[English] 日本語
Yorodumi
- PDB-1ofc: nucleosome recognition module of ISWI ATPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ofc
Titlenucleosome recognition module of ISWI ATPase
ComponentsISWI PROTEIN
KeywordsNUCLEAR PROTEIN / CHROMATIN REMODELING FACTOR / ISWI / ATPASE / SANT DOMAIN / NUCLEOSOME RECOGNITION
Function / homology
Function and homology information


ISWI-type complex / nuclear speck organization / : / : / sperm DNA decondensation / RSF complex / ACF complex / ecdysone receptor signaling pathway / chromatin organization => GO:0006325 / chromatin remodeling => GO:0006338 ...ISWI-type complex / nuclear speck organization / : / : / sperm DNA decondensation / RSF complex / ACF complex / ecdysone receptor signaling pathway / chromatin organization => GO:0006325 / chromatin remodeling => GO:0006338 / CHRAC / ATP-dependent chromatin remodeler activity => GO:0140658 / sperm DNA condensation / polytene chromosome / NURF complex / transcription factor binding / ATP-dependent activity, acting on DNA / nucleosome binding / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of circadian rhythm / nucleosome assembly / chromatin organization / spermatogenesis / transcription regulator complex / chromatin remodeling / nucleotide binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Similarity search - Function
: / ISWI, HAND domain / iswi atpase / DBINO domain / DNA-binding domain / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE ...: / ISWI, HAND domain / iswi atpase / DBINO domain / DNA-binding domain / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / SANT domain profile. / SANT domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-deoxy-alpha-D-glucopyranose / alpha-D-glucopyranose / Chromatin-remodeling complex ATPase chain Iswi
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsGrune, T. / Muller, C.W.
CitationJournal: Mol.Cell / Year: 2003
Title: Crystal Structure and Functional Analysis of a Nucleosome Recognition Module of the Remodeling Factor Iswi
Authors: Grune, T. / Brzeski, J. / Eberharter, A. / Clapier, C.R. / Corona, D.F.V. / Becker, P.B. / Muller, C.W.
History
DepositionApr 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: ISWI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3224
Polymers35,8861
Non-polymers4363
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.470, 66.340, 82.830
Angle α, β, γ (deg.)90.00, 124.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-2002-

HOH

-
Components

#1: Protein ISWI PROTEIN / IMITATION SWI PROTEIN / NUCLEOSOME REMODELING FACTOR 140 KDA SUBUNIT / NURF-140 / CHRAC 140 KDA SUBUNIT


Mass: 35885.770 Da / Num. of mol.: 1
Fragment: NUCLEOSOME RECOGNITION MODULE (C-TERMINAL THIRD) RESIDUES 691-991
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: HTB-C2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q24368
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-G4D / 4-deoxy-alpha-D-glucopyranose / 4-DEOXY-ALPHA-D-GLUCOSE / 4-deoxy-D-glucose / 4-deoxy-glucose


Type: D-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
a-D-4-deoxy-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 691-991 PLUS THREE ADDITIONAL RESIDUES AT THE N-TERMINUS (GAM)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 65.9 %
Description: MERGING R IS R_MEASURED (MULTIPLICITY INDEPENDENT)
Crystal growpH: 7
Details: 1MUL PROTEIN AT 60MG/ML IN 20MM HEPES, 0.5M NACL, PH 7, WAS MIXED WITH 4MUL, 0.125M HEPES PH 7.0, 5% PEG 6000 RESERVOIR 0.1M HEPES, 4% PEG 6000, 0.1M NACL CRYSTALS GROWTH INDUCED BY MICRO SEEDING
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 %PEG60001reservoir
20.1 MHEPES1reservoirpH7.0
350 mMTris-Cl1droppH7.6
4100 mM1dropNaCl
550 %glycerol1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939281
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 13, 2002 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939281 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 38275 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 19 Å / Num. measured all: 141793 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 99.1 % / Num. unique obs: 5452 / Num. measured obs: 20046 / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1

-
Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→18.8 Å / SU B: 3.413 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.25344 1876 4.9 %RANDOM
Rwork0.21775 ---
obs0.21946 36396 98.6 %-
Displacement parametersBiso mean: 31.224 Å2
Baniso -1Baniso -2Baniso -3
1--3.45 Å20 Å2-2.99 Å2
2--0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 29 48 2255
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 19 Å / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.019
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.701

+
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