[English] 日本語
Yorodumi
- PDB-8f6g: Crystal structure of BPTF bromodomain in complex with BZ2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f6g
TitleCrystal structure of BPTF bromodomain in complex with BZ2
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION / BPTF / BROMODOMAIN / BROMODOMAIN INHIBITOR
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / 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
Similarity search - Domain/homology
: / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsNithianantham, S. / Fischer, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM142772-01 United States
CitationJournal: To Be Published
Title: Crystal structure of BPTF bromodomain in complex with BZ2
Authors: Nithianantham, S. / Fischer, M.
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7342
Polymers14,4551
Non-polymers2791
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.976, 66.859, 39.564
Angle α, β, γ (deg.)90.00, 104.94, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Nucleosome-remodeling factor subunit BPTF / Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal ...Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal Alzheimer antigen


Mass: 14455.415 Da / Num. of mol.: 1 / Fragment: BPTF bromodomain (uniprot residues 2917-3037)
Source method: isolated from a genetically manipulated source
Details: The following residues were not located. SER A 2915 MET A 2916
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q12830
#2: Chemical ChemComp-XHK / 6-[4-(2-aminoethyl)anilino]-5-chloro-3-methylpyrimidin-4(3H)-one


Mass: 278.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15ClN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0. 2 M NaCl and 23% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→33.43 Å / Num. obs: 9052 / % possible obs: 90.9 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.105 / Χ2: 0.081 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.95-1.981.90.6094040.722183
1.98-2.0220.5624390.773190.5
2.02-2.062.20.4854630.777191.5
2.06-2.12.20.4244610.731192.6
2.1-2.152.30.3874400.885192.8
2.15-2.22.30.3454780.828192.6
2.2-2.252.30.2824660.853192.5
2.25-2.312.40.2924580.829193.9
2.31-2.382.40.2494510.794194
2.38-2.462.30.2134800.845191.8
2.46-2.542.30.194220.9189.2
2.54-2.652.30.1584420.809188.4
2.65-2.772.10.1334270.833184.1
2.77-2.912.40.1114090.765185.4
2.91-3.12.50.14690.786192.5
3.1-3.332.40.0854690.747193.2
3.33-3.672.40.0724560.818192.9
3.67-4.22.40.0564590.709191.3
4.2-5.292.20.0584660.74190.7
5.29-33.432.30.0524930.626195.4

-
Processing

Software
NameVersionClassification
PHENIX1.2refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIX1.2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7M2E

7m2e


Resolution: 1.95→33.43 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 392 4.59 %
Rwork0.1914 --
obs0.1932 8537 85.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 19 120 1136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041074
X-RAY DIFFRACTIONf_angle_d0.7161458
X-RAY DIFFRACTIONf_dihedral_angle_d25.21409
X-RAY DIFFRACTIONf_chiral_restr0.042149
X-RAY DIFFRACTIONf_plane_restr0.007191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.230.2841050.22432402X-RAY DIFFRACTION76
2.23-2.810.25161330.21042807X-RAY DIFFRACTION89
2.81-33.430.20671540.17412936X-RAY DIFFRACTION92
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)
10.919-0.3044-1.10284.80831.66431.6489-0.0687-0.05410.0744-0.02030.2848-0.3689-0.06060.3208-0.22680.12880.0178-0.03130.1554-0.00490.153215.29417.43546.3752
27.82451.99160.51586.10530.71062.59550.0180.1324-1.03440.0230.46780.58360.3709-0.3562-0.38440.1794-0.03640.00240.20080.00210.39080.1758-3.02123.3248
31.46120.3989-0.36082.6935-0.01571.11290.0254-0.00350.02210.00360.01920.06240.03270.0117-0.04180.13750.0045-0.0080.1713-0.00630.11710.61949.0649.1486
49.991-5.07418.01361.9999-2.63222.00010.1671-0.1323-0.42640.1852-0.6039-0.5206-0.59241.13310.45420.7849-0.46340.2450.79350.06351.079827.069527.307610.4887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2917 through 2952 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2953 through 2963 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2964 through 3036 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3037 through 3037 )

+
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