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- PDB-7l9k: Crystal structure of the second bromodomain (BD2) of human BRD2 b... -

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Basic information

Entry
Database: PDB / ID: 7l9k
TitleCrystal structure of the second bromodomain (BD2) of human BRD2 bound to LRRK2-IN-1
ComponentsBromodomain-containing protein 2
KeywordsGENE REGULATION / BET / ERK5 / dual BRD-kinase inhibitor
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-4K4 / 1,4-BUTANEDIOL / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 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 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5536
Polymers26,7512
Non-polymers1,8024
Water3,477193
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6074
Polymers13,3751
Non-polymers1,2313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9462
Polymers13,3751
Non-polymers5711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.400, 72.530, 52.680
Angle α, β, γ (deg.)90.000, 119.890, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-700-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 347 through 357 or resid 359...
21(chain B and (resid 347 through 357 or resid 359...

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
11SERSERLEULEU(chain A and (resid 347 through 357 or resid 359...AA347 - 3576 - 16
12GLUGLUSERSER(chain A and (resid 347 through 357 or resid 359...AA359 - 36218 - 21
13GLYGLYASPASP(chain A and (resid 347 through 357 or resid 359...AA344 - 4553 - 114
14HISHISASNASN(chain A and (resid 347 through 357 or resid 359...AA392 - 40551 - 64
15ASPASPALAALA(chain A and (resid 347 through 357 or resid 359...AA407 - 45166 - 110
16METMETASPASP(chain A and (resid 347 through 357 or resid 359...AA453 - 455112 - 114
21SERSERLEULEU(chain B and (resid 347 through 357 or resid 359...BB347 - 3576 - 16
22GLUGLUSERSER(chain B and (resid 347 through 357 or resid 359...BB359 - 36218 - 21
23SERSERASPASP(chain B and (resid 347 through 357 or resid 359...BB347 - 4556 - 114
24HISHISASNASN(chain B and (resid 347 through 357 or resid 359...BB392 - 40551 - 64
25ASPASPALAALA(chain B and (resid 347 through 357 or resid 359...BB407 - 45166 - 110
26METMETASPASP(chain B and (resid 347 through 357 or resid 359...BB453 - 455112 - 114

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Components

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


Mass: 13375.410 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: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-4K4 / 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 570.685 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C31H38N8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES 7.5, 2.0 M Ammonium sulfate

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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: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→42.02 Å / Num. obs: 17720 / % possible obs: 95.6 % / Redundancy: 3.781 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.077 / Χ2: 0.955 / Net I/σ(I): 13.88 / Num. measured all: 66998 / Scaling rejects: 65
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
1.95-23.7830.4253.44695132712410.9220.49493.5
2-2.063.8090.3144.614815134912640.9380.36593.7
2.06-2.123.8180.2286.214647129012170.9670.26594.3
2.12-2.183.790.1936.944472124711800.9760.22594.6
2.18-2.253.8120.1787.664441121711650.9790.20795.7
2.25-2.333.7880.1588.354239118311190.9860.18494.6
2.33-2.423.7750.1349.464164116411030.9880.15694.8
2.42-2.523.8290.1229.523902107010190.9910.14295.2
2.52-2.633.7930.10511.473899107010280.9910.12296.1
2.63-2.763.810.08413.3436929999690.9940.09897
2.76-2.913.8340.07315.5135169499170.9960.08496.6
2.91-3.083.8070.0617.7833359058760.9970.0796.8
3.08-3.33.8190.04821.332128758410.9980.05596.1
3.3-3.563.7970.04125.2229207857690.9980.04798
3.56-3.93.7090.04128.5626307277090.9980.04897.5
3.9-4.363.6980.03529.7624336776580.9980.04197.2
4.36-5.033.7120.03530.9520865785620.9970.04197.2
5.03-6.173.7010.03629.6718435094980.9980.04297.8
6.17-8.723.6410.03529.6813983973840.9980.04196.7
8.72-42.023.2790.03532.146592242010.9970.04289.7

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L9G

7l9g


Resolution: 1.95→42.02 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 1064 6.01 %
Rwork0.1881 16652 -
obs0.1903 17716 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.18 Å2 / Biso mean: 29.5677 Å2 / Biso min: 14.87 Å2
Refinement stepCycle: final / Resolution: 1.95→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 132 193 2131
Biso mean--44.58 32.7 -
Num. residues----221
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A596X-RAY DIFFRACTION0.362TORSIONAL
12B596X-RAY DIFFRACTION0.362TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.040.3011290.24512012214194
2.04-2.150.21511300.18942032216295
2.15-2.280.24011320.1872071220395
2.28-2.460.22251300.22044217496
2.46-2.70.27291340.19742099223396
2.7-3.090.24221350.19652111224697
3.1-3.90.2071350.17022122225798
3.9-42.020.20121390.18082161230097
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)
12.58921.18111.59714.26021.334.5023-0.09490.0841-0.1923-0.17850.18070.0201-0.0319-0.0398-0.15180.2099-0.00820.09570.08660.03760.20459.6084-13.150220.771
21.9272-0.0448-0.22432.58111.38950.9628-0.1066-0.17450.04760.50640.0160.3505-0.0557-0.09530.05970.33830.03060.10420.12720.00340.23293.70036.180727.361
34.08833.10142.43923.32140.71452.90150.23910.13720.08710.51160.00490.83420.2909-0.5886-0.05990.2834-0.03310.08870.26370.02630.3565-0.5102-9.50922.3881
42.2135-0.17020.34543.07710.81873.6038-0.0044-0.0489-0.1408-0.2010.0741-0.1925-0.1157-0.2322-0.07220.22630.00590.08520.10840.01360.17036.7966-1.236517.5012
52.3183-0.663-0.83073.91380.96422.383-0.09450.0726-0.1754-0.1609-0.0365-0.15210.2502-0.02110.10140.2428-0.00790.09130.10890.02860.193815.6645-7.619716.2222
61.9313-0.19050.10023.67070.09670.5527-0.03640.1810.0579-0.2830.1265-0.1234-0.1281-0.054-0.05280.2774-0.02030.10310.13960.01470.160321.1198-0.19160.1088
73.029-2.44711.03252.5598-2.56186.45460.31641.02840.4105-1.0375-0.3746-0.35220.0199-0.2347-0.11090.41470.00160.01570.30170.04540.220915.84535.3706-5.624
80.14430.24840.10543.2125-2.70414.75330.03011.32890.3219-0.3316-0.24680.6267-0.118-0.34730.14390.27140.0325-0.11140.51140.00320.47717.44177.2507-4.8713
91.98350.1429-0.45572.99590.35492.5873-0.0826-0.00610.03920.24730.0687-0.0202-0.0325-0.0525-0.05860.2456-0.02130.07530.09880.00780.155917.9028-1.20318.3503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 344 through 372 )A344 - 372
2X-RAY DIFFRACTION2chain 'A' and (resid 373 through 395 )A373 - 395
3X-RAY DIFFRACTION3chain 'A' and (resid 396 through 404 )A396 - 404
4X-RAY DIFFRACTION4chain 'A' and (resid 405 through 433 )A405 - 433
5X-RAY DIFFRACTION5chain 'A' and (resid 434 through 455 )A434 - 455
6X-RAY DIFFRACTION6chain 'B' and (resid 347 through 395 )B347 - 395
7X-RAY DIFFRACTION7chain 'B' and (resid 396 through 404 )B396 - 404
8X-RAY DIFFRACTION8chain 'B' and (resid 405 through 410 )B405 - 410
9X-RAY DIFFRACTION9chain 'B' and (resid 411 through 455 )B411 - 455

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