[English] 日本語
Yorodumi
- PDB-7lbt: Crystal structure of the second bromodomain (BD2) of human BRD3 b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lbt
TitleCrystal structure of the second bromodomain (BD2) of human BRD3 bound to ERK5-IN-1
ComponentsBromodomain-containing protein 3
KeywordsGENE REGULATION/INHIBITOR / BET / ERK5 / dual BRD-kinase inhibitor / GENE REGULATION / GENE REGULATION-INHIBITOR complex
Function / homology
Function and homology information


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 ...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, 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
Chem-VYJ / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKarim, M.R. / Bikowitz, M.J. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors.
Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E.
History
DepositionJan 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: Bromodomain-containing protein 3
D: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9128
Polymers52,3574
Non-polymers2,5554
Water1,40578
1
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7282
Polymers13,0891
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7282
Polymers13,0891
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7282
Polymers13,0891
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7282
Polymers13,0891
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.290, 165.190, 108.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))
21(chain B and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))
31(chain C and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))
41(chain D and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLY(chain A and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))AA308 - 3673 - 62
12GLUGLUMETMET(chain A and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))AA369 - 41064 - 105
13PHEPHEPROPRO(chain A and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))AA412 - 416107 - 111
21LEULEUGLYGLY(chain B and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))BB308 - 3673 - 62
22GLUGLUMETMET(chain B and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))BB369 - 41064 - 105
23PHEPHEPROPRO(chain B and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))BB412 - 416107 - 111
31LEULEUGLYGLY(chain C and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))CC308 - 3673 - 62
32GLUGLUMETMET(chain C and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))CC369 - 41064 - 105
33PHEPHEPROPRO(chain C and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))CC412 - 416107 - 111
41LEULEUGLYGLY(chain D and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))DD308 - 3673 - 62
42GLUGLUMETMET(chain D and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))DD369 - 41064 - 105
43PHEPHEPROPRO(chain D and (resid 308 through 367 or resid 369 through 410 or resid 412 through 416))DD412 - 416107 - 111

-
Components

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


Mass: 13089.126 Da / Num. of mol.: 4
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-VYJ / 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 638.802 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H46N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 4.3 Å3/Da / Density % sol: 71.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol, 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1MBuffer System 3 (pH 8.5 Tris (base) and BICINE 1. ...Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol, 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1MBuffer System 3 (pH 8.5 Tris (base) and BICINE 1.0M each), 37.5% v/vPrecipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→19.4 Å / Num. obs: 24881 / % possible obs: 98.8 % / Redundancy: 7.421 % / Biso Wilson estimate: 27.984 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.182 / Χ2: 0.943 / Net I/σ(I): 13.52 / Num. measured all: 184642 / Scaling rejects: 36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.777.510.673.7413586184218090.8930.71998.2
2.77-2.857.4840.6153.9513247179817700.90.66198.4
2.85-2.937.5030.5164.612762172617010.9230.55498.6
2.93-3.027.5080.4645.0412621170616810.9340.49898.5
3.02-3.127.5050.3865.912211164516270.9520.41598.9
3.12-3.237.5090.2927.811826158915750.9680.31399.1
3.23-3.357.4680.2289.7211336152815180.9790.24599.3
3.35-3.497.4940.17312.8910904146614550.9880.18699.2
3.49-3.647.4780.14315.2510663143914260.9920.15499.1
3.64-3.827.4590.12217.2710129136413580.9930.13199.6
3.82-4.037.4220.10718.979648130713000.9960.11599.5
4.03-4.277.4580.09720.959047121912130.9960.10499.5
4.27-4.567.3140.08922.38528117011660.9960.09699.7
4.56-4.937.4250.08223.717952107410710.9970.08899.7
4.93-5.47.3540.08621.977450101410130.9970.09299.9
5.4-6.047.2950.11716.8665959059040.9940.12699.9
6.04-6.977.2950.10118.7859168148110.9960.10999.6
6.97-8.547.1360.05828.7449816986980.9990.062100
8.54-12.086.8470.03741.137525505480.9990.0499.6
12.08-19.46.2780.03437.7214883252370.9990.03872.9

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L9L

7l9l


Resolution: 2.7→19.4 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 996 4 %
Rwork0.1931 23880 -
obs0.1947 24876 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.46 Å2 / Biso mean: 26.7621 Å2 / Biso min: 13.19 Å2
Refinement stepCycle: final / Resolution: 2.7→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 188 78 3917
Biso mean--49.55 18.73 -
Num. residues----441
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1272X-RAY DIFFRACTION6.744TORSIONAL
12B1272X-RAY DIFFRACTION6.744TORSIONAL
13C1272X-RAY DIFFRACTION6.744TORSIONAL
14D1272X-RAY DIFFRACTION6.744TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.84190.33451400.2696335098
2.8419-3.01940.29521390.254334399
3.0194-3.25150.32381400.2513336099
3.2515-3.57680.22521420.1896339999
3.5768-4.09020.20031410.1692340099
4.0902-5.13730.18341440.15083456100
5.1373-19.40.18881500.16773572100
Refinement TLS params.Method: refined / Origin x: -12.3268 Å / Origin y: -26.4237 Å / Origin z: -0.7802 Å
111213212223313233
T0.1604 Å2-0.0082 Å2-0.0111 Å2-0.1819 Å2-0.0084 Å2--0.1736 Å2
L0.1409 °2-0.0251 °2-0.0461 °2-0.278 °2-0.2251 °2--0.3884 °2
S-0.0059 Å °-0.0162 Å °0.0061 Å °0.0432 Å °0.0125 Å °-0.0119 Å °-0.0601 Å °-0.0542 Å °-0.0075 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA306 - 416
2X-RAY DIFFRACTION1allB308 - 416
3X-RAY DIFFRACTION1allC307 - 416
4X-RAY DIFFRACTION1allD306 - 416
5X-RAY DIFFRACTION1allI1 - 4
6X-RAY DIFFRACTION1allQ1 - 78

+
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