[English] 日本語
Yorodumi
- PDB-5ffy: Crystal structure of the bromodomain of human BRPF1 in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ffy
TitleCrystal structure of the bromodomain of human BRPF1 in complex with a benzimidazole ligand
ComponentsPeregrin
KeywordsTRANSCRIPTION / Peregrin / MOZ-MORF complex
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTallant, C. / Savitsky, P. / Nunez-Alonso, G. / Kopec, J. / Fedorov, O. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
CitationJournal: To Be Published
Title: Crystal structure of the bromodomain of human BRPF1 in complex with a benzimidazole ligand
Authors: Tallant, C. / Savitsky, P. / Nunez-Alonso, G. / Kopec, J. / Fedorov, O. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
History
DepositionDec 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0792
Polymers13,7041
Non-polymers3751
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.545, 59.869, 51.236
Angle α, β, γ (deg.)90.00, 100.43, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-958-

HOH

21A-985-

HOH

31A-1003-

HOH

41A-1024-

HOH

-
Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 13703.698 Da / Num. of mol.: 1 / Fragment: UNP residues 626-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Chemical ChemComp-5XD / 4-ethyl-~{N}-(6-methoxy-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)benzenesulfonamide


Mass: 375.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N3O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.05 % / Description: Rod
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M bis tris propane pH 9, 10% ethylene glycol, 0.15 M sodium nitrate
PH range: 9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.55→25.19 Å / Num. all: 20656 / Num. obs: 20656 / % possible obs: 98.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.022 / Net I/σ(I): 19.1
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.1 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.55→23.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.514 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 1058 5.1 %RANDOM
Rwork0.18319 ---
obs0.18475 19595 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.718 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å2-0 Å20.73 Å2
2---0.82 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.55→23.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 26 124 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02994
X-RAY DIFFRACTIONr_bond_other_d0.0010.02969
X-RAY DIFFRACTIONr_angle_refined_deg1.6332.0151346
X-RAY DIFFRACTIONr_angle_other_deg0.7943.0072223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8515116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60323.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22715186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.913159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211114
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
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_it3.9833.224449
X-RAY DIFFRACTIONr_mcbond_other3.9353.207448
X-RAY DIFFRACTIONr_mcangle_it4.945.953561
X-RAY DIFFRACTIONr_mcangle_other4.9355.975562
X-RAY DIFFRACTIONr_scbond_it9.5114.528545
X-RAY DIFFRACTIONr_scbond_other9.5024.528546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.77.795783
X-RAY DIFFRACTIONr_long_range_B_refined12.12220.4761304
X-RAY DIFFRACTIONr_long_range_B_other12.1220.4771305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 67 -
Rwork0.296 1424 -
obs--98.35 %
Refinement TLS params.Method: refined / Details: Chain A / Origin x: 18.684 Å / Origin y: -18.259 Å / Origin z: 10.2441 Å
111213212223313233
T0.0306 Å2-0.0108 Å20.0052 Å2-0.0372 Å2-0.0079 Å2--0.0386 Å2
L0.8112 °2-1.2858 °2-0.4103 °2-2.5016 °20.448 °2--0.3056 °2
S-0.0032 Å °-0.0285 Å °0.1695 Å °-0.0821 Å °0.086 Å °-0.266 Å °0.047 Å °-0.0194 Å °-0.0828 Å °

+
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