[English] 日本語
Yorodumi
- PDB-7s3p: BD2 domain of human BRD3 bound to Physachenolide C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s3p
TitleBD2 domain of human BRD3 bound to Physachenolide C
ComponentsBromodomain-containing protein 3
KeywordsTRANSCRIPTION / inhibitor / bromodomain / epigenetics
Function / homology
Function and homology information


histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / : / protein localization to chromatin / molecular condensate scaffold activity / histone binding ...histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / : / protein localization to chromatin / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Physachenolide C / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsHorton, N.C. / Chapman, E. / Sivinski, J. / Zerio, C. / Ghadirian, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Physachenolide C is a Potent, Selective BET Inhibitor.
Authors: Zerio, C.J. / Sivinski, J. / Wijeratne, E.M.K. / Xu, Y.M. / Ngo, D.T. / Ambrose, A.J. / Villa-Celis, L. / Ghadirian, N. / Clarkson, M.W. / Zhang, D.D. / Horton, N.C. / Gunatilaka, A.A.L. / ...Authors: Zerio, C.J. / Sivinski, J. / Wijeratne, E.M.K. / Xu, Y.M. / Ngo, D.T. / Ambrose, A.J. / Villa-Celis, L. / Ghadirian, N. / Clarkson, M.W. / Zhang, D.D. / Horton, N.C. / Gunatilaka, A.A.L. / Fromme, R. / Chapman, E.
History
DepositionSep 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
K: Bromodomain-containing protein 3
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: Bromodomain-containing protein 3
D: Bromodomain-containing protein 3
E: Bromodomain-containing protein 3
F: Bromodomain-containing protein 3
G: Bromodomain-containing protein 3
H: Bromodomain-containing protein 3
I: Bromodomain-containing protein 3
J: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,83428
Polymers144,60811
Non-polymers6,22617
Water1,27971
1
K: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
E: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
F: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
G: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
H: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
I: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
J: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.448, 158.535, 293.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 309 or (resid 310 and (name...
d_2ens_1(chain "B" and (resid 309 or (resid 310 and (name...
d_3ens_1(chain "C" and (resid 309 or (resid 310 and (name...
d_4ens_1(chain "D" and (resid 309 or (resid 310 and (name...
d_5ens_1(chain "E" and (resid 309 or (resid 310 and (name...
d_6ens_1(chain "F" and (resid 309 or (resid 310 and (name...
d_7ens_1(chain "G" and (resid 309 or (resid 310 and (name...
d_8ens_1(chain "H" and (resid 309 or (resid 310 and (name...
d_9ens_1(chain "I" and (resid 309 or (resid 310 and (name...
d_10ens_1(chain "J" and (resid 309 through 312 or (resid 313...
d_11ens_1(chain "K" and (resid 309 or (resid 310 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPROA1 - 108
d_21ens_1SERPROB1 - 108
d_31ens_1SERPROC1 - 108
d_41ens_1SERPROD1 - 108
d_51ens_1SERPROE2 - 109
d_61ens_1SERPROF1 - 108
d_71ens_1SERPROG1 - 108
d_81ens_1SERPROH1 - 108
d_91ens_1SERPROI1 - 108
d_101ens_1SERPROJ1 - 108
d_111ens_1SERPROK1 - 108

NCS oper:
IDCodeMatrixVector
1given(-0.967952648823, 0.249625658921, -0.0274718045599), (-0.250922645713, -0.965812681566, 0.0651436105463), (-0.0102711005223, 0.0699492282648, 0.997497674162)47.8729404234, 80.7998494501, 52.1147938977
2given(0.844581559532, -0.524340565757, 0.108392621521), (-0.528220115233, -0.849064500148, 0.00854309374756), (0.0875528364028, -0.0644705024709, -0.994071453744)54.7364890962, 78.2966582985, -105.924370635
3given(-0.437012946597, 0.899437063678, 0.00571427938004), (0.899450089126, 0.436980187693, 0.006152457624), (0.00303672154371, 0.00782841273275, -0.999964746517)-0.460003317798, 0.668952766322, -66.3143023027
4given(0.63902606648, -0.76901670146, 0.0160934531738), (0.766124864487, 0.638208858553, 0.0757769416131), (-0.0685447180663, -0.036093846297, 0.996994912667)0.116615345819, 3.55409816199, 14.3365016201
5given(0.167997692316, -0.981540356023, 0.0914073567906), (-0.984887471148, -0.171082380509, -0.0269719901792), (0.0421122850388, -0.0854947283666, -0.995448244195)53.1989397545, 77.4877869792, -118.867152403
6given(-0.829466519171, -0.557974253854, -0.0254955998344), (0.55251839976, -0.826338176031, 0.109035025384), (-0.0819067243963, 0.0763541149511, 0.993710892377)46.7848299223, 83.0041097954, 39.506698671
7given(0.41563379029, 0.907232387451, 0.0646370445624), (0.907113680756, -0.41865951236, 0.0432317348259), (0.0662821435566, 0.0406645775997, -0.996971950244)2.49001789819, 2.07687787087, -80.3816545792
8given(-0.142949314542, -0.989711658275, -0.00602718400837), (0.984136167557, -0.14278528475, 0.105301311319), (-0.105078528629, 0.00912118050222, 0.994422096942)98.6515921838, 4.58774027046, 27.1222012538
9given(0.628479579629, 0.775361878194, -0.0618657888811), (-0.777825152397, 0.626364618401, -0.0515305454513), (-0.00120427926084, 0.0805066622079, 0.996753343135)-1.53402021018, -1.68668762248, -14.6323572884
10given(0.956413332372, 0.262001915317, 0.128951673242), (0.26050018664, -0.965047688188, 0.0286812182944), (0.131959048277, 0.00616083538171, -0.991236023198)6.17639648132, 1.2354571067, -94.3197207858

-
Components

#1: Protein
Bromodomain-containing protein 3 / RING3-like protein


Mass: 13146.177 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059
#2: Chemical
ChemComp-8L6 / Physachenolide C


Mass: 546.649 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C30H42O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4.03 Å3/Da / Density % sol: 69.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.89→39.49 Å / Num. obs: 53287 / % possible obs: 99.84 % / Redundancy: 2 % / Biso Wilson estimate: 55.77 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05044 / Rpim(I) all: 0.05044 / Rrim(I) all: 0.07134 / Net I/σ(I): 7.67
Reflection shellResolution: 2.89→2.993 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3034 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 5273 / CC1/2: 0.936 / CC star: 0.983 / Rpim(I) all: 0.3034 / Rrim(I) all: 0.4291 / % possible all: 99.79

-
Processing

Software
NameVersionClassification
PHENIX1.19_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Blu-Icedata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2oo1

2oo1


Resolution: 2.89→39.49 Å / SU ML: 0.3791 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2402 1995 3.75 %
Rwork0.2071 51241 -
obs0.2084 53236 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.95 Å2
Refinement stepCycle: LAST / Resolution: 2.89→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9478 0 435 71 9984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009510248
X-RAY DIFFRACTIONf_angle_d1.186214085
X-RAY DIFFRACTIONf_chiral_restr0.07061465
X-RAY DIFFRACTIONf_plane_restr0.00951789
X-RAY DIFFRACTIONf_dihedral_angle_d16.30263670
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EX-RAY DIFFRACTIONTorsion NCS0.394033399352
ens_1d_3EX-RAY DIFFRACTIONTorsion NCS0.451084782878
ens_1d_4EX-RAY DIFFRACTIONTorsion NCS0.309352760894
ens_1d_5EX-RAY DIFFRACTIONTorsion NCS0.398932958066
ens_1d_6EX-RAY DIFFRACTIONTorsion NCS0.418643940463
ens_1d_7EX-RAY DIFFRACTIONTorsion NCS0.418444572586
ens_1d_8EX-RAY DIFFRACTIONTorsion NCS0.417768500383
ens_1d_9EX-RAY DIFFRACTIONTorsion NCS0.401618513901
ens_1d_10EX-RAY DIFFRACTIONTorsion NCS0.397733411259
ens_1d_11EX-RAY DIFFRACTIONTorsion NCS0.428834710119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.35691390.30093613X-RAY DIFFRACTION99.81
2.96-3.040.33271420.26943633X-RAY DIFFRACTION99.89
3.04-3.130.30751410.24573625X-RAY DIFFRACTION99.97
3.13-3.230.28371410.22733620X-RAY DIFFRACTION99.95
3.23-3.350.31741400.2233618X-RAY DIFFRACTION100
3.35-3.480.31381430.25033647X-RAY DIFFRACTION99.89
3.48-3.640.25181410.21563633X-RAY DIFFRACTION99.97
3.64-3.830.24241420.19463610X-RAY DIFFRACTION99.87
3.83-4.070.25541420.20693666X-RAY DIFFRACTION99.74
4.07-4.390.20331420.18213636X-RAY DIFFRACTION100
4.39-4.830.18321430.16293681X-RAY DIFFRACTION100
4.83-5.520.19691450.17913702X-RAY DIFFRACTION100
5.52-6.950.22981440.22443707X-RAY DIFFRACTION99.97
6.95-39.490.20791500.19933850X-RAY DIFFRACTION99.5

+
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