[English] 日本語
Yorodumi
- PDB-9mpl: BRD2-BD1 in complex with cyclic peptide 2.1C-W11A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mpl
TitleBRD2-BD1 in complex with cyclic peptide 2.1C-W11A
Components
  • 2.1C-W11A
  • Bromodomain-containing protein 2
KeywordsGENE REGULATION / BRD2 / cyclic peptide
Function / homology
Function and homology information


acetylation-dependent protein binding / histone H3K14ac reader activity / chromatin looping / histone H4K5ac reader activity / RUNX3 regulates p14-ARF / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...acetylation-dependent protein binding / histone H3K14ac reader activity / chromatin looping / histone H4K5ac reader activity / RUNX3 regulates p14-ARF / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / histone binding / spermatogenesis / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsPatel, K. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: BRD2-BD1 in complex with cyclic peptide 2.1C-W11A
Authors: Patel, K. / Mackay, J.P.
History
DepositionDec 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: 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
G: 2.1C-W11A
C: 2.1C-W11A


Theoretical massNumber of molelcules
Total (without water)34,9094
Polymers34,9094
Non-polymers00
Water00
1
A: Bromodomain-containing protein 2
C: 2.1C-W11A


Theoretical massNumber of molelcules
Total (without water)17,4542
Polymers17,4542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-12 kcal/mol
Surface area7440 Å2
MethodPISA
2
G: 2.1C-W11A

B: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)17,4542
Polymers17,4542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z+1/41
Buried area1450 Å2
ΔGint-12 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.992, 77.992, 57.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

-
Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1


Mass: 15836.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Protein/peptide 2.1C-W11A


Mass: 1617.867 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium chloride, 0.1 M Sodium acetate pH 5.0, 20 % w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→46.31 Å / Num. obs: 6315 / % possible obs: 99.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 49.68 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.3
Reflection shellResolution: 3.1→3.32 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.387 / Num. unique obs: 1109 / CC1/2: 0.742 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→46.31 Å / SU ML: 0.2751 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.8251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2678 322 5.1 %
Rwork0.2105 5993 -
obs0.2134 6315 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.01 Å2
Refinement stepCycle: LAST / Resolution: 3.11→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 8 0 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152228
X-RAY DIFFRACTIONf_angle_d0.42793016
X-RAY DIFFRACTIONf_chiral_restr0.0375316
X-RAY DIFFRACTIONf_plane_restr0.0037380
X-RAY DIFFRACTIONf_dihedral_angle_d10.4748832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.920.3491600.26042944X-RAY DIFFRACTION99.26
3.92-46.310.22111620.18023049X-RAY DIFFRACTION99.97
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)
12.519014184190.4032966609480.3539568572273.243353130450.1214391023961.892758375910.4380610208980.509637698092-0.45633892023-0.5143766499270.262653680892-0.2166759929290.6214157920670.0755685120737-0.4366269208790.393730252763-0.02229467568970.02717645556910.3762707366050.02978345103910.20005298303325.845482089725.5919276228-2.33143211161
24.491858913280.45430236645-1.257976309832.523761843640.7450368594958.436860338340.231461752821-0.287039376907-0.2985880495170.3825559082460.06487554727810.08982109863120.711974942684-0.754247597324-0.5842544099310.4279200749580.049408430167-0.02466935497780.4731559027440.08446250867310.19250875501622.382669680524.190522026918.7087285903
33.872522984861.19887081087-0.5146593453083.373699211531.711843092113.934085058880.331033984613-0.03070490031970.15696254069-0.608737365098-0.2015466754180.614368707032-0.330175722061-1.24173425794-0.2314971147340.4347011505390.0185059647324-0.1387312973920.3919339592370.01795604450280.34413858081416.359881447126.73350436065.77303881759
43.61684648897-0.312669695242.497135957031.04299165916-0.786020867448.24116907433-0.676828322341-0.340873549921.03507220736-0.526033105431-0.01325393427560.367571490938-1.52397650241-0.06096176948540.4632365577940.5936224640.00866434196582-0.05555151910520.213340411137-0.03984523029650.47332896887920.984197820734.18909067916.83473779786
52.23453942072-1.97712900650.1749690903693.42056632273-1.633396019561.27170060112-0.1573183011010.1624132907220.296210292797-0.297594003933-0.406094096935-0.5211907787440.341942469169-0.2966368271160.5139254686380.265031274955-0.05339913302340.04316999371560.403815786046-0.07922571780960.32626565220628.269080077234.09949876581.72857663237
63.22930991119-0.0496212151742-0.8990964255134.938744115671.344689898363.53028109396-0.186241076093-0.556131525436-0.1366865168850.4180752880950.136322889107-0.3676900221430.2566793574590.1859678139240.06150208416230.3714150732490.0952807230476-0.09263830000780.4298272897810.06680845809020.465604948419.682783207-3.417670792834.47277386209
71.91848028246-1.00130910270.03601979881024.05203827476-1.5618119137.23232674576-0.141701825166-0.6230107137750.2974553160330.6043087628370.299426972041-0.690077088325-0.4662690862460.573883365259-0.1180906972770.4165652070630.0207492521932-0.207222627350.4669519172480.0007409721797580.81637244038922.47999450353.949194089032.67264876023
81.93807290144-0.704616474562-0.06292512686842.716013781410.6396271206372.82727123546-0.333400045598-0.120332315290.1582195578040.6527240880570.103280201479-0.164605644743-0.6797155283780.4786425966920.1689052156670.493274753565-0.01755473373-0.07318459270970.272680574758-0.01351213128290.37139953414111.79729307871.981696694687.23265040738
94.80400780201-0.503254842263-1.495822456411.866855211771.164832065511.349644730330.1940554382310.9516502290790.622644661759-0.694325097063-0.456740060556-0.331549680604-1.39082681353-0.505906806765-0.1394229216480.5089113957680.0349471128459-0.04849004276880.3880645152440.1409697759910.2427343884398.528659439714.53672749662.55046463106
107.386791901670.4284026137560.2446280557695.75934990177-2.616546510791.41675281050.117858413516-1.28633325524-0.636941768680.6250054413140.0516556298275-0.1572017681620.331044840138-0.721951005784-0.06995286682740.336133826082-0.04799113506970.05888901073970.3947358755420.04013855250460.23207470164531.482649286723.956121164420.9029854722
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 72 through 98 )AA72 - 981 - 27
22chain 'A' and (resid 99 through 112 )AA99 - 11228 - 41
33chain 'A' and (resid 113 through 137 )AA113 - 13742 - 66
44chain 'A' and (resid 138 through 155 )AA138 - 15567 - 84
55chain 'A' and (resid 156 through 187 )AA156 - 18785 - 116
66chain 'B' and (resid 72 through 112 )BB72 - 1121 - 41
77chain 'B' and (resid 113 through 155 )BB113 - 15542 - 84
88chain 'B' and (resid 156 through 187 )BB156 - 18785 - 116
99chain 'G' and (resid 1 through 13 )CC1 - 132 - 14
1010chain 'C' and (resid 1 through 13 )DD1 - 132 - 14

+
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