[English] 日本語
Yorodumi
- PDB-3aad: Structure of the histone chaperone CIA/ASF1-double bromodomain co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3aad
TitleStructure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction
Components
  • Histone chaperone ASF1A
  • Transcription initiation factor TFIID subunit 1
KeywordsTRANSCRIPTION/CHAPERONE / PROTEIN-PROTEIN COMPLEX / BROMODOMAIN / TRANSCRIPTION / TRANSCRIPTION REGULATION / CHAPERONE / CHROMATIN REGULATOR / TRANSCRIPTION-CHAPERONE COMPLEX
Function / homology
Function and homology information


positive regulation of androgen receptor signaling pathway / histone chaperone activity / negative regulation of protein autoubiquitination / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / histone H4K16ac reader activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / negative regulation of signal transduction by p53 class mediator / RNA polymerase II general transcription initiation factor binding ...positive regulation of androgen receptor signaling pathway / histone chaperone activity / negative regulation of protein autoubiquitination / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / histone H4K16ac reader activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / negative regulation of signal transduction by p53 class mediator / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / DNA repair-dependent chromatin remodeling / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / midbrain development / ubiquitin conjugating enzyme activity / replication fork processing / transcription initiation at RNA polymerase I promoter / histone acetyltransferase activity / MLL1 complex / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / transcription regulator inhibitor activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / regulation of signal transduction by p53 class mediator / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / mRNA transcription by RNA polymerase II / protein polyubiquitination / osteoblast differentiation / cellular response to UV / p53 binding / kinase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosome assembly / site of double-strand break / protein autophosphorylation / ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / histone binding / transcription by RNA polymerase II / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA damage response / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle ...Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain (BrD) profile. / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 1 / Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAkai, Y. / Adachi, N. / Hayashi, Y. / Eitoku, M. / Sano, N. / Natsume, R. / Kudo, N. / Tanokura, M. / Senda, T. / Horikoshi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction
Authors: Akai, Y. / Adachi, N. / Hayashi, Y. / Eitoku, M. / Sano, N. / Natsume, R. / Kudo, N. / Tanokura, M. / Senda, T. / Horikoshi, M.
History
DepositionNov 16, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1
B: Histone chaperone ASF1A
D: Histone chaperone ASF1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2154
Polymers70,1193
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.120, 102.120, 271.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID 250 kDa subunit / TAF(II)250 / TAFII-250 / TAFII250 / TBP- ...Transcription initiation factor TFIID 250 kDa subunit / TAF(II)250 / TAFII-250 / TAFII250 / TBP-associated factor 250 kDa / p250 / Cell cycle gene 1 protein


Mass: 34183.207 Da / Num. of mol.: 1 / Fragment: Bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCG1, TAF1, TAFII250 / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CODON PLUS-RIL
References: UniProt: P21675, non-specific serine/threonine protein kinase
#2: Protein Histone chaperone ASF1A / Anti-silencing function protein 1 homolog A / hAsf1 / hAsf1a / CCG1-interacting factor A / CIA / hCIA


Mass: 17968.043 Da / Num. of mol.: 2 / Fragment: Residues 1-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CIA-I / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CODON PLUS-RIL / References: UniProt: Q9Y294
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.65
Details: 0.1M MES, 1.1M AMMONIUM SULFATE, 0.25M LITHIUM SULFATE, pH 5.65, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2006
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→37.18 Å / Num. obs: 17814 / % possible obs: 99.2 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 6.3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→31.65 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.84 / SU B: 78.508 / SU ML: 0.584 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.608 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS-PARAMETERS WERE REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 -5 %RANDOM
Rwork0.237 ---
obs0.24 12345 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 3.3→31.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4612 0 5 0 4617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224724
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9656430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2095565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.14924.958238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.39815807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4031526
X-RAY DIFFRACTIONr_chiral_restr0.1040.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023625
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.22210
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.23132
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.52935
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it024701
X-RAY DIFFRACTIONr_scbond_it032007
X-RAY DIFFRACTIONr_scangle_it04.51729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 49 -
Rwork0.285 887 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
121.23517.36252.620524.086110.58968.27770.5247-0.2971.6131.2898-0.23671.194-0.17180.2605-0.28790.1841-0.05840.0254-0.23440.1507-0.3623-63.12943.53622.206
29.3064-1.7692-4.16964.53581.09944.2261-0.37830.6889-0.5667-1.0757-0.16920.7862-0.1319-0.65470.54740.5497-0.567-0.00140.3233-0.35070.4942-72.73415.995-8.788
36.3592-4.4766-0.9979.7553-2.08362.25190.14550.34690.0889-0.8188-0.1081-0.0652-0.05340.4782-0.03740.0092-0.16640.0131-0.11890.0089-0.4728-52.88430.58810.894
420.27728.84442.147513.16081.703111.4370.0434-0.41661.25280.2605-0.13752.1657-0.367-1.41910.09420.26820.0844-0.0903-0.13450.10740.0436-73.37841.8414.684
56.70090.3934.8813.17110.766213.78980.07190.23780.17160.4592-0.37520.25432.0905-0.15220.30330.813-0.23120.6147-0.75960.2327-0.2212-36.68611.991-8.9
64.3029-0.5812-0.730513.17853.74746.8629-0.35460.67580.4894-0.83820.4523-0.3213-0.55830.962-0.09770.3468-0.2982-0.19050.16880.4051-0.1568-63.50956.178-2.326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1353 - 1366
2X-RAY DIFFRACTION2A1379 - 1495
3X-RAY DIFFRACTION3A1496 - 1608
4X-RAY DIFFRACTION4A1609 - 1628
5X-RAY DIFFRACTION5B1 - 153
6X-RAY DIFFRACTION6D1 - 152

+
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