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- PDB-7lbt: Crystal structure of the second bromodomain (BD2) of human BRD3 b... -

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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


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, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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)

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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

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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

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