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- PDB-5d5v: Crystal structure of human Hsf1 with Satellite III repeat DNA -

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Basic information

Entry
Database: PDB / ID: 5d5v
TitleCrystal structure of human Hsf1 with Satellite III repeat DNA
Components
  • (DNA) x 2
  • Heat shock factor protein 1
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / double helix / helix-turn-helix / transcription-DNA complex
Function / homology
Function and homology information


cellular response to nitroglycerin / embryonic process involved in female pregnancy / sequence-specific single stranded DNA binding / cellular response to diamide / response to hypobaric hypoxia / negative regulation of double-strand break repair via nonhomologous end joining / cellular response to L-glutamine / positive regulation of stress granule assembly / positive regulation of apoptotic DNA fragmentation / response to peptide ...cellular response to nitroglycerin / embryonic process involved in female pregnancy / sequence-specific single stranded DNA binding / cellular response to diamide / response to hypobaric hypoxia / negative regulation of double-strand break repair via nonhomologous end joining / cellular response to L-glutamine / positive regulation of stress granule assembly / positive regulation of apoptotic DNA fragmentation / response to peptide / cellular response to sodium arsenite / translation elongation factor binding / negative regulation of inclusion body assembly / nuclear stress granule / female meiotic nuclear division / positive regulation of macrophage differentiation / positive regulation of inclusion body assembly / positive regulation of multicellular organism growth / pronucleus / cellular response to potassium ion / protein folding chaperone complex / negative regulation of cardiac muscle cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / STAT family protein binding / response to psychosocial stress / mitotic spindle pole / response to testosterone / cellular response to cadmium ion / cellular response to angiotensin / negative regulation of tumor necrosis factor production / general transcription initiation factor binding / HSF1-dependent transactivation / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / mRNA transport / Mitochondrial unfolded protein response (UPRmt) / HSF1 activation / embryonic placenta development / Attenuation phase / negative regulation of protein-containing complex assembly / heterochromatin / regulation of cellular response to heat / heat shock protein binding / response to nutrient / positive regulation of mitotic cell cycle / cellular response to copper ion / positive regulation of apoptotic signaling pathway / epithelial cell proliferation / response to activity / cellular response to estradiol stimulus / Hsp90 protein binding / chromatin DNA binding / promoter-specific chromatin binding / euchromatin / cellular response to gamma radiation / defense response / PML body / kinetochore / Aggrephagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / mRNA processing / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / MAPK cascade / positive regulation of cold-induced thermogenesis / cellular response to heat / cellular response to lipopolysaccharide / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / ribonucleoprotein complex / DNA repair / centrosome / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Heat shock factor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsNeudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of human heat-shock transcription factor 1 in complex with DNA.
Authors: Neudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 20, 2016Group: Structure summary
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Heat shock factor protein 1
D: Heat shock factor protein 1
A: DNA
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4756
Polymers36,4264
Non-polymers492
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-26 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.813, 112.678, 39.865
Angle α, β, γ (deg.)90.000, 92.560, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 14 - 120 / Label seq-ID: 25 - 131

Dom-IDAuth asym-IDLabel asym-ID
1BA
2DB

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Components

#1: Protein Heat shock factor protein 1 / HSF 1 / Heat shock transcription factor 1 / HSTF 1


Mass: 14550.622 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN, UNP residues 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF1, HSTF1 / Plasmid: pProEx-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: Q00613
#2: DNA chain DNA


Mass: 3751.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA


Mass: 3573.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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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: 4.69 Å3/Da / Density % sol: 73.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 31 % PEG-4000, 0.09 M Mg-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.55→39.83 Å / Num. obs: 15087 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.069 / Net I/σ(I): 9.3 / Num. measured all: 66855
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.55-2.664.10.6692.2748318210.6760.37597.2
8.83-39.834.60.04925.517313790.9970.02598.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation39.83 Å2.9 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
MOLREP11.0.05phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D5U

5d5u


Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.173 / FOM work R set: 0.847 / SU B: 7.85 / SU ML: 0.171 / SU R Cruickshank DPI: 0.3225 / SU Rfree: 0.2408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 731 4.8 %RANDOM
Rwork0.19 ---
obs0.1921 14354 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.82 Å2 / Biso mean: 32.413 Å2 / Biso min: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å2-0 Å2-0.32 Å2
2---0.9 Å2-0 Å2
3----1.79 Å2
Refinement stepCycle: final / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 488 108 2265
Biso mean--24.39 27.68 -
Num. residues----203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0172258
X-RAY DIFFRACTIONr_bond_other_d0.0040.021879
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.7293152
X-RAY DIFFRACTIONr_angle_other_deg1.12734336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7324.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49415291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.913159
X-RAY DIFFRACTIONr_chiral_restr0.080.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212225
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02552
Refine LS restraints NCS

Ens-ID: 1 / Number: 5333 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2D
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 54 -
Rwork0.315 1030 -
all-1084 -
obs--98.46 %

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