[English] 日本語
Yorodumi
- PDB-4b4c: Crystal structure of the DNA-binding domain of human CHD1. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b4c
TitleCrystal structure of the DNA-binding domain of human CHD1.
ComponentsCHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
KeywordsTRANSCRIPTION / CHROMODOMAIN / CHROMATIN-REMODELING / HISTONE ACETYLATION COMPLEX / CHROMATIN REGULATION
Function / homology
Function and homology information


nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / methylated histone binding / helicase activity / histone binding / DNA helicase / Estrogen-dependent gene expression / chromatin remodeling ...nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / methylated histone binding / helicase activity / histone binding / DNA helicase / Estrogen-dependent gene expression / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Homeodomain-like / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsAllerston, C.K. / Cooper, C.D.O. / Shrestha, L. / Vollmar, M. / Burgess-Brown, N. / Yue, W.W. / Carpenter, E.P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. ...Allerston, C.K. / Cooper, C.D.O. / Shrestha, L. / Vollmar, M. / Burgess-Brown, N. / Yue, W.W. / Carpenter, E.P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal Structure of the DNA-Binding Domain of Human Chd1.
Authors: Allerston, C.K. / Cooper, C.D.O. / Shrestha, L. / Vollmar, M. / Burgess-Brown, N. / Yue, W.W. / Carpenter, E.P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
History
DepositionJul 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary
Revision 1.2Mar 25, 2015Group: Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3349
Polymers23,7131
Non-polymers6218
Water3,369187
1
A: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
hetero molecules

A: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,66718
Polymers47,4262
Non-polymers1,24116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3750 Å2
ΔGint-25.5 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.464, 62.464, 128.085
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2158-

HOH

-
Components

#1: Protein CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1 / CHD-1 / CHD1 / ATP-DEPENDENT HELICASE CHD1


Mass: 23713.076 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 1119-1327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O14646, DNA helicase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.35 Å3/Da / Density % sol: 47.77 % / Description: NONE
Crystal growpH: 7.5 / Details: 2M AMMONIUM SULFATE, 0.1M CITRATE PH 3.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→128.09 Å / Num. obs: 32880 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 29.53 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 36.2
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
AutoPROCdata reduction
AP_SCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BALBES

Resolution: 1.62→29.34 Å / Cor.coef. Fo:Fc: 0.9546 / Cor.coef. Fo:Fc free: 0.9469 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.084
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1664 5.07 %RANDOM
Rwork0.192 ---
obs0.1936 32793 99.16 %-
Displacement parametersBiso mean: 36.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.8705 Å20 Å20 Å2
2---1.8705 Å20 Å2
3---3.741 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 1.62→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 39 187 1680
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011567HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12110HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d747SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes225HARMONIC5
X-RAY DIFFRACTIONt_it1567HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion2.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion202SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2050SEMIHARMONIC4
LS refinement shellResolution: 1.62→1.67 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2386 134 4.96 %
Rwork0.1909 2567 -
all0.1931 2701 -
obs--99.16 %
Refinement TLS params.Method: refined / Origin x: 18.7622 Å / Origin y: 1.528 Å / Origin z: 21.6082 Å
111213212223313233
T-0.0414 Å2-0.0102 Å20.0092 Å2--0.0788 Å20.0288 Å2---0.0531 Å2
L0.5575 °20.0192 °20.0441 °2-1.2934 °2-0.9795 °2--1.8312 °2
S-0.0395 Å °-0.0179 Å °0.0086 Å °0.0149 Å °-0.0989 Å °-0.1334 Å °-0.0957 Å °0.1746 Å °0.1384 Å °
Refinement TLS groupSelection details: CHAIN A

+
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