[English] 日本語
Yorodumi
- PDB-8ugv: Crystal structure of the second bromodomain of human BRD2 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ugv
TitleCrystal structure of the second bromodomain of human BRD2 in complex with 6IND
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / BRD2 / BROMODOMAIN / BROMODOMAIN INHIBITOR / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / histone reader activity / : / neural tube closure / nucleosome assembly / spermatogenesis ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / histone reader activity / : / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 United States
CitationJournal: to be published
Title: Development of synthetic molecules for bromodomain-selective recruitment of transcriptional regulators to targeted genomic loci
Authors: Chowdhury, N. / Nithianantham, S. / Lang, W. / Young, S. / Philips, S. / Das, S. / Shelat, A. / Fischer, M. / Ansari, A. / Jaisankar, P.
History
DepositionOct 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8804
Polymers27,0492
Non-polymers8312
Water3,261181
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9402
Polymers13,5241
Non-polymers4151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9402
Polymers13,5241
Non-polymers4151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.799, 117.799, 42.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13524.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25440
#2: Chemical ChemComp-WNX / methyl [(4S,6P,10aM)-6-(1H-indol-6-yl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]acetate


Mass: 415.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H21N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.93 % / Description: Tetragonal prism
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS-HCl pH 8.5 and 28% (v/v) PEG 550 MME

-
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: Mar 11, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 20923 / % possible obs: 99.5 % / Redundancy: 11.2 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.035 / Rrim(I) all: 0.117 / Χ2: 0.876 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.99-2.0312.21.78210200.8490.9580.5161.8560.647100
2.03-2.079.51.43810180.670.8960.5081.530.97699.8
2.07-2.119.61.20410280.8550.960.4151.2770.999.9
2.11-2.1511.70.77810220.940.9840.2330.8130.69698.9
2.15-2.210.90.73810240.920.9790.2350.7760.68999.5
2.2-2.257.60.61910070.8930.9710.2420.6671.59596.9
2.25-2.3110.40.50610240.940.9840.1620.5330.815100
2.31-2.37130.37510480.9830.9960.1060.390.703100
2.37-2.4413.30.34210100.9830.9960.0960.3550.712100
2.44-2.5212.80.25810610.9910.9980.0730.2680.722100
2.52-2.6112.80.21410320.9910.9980.0610.2230.76100
2.61-2.7110.50.20710350.9910.9980.0670.2181.29100
2.71-2.8412.50.11710570.9960.9990.0340.1220.759100
2.84-2.99120.09310420.9970.9990.0270.0970.776100
2.99-3.1710.90.07510290.9970.9990.0230.0790.80398.6
3.17-3.4211.10.05410610.9980.9990.0170.0560.85799.7
3.42-3.769.90.04810550.9980.9990.0160.0511.5398.6
3.76-4.3110.80.03610870.9980.9990.0110.0381.0699.6
4.31-5.4311.80.03310950.99810.010.0340.9299.9
5.43-5010.50.02911680.99910.010.0310.83798.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→40.03 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 981 5 %Random
Rwork0.1761 ---
obs0.1776 19627 93.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 62 181 2039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041918
X-RAY DIFFRACTIONf_angle_d0.862597
X-RAY DIFFRACTIONf_dihedral_angle_d12.917705
X-RAY DIFFRACTIONf_chiral_restr0.04254
X-RAY DIFFRACTIONf_plane_restr0.004333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.10.27351140.24241919X-RAY DIFFRACTION69
2.1-2.230.23941290.20592544X-RAY DIFFRACTION90
2.23-2.40.22431410.20142650X-RAY DIFFRACTION95
2.4-2.640.2441550.18472817X-RAY DIFFRACTION100
2.64-3.030.25051580.18392837X-RAY DIFFRACTION100
3.03-3.810.18951290.16872867X-RAY DIFFRACTION99
3.81-40.030.16351550.15373012X-RAY DIFFRACTION99
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)
12.76480.2354-0.64892.9922-0.98533.5686-0.0027-0.0470.25830.31030.0706-0.0516-0.28170.0847-0.05150.18820.0265-0.01350.129-0.01820.219529.887115.14357.4914
25.7276-1.2514-3.3823.25451.09556.4408-0.11130.03450.01610.1560.11780.12350.0927-0.341-0.00670.18440.015-0.01180.14320.02270.164324.998311.8827.1558
36.90861.9375-4.14336.2241-3.66979.3198-0.3129-0.3746-0.15050.34320.0478-0.18880.48830.1060.31440.25710.0526-0.02390.1348-0.01240.179531.97574.26412.3286
47.2929-1.52.10944.6441-0.99274.69460.06110.8206-0.2372-0.6034-0.0953-0.10720.0292-0.00680.04570.29-0.00460.01160.1781-0.03790.204731.0775-9.5947-2.2955
54.4509-0.5708-0.99024.45710.50576.1437-0.029-0.2881-0.41570.4315-0.00370.27190.0375-0.3779-0.0690.28590.0268-0.01030.22850.0320.296726.2178-16.164516.9669
63.12841.26842.13174.83740.2117.05890.02160.0442-0.14190.03420.27630.35640.0453-0.461-0.24040.20330.0278-0.01260.1930.01290.222524.3406-8.78286.4921
74.0324-1.37571.69826.6561-4.21732.89-0.26830.08810.1948-0.09290.0632-0.3386-0.2817-0.22190.17880.31860.0186-0.01170.1881-0.01620.19732.7952-1.98972.4885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 347 through 395 )
2X-RAY DIFFRACTION2chain 'A' and (resid 396 through 433 )
3X-RAY DIFFRACTION3chain 'A' and (resid 434 through 455 )
4X-RAY DIFFRACTION4chain 'B' and (resid 347 through 372 )
5X-RAY DIFFRACTION5chain 'B' and (resid 373 through 395 )
6X-RAY DIFFRACTION6chain 'B' and (resid 396 through 433 )
7X-RAY DIFFRACTION7chain 'B' and (resid 434 through 455 )

+
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