[English] 日本語
Yorodumi
- PDB-5d8k: Human HSF2 DNA-Binding Domain bound to 2-site HSE DNA at 1.73 Ang... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d8k
TitleHuman HSF2 DNA-Binding Domain bound to 2-site HSE DNA at 1.73 Angstroms Resolution
Components
  • DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
  • Heat shock factor protein 2
Keywordstranscription/dna / transcription factor / DNA / HSF / transcription-dna complex
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / 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 ...Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.728 Å
AuthorsJaeger, A.M. / Pemble, C.W. / Thiele, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structures of HSF2 reveal mechanisms for differential regulation of human heat-shock factors.
Authors: Jaeger, A.M. / Pemble, C.W. / Sistonen, L. / Thiele, D.J.
History
DepositionAug 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
B: Heat shock factor protein 2


Theoretical massNumber of molelcules
Total (without water)16,7122
Polymers16,7122
Non-polymers00
Water1,910106
1
A: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
B: Heat shock factor protein 2

A: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
B: Heat shock factor protein 2


Theoretical massNumber of molelcules
Total (without water)33,4254
Polymers33,4254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4690 Å2
ΔGint-36 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.883, 39.631, 39.393
Angle α, β, γ (deg.)90.00, 91.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-130-

HOH

-
Components

#1: DNA chain DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Heat shock factor protein 2 / / HSF 2 / Heat shock transcription factor 2 / HSTF 2


Mass: 13049.851 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF2, HSTF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03933
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 7 mg/ml protein:DNA complexes were mixed at a ratio of 1:1.2 protein:DNA in 25 mM HEPES pH 7.5 and 150 mM NaCl and crystallized against 100 mM NaCl, 100 mM BICINE pH 9, and 30% PEG 550 MME. ...Details: 7 mg/ml protein:DNA complexes were mixed at a ratio of 1:1.2 protein:DNA in 25 mM HEPES pH 7.5 and 150 mM NaCl and crystallized against 100 mM NaCl, 100 mM BICINE pH 9, and 30% PEG 550 MME. Crystals grew overnight at room temperature

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.728→21.21 Å / Num. obs: 13023 / % possible obs: 93.89 % / Redundancy: 5.1 % / Net I/σ(I): 22.8
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 4.1 % / % possible all: 89.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1675refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.728→21.21 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 1313 10.08 %
Rwork0.1479 --
obs0.1531 13023 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.728→21.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 243 0 106 1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111241
X-RAY DIFFRACTIONf_angle_d1.3961728
X-RAY DIFFRACTIONf_dihedral_angle_d20.573485
X-RAY DIFFRACTIONf_chiral_restr0.058181
X-RAY DIFFRACTIONf_plane_restr0.008184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7281-1.79730.27781370.24071180X-RAY DIFFRACTION86
1.7973-1.8790.28491380.2141271X-RAY DIFFRACTION92
1.879-1.9780.25791390.1971267X-RAY DIFFRACTION93
1.978-2.10180.23061460.17221270X-RAY DIFFRACTION93
2.1018-2.2640.24561420.16961309X-RAY DIFFRACTION94
2.264-2.49150.21941500.15731321X-RAY DIFFRACTION95
2.4915-2.85130.19861500.16811334X-RAY DIFFRACTION96
2.8513-3.58950.18851500.14141356X-RAY DIFFRACTION96
3.5895-21.21570.16361610.11461402X-RAY DIFFRACTION98

+
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