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- PDB-3aad: Structure of the histone chaperone CIA/ASF1-double bromodomain co... -

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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


histone chaperone activity / negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / DNA replication-dependent chromatin assembly / positive regulation of androgen receptor activity / muscle cell differentiation / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / midbrain development ...histone chaperone activity / negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / DNA replication-dependent chromatin assembly / positive regulation of androgen receptor activity / muscle cell differentiation / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / midbrain development / cellular response to ATP / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / replication fork processing / ubiquitin conjugating enzyme activity / transcription initiation at RNA polymerase I promoter / MLL1 complex / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of ubiquitin-dependent protein catabolic process / histone acetyltransferase 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 / peptidyl-threonine phosphorylation / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / protein polyubiquitination / osteoblast differentiation / cellular response to UV / p53 binding / positive regulation of protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosome assembly / kinase activity / site of double-strand break / histone binding / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / 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 / Bromodomain profile. / bromo domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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