[English] 日本語
Yorodumi
- PDB-5d5w: Crystal structure of Chaetomium thermophilum Skn7 with HSE DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d5w
TitleCrystal structure of Chaetomium thermophilum Skn7 with HSE DNA
Components
  • HSE DNA
  • Putative transcription factor
KeywordsTRANSCRIPTION / protein-DNA complex / double helix / helix-turn-helix
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity / identical protein binding / nucleus
Similarity search - Function
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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 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) / Transcription factor SKN7
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HSE DNA
B: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)16,2802
Polymers16,2802
Non-polymers00
Water39622
1
A: HSE DNA
B: Putative transcription factor

A: HSE DNA
B: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)32,5614
Polymers32,5614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4840 Å2
ΔGint-25 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.771, 78.397, 90.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11B-207-

HOH

-
Components

#1: DNA chain HSE DNA


Mass: 3662.404 Da / Num. of mol.: 1 / Fragment: DNA binding domain / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Putative transcription factor / CtSkn7


Mass: 12618.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0048700 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0SB31
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 11 % PEG-3350, 0.18 M tri-Ammonium Citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97702 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 2.349→45.042 Å / Num. all: 6090 / Num. obs: 6090 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 61.1 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.051 / Rsym value: 0.045 / Net I/av σ(I): 9.6 / Net I/σ(I): 17.4 / Num. measured all: 28671
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.349-2.484.80.9580.842028700.4690.9581.899.2
2.48-2.634.60.561.438178280.2820.562.799.6
2.63-2.8150.3482.239537900.1680.3484.799.9
2.81-3.034.80.1744.535037280.0860.1748.399.8
3.03-3.324.60.0544.531356760.030.05415.498.3
3.32-3.714.90.0461329476070.0230.04625.298.5
3.71-4.294.50.03318.324135360.0170.03334.398.1
4.29-5.254.70.02622.322184680.0130.02644.698.5
5.25-7.434.30.02624.715983680.0130.02643.797
7.43-45.04240.01929.28852190.010.01952.396.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HTS

3hts


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2383 / WRfactor Rwork: 0.201 / FOM work R set: 0.6975 / SU B: 13.086 / SU ML: 0.277 / SU R Cruickshank DPI: 0.4434 / SU Rfree: 0.2592 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 280 4.6 %RANDOM
Rwork0.2154 ---
obs0.2173 5791 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.63 Å2 / Biso mean: 72.272 Å2 / Biso min: 35.01 Å2
Baniso -1Baniso -2Baniso -3
1--6.22 Å20 Å20 Å2
2--4.6 Å2-0 Å2
3---1.62 Å2
Refinement stepCycle: final / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 243 0 22 1081
Biso mean---60.77 -
Num. residues----106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0171112
X-RAY DIFFRACTIONr_bond_other_d0.0010.02915
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.7131544
X-RAY DIFFRACTIONr_angle_other_deg1.39732110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.563592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31722.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.215149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.042159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.712 23 -
Rwork0.455 411 -
all-434 -
obs--99.77 %

+
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://pdbjlvh1.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