[English] 日本語
Yorodumi
- PDB-5fe8: Crystal structure of human PCAF bromodomain in complex with compo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fe8
TitleCrystal structure of human PCAF bromodomain in complex with compound SL1126 (compound 12)
ComponentsHistone acetyltransferase KAT2B
KeywordsSIGNALING PROTEIN / bromodomain / Histone acetyltransferase KAT2B / histone / acetylation / acetyllysine / epigenetics / structural genomics consortium (SGC)
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / peptidyl-lysine acetylation ...regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / YAP1- and WWTR1 (TAZ)-stimulated gene expression / actomyosin / positive regulation of fatty acid biosynthetic process / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / ATAC complex / I band / cellular response to parathyroid hormone stimulus / Regulation of FOXO transcriptional activity by acetylation / limb development / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / A band / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / histone acetyltransferase binding / protein acetylation / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / histone acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / positive regulation of glycolytic process / transcription initiation-coupled chromatin remodeling / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / memory / kinetochore / Pre-NOTCH Transcription and Translation / histone deacetylase binding / positive regulation of neuron projection development / cellular response to insulin stimulus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / vasodilation / rhythmic process / heart development / HATs acetylate histones / cellular response to oxidative stress / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / negative regulation of cell population proliferation / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A ...PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5WT / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2016
Title: Structure-Based Identification of Inhibitory Fragments Targeting the p300/CBP-Associated Factor Bromodomain.
Authors: Chaikuad, A. / Lang, S. / Brennan, P.E. / Temperini, C. / Fedorov, O. / Hollander, J. / Nachane, R. / Abell, C. / Muller, S. / Siegal, G. / Knapp, S.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone acetyltransferase KAT2B
B: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,15012
Polymers28,3452
Non-polymers80510
Water4,216234
1
A: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6516
Polymers14,1721
Non-polymers4795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint3 kcal/mol
Surface area6800 Å2
MethodPISA
2
B: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4996
Polymers14,1721
Non-polymers3265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint11 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.670, 99.670, 99.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 724 - 831 / Label seq-ID: 12 - 119

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Histone acetyltransferase KAT2B / Histone acetyltransferase PCAF / Histone acetylase PCAF / Lysine acetyltransferase 2B / P300/CBP- ...Histone acetyltransferase PCAF / Histone acetylase PCAF / Lysine acetyltransferase 2B / P300/CBP-associated factor / P/CAF


Mass: 14172.371 Da / Num. of mol.: 2 / Fragment: PCAF bromodomain, UNP residues 715-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2B, PCAF / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 / References: UniProt: Q92831, histone acetyltransferase
#2: Chemical ChemComp-5WT / ~{N}-(1,4-dimethyl-2-oxidanylidene-quinolin-7-yl)ethanamide


Mass: 230.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54165 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54165 Å / Relative weight: 1
ReflectionResolution: 2.1→39.6 Å / Num. obs: 21523 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PROTEUM PLUSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 3GG3

3gg3


Resolution: 2.1→33.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.68 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23252 1103 5.1 %RANDOM
Rwork0.19344 ---
obs0.19545 20417 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å2-0 Å2
2--0.16 Å2-0 Å2
3----0.51 Å2
Refine analyzeLuzzati coordinate error obs: 0.285 Å
Refinement stepCycle: 1 / Resolution: 2.1→33.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 53 234 2095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021916
X-RAY DIFFRACTIONr_bond_other_d0.0070.021841
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9932568
X-RAY DIFFRACTIONr_angle_other_deg1.3653.0024259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13723.93389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4051510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212078
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02440
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2312.384868
X-RAY DIFFRACTIONr_mcbond_other1.2082.381867
X-RAY DIFFRACTIONr_mcangle_it1.943.5611083
X-RAY DIFFRACTIONr_mcangle_other1.943.5641084
X-RAY DIFFRACTIONr_scbond_it1.6782.7251048
X-RAY DIFFRACTIONr_scbond_other1.6772.7281049
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.683.9451483
X-RAY DIFFRACTIONr_long_range_B_refined7.14221.7642462
X-RAY DIFFRACTIONr_long_range_B_other7.14121.7812463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12064 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 74 -
Rwork0.27 1492 -
obs--99.75 %
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)
16.83350.316-2.05063.14390.59864.8070.15271.00310.0516-0.18030.0307-0.20650.029-0.3169-0.18340.02210.0342-0.00630.1779-0.03580.083720.38446.772889.4655
25.02051.2319-1.92463.6658-1.80196.71430.28060.24140.25130.2466-0.1936-0.0335-0.2893-0.1578-0.0870.03360.0133-0.00830.0508-0.00790.066716.183413.308196.0924
39.51061.4353-2.32425.9148-2.10566.87610.06190.284-0.1760.0011-0.1575-0.47590.11620.47490.09560.08070.0427-0.07780.0674-0.02560.113325.8294.473998.9831
415.88730.6251-3.62323.10071.10277.40730.0810.00640.67780.2731-0.29450.3788-0.2998-0.5690.21350.22480.04250.01880.1502-0.0220.187714.881829.0848121.5803
56.2485-2.3761-0.52397.16490.57284.15060.3598-0.54960.1270.7959-0.0978-0.3199-0.04240.2664-0.26210.2873-0.0756-0.12270.0776-0.01580.09729.230615.3827119.3941
60.95690.10810.24816.66771.17863.95690.15830.22690.0170.1237-0.0896-0.2065-0.0924-0.0748-0.06870.11520.0148-0.07620.07190.02980.082327.14415.8636111.5901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A724 - 754
2X-RAY DIFFRACTION2A755 - 806
3X-RAY DIFFRACTION3A807 - 831
4X-RAY DIFFRACTION4B724 - 729
5X-RAY DIFFRACTION5B730 - 754
6X-RAY DIFFRACTION6B755 - 831

+
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