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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lvq
TitleCrystal structure of human PCAF bromodomain in complex with compound-D (CPD-D), N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide
ComponentsHistone acetyltransferase KAT2B
KeywordsTRANSFERASE / SIGNALING 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 / 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 / peptidyl-lysine acetylation / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor ...regulation of protein ADP-ribosylation / negative regulation of rRNA processing / 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 / peptidyl-lysine acetylation / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / YAP1- and WWTR1 (TAZ)-stimulated gene expression / positive regulation of fatty acid biosynthetic process / actomyosin / 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 / A band / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / limb development / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / cellular response to parathyroid hormone stimulus / regulation of tubulin deacetylation / protein-lysine-acetyltransferase activity / histone acetyltransferase binding / protein acetylation / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / histone acetyltransferase activity / Formation of paraxial mesoderm / acetyltransferase activity / regulation of RNA splicing / regulation of cell division / regulation of embryonic development / RNA Polymerase I Transcription Initiation / regulation of DNA repair / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / positive regulation of glycolytic process / 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 / kinetochore / positive regulation of neuron projection development / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / memory / mitotic spindle / Metalloprotease DUBs / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to insulin stimulus / vasodilation / rhythmic process / HATs acetylate histones / heart development / 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
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
N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsChaikuad, A. / Filippakopoulos, P. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hopkins, A.L. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: ACS Med Chem Lett / Year: 2016
Title: Discovery of New Bromodomain Scaffolds by Biosensor Fragment Screening.
Authors: Navratilova, I. / Aristotelous, T. / Picaud, S. / Chaikuad, A. / Knapp, S. / Filappakopoulos, P. / Hopkins, A.L.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)28,9689
Polymers28,3452
Non-polymers6247
Water2,288127
1
A: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5945
Polymers14,1721
Non-polymers4214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3754
Polymers14,1721
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.859, 99.859, 100.762
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: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 724 - 829 / Label seq-ID: 12 - 117

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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2B, PCAF / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-pRARE2 / References: UniProt: Q92831, histone acetyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-2LX / N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide


Mass: 235.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO3
#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.: 127 / 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: 3.41 Å3/Da / Density % sol: 63.94 %
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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91997 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91997 Å / Relative weight: 1
ReflectionResolution: 2.05→65.62 Å / Num. obs: 23526 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.9
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.05→43.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.543 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21795 1212 5.2 %RANDOM
Rwork0.18045 ---
obs0.18235 22306 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.896 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.05→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 41 127 1960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191903
X-RAY DIFFRACTIONr_bond_other_d0.0060.021808
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9772556
X-RAY DIFFRACTIONr_angle_other_deg1.20234184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9323.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34415347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1771511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212124
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02447
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_it3.7784.21871
X-RAY DIFFRACTIONr_mcbond_other3.7764.212872
X-RAY DIFFRACTIONr_mcangle_it5.3166.2731087
X-RAY DIFFRACTIONr_mcangle_other5.3156.2761088
X-RAY DIFFRACTIONr_scbond_it4.8664.7461032
X-RAY DIFFRACTIONr_scbond_other4.8644.7471033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1556.8941466
X-RAY DIFFRACTIONr_long_range_B_refined9.81534.9732345
X-RAY DIFFRACTIONr_long_range_B_other9.81434.9862346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5972 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 86 -
Rwork0.294 1652 -
obs--99.83 %
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)
13.1546-0.15971.68993.65440.71661.37020.36940.09670.12430.2705-0.51270.04120.1513-0.10360.14330.1211-0.0479-0.00210.1893-0.0430.041821.731912.829953.5073
22.89940.1043-0.52083.55230.89412.96680.06960.3222-0.07220.2539-0.03480.4934-0.06910.0525-0.03480.0802-0.0258-0.01440.05320.00260.139132.59817.24672.2592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A724 - 831
2X-RAY DIFFRACTION2B723 - 830

+
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