HspB2 or ... , 5 types, 9 molecules MNO123WXY

#5: Protein/peptide Unknown peptide from HspB2 or HspB3


Mass: 869.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#6: Protein/peptide Unknown peptide from HspB2 or HspB3


Mass: 613.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#7: Protein/peptide Unknown peptide from HspB2 or HspB3


Mass: 528.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#8: Protein/peptide Unknown peptide from HspB2 or HspB3


Mass: 443.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#9: Protein/peptide Unknown peptide from HspB2 or HspB3


Mass: 1039.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Details

Sequence detailsIn the chains QTV and JDF it is not certain if this entity maps to HspB3 or HspB2. Here it is ...In the chains QTV and JDF it is not certain if this entity maps to HspB3 or HspB2. Here it is mapped to the "most likely" protein

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.6M SODIUM FORMATE, 0.1 M TRIS HCL pH7.8, 7.8% PGA, 2mM GTP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.9→126.46 Å / Num. obs: 147958 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 123.8 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.5
Reflection shellResolution: 3.9→4.11 Å / Rmerge(I) obs: 1.163 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENSEMBLE OF 3Q9P, 2WJ5, 2WJ7

3q9p

2wj5

2wj7


Resolution: 3.9→78 Å / Cor.coef. Fo:Fc: 0.801 / Cor.coef. Fo:Fc free: 0.755 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.013 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.873 / SU Rfree Blow DPI: 0.502 / SU Rfree Cruickshank DPI: 0.53
RfactorNum. reflection% reflectionSelection details
Rfree0.313 2088 5.17 %RANDOM
Rwork0.297 ---
obs0.298 40354 99.8 %-
Displacement parametersBiso mean: 144.7 Å2
Baniso -1Baniso -2Baniso -3
1-21.0901 Å20 Å20 Å2
2--21.0901 Å20 Å2
3----42.1803 Å2
Refine analyzeLuzzati coordinate error obs: 1.01 Å
Refinement stepCycle: LAST / Resolution: 3.9→78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7592 0 0 0 7592
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097652HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1910574HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1848SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1334HARMONIC5
X-RAY DIFFRACTIONt_it7652HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion24.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1290SEMIHARMONIC5
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_contact7181SEMIHARMONIC4
LS refinement shellResolution: 3.9→4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 140 4.73 %
Rwork0.23 2819 -
all0.231 2959 -
obs--99.39 %

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