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- PDB-7vrh: crystal structure of BRD2-BD1 in complex with guanosine analog -

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Basic information

Entry
Database: PDB / ID: 7vrh
Titlecrystal structure of BRD2-BD1 in complex with guanosine analog
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION/INHIBITOR / BET family / BET inhibitor / Bromodomain Inhibitor / BRD2-BD1 inhibitor / TRANSCRIPTION-INHIBITOR COMPLEX
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-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
9-HYROXYETHOXYMETHYLGUANINE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPadmanabhan, B. / Arole, A. / Deshmukh, P. / Ashok, S. / Mathur, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and biochemical insights into purine-based drug molecules in hBRD2 delineate a unique binding mode opening new vistas in the design of inhibitors of the BET family.
Authors: Arole, A.H. / Deshmukh, P. / Sridhar, A. / Mathur, S. / Mahalingaswamy, M. / Subramanya, H. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B.
History
DepositionOct 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1167
Polymers43,4163
Non-polymers7014
Water2,882160
1
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5485
Polymers28,9442
Non-polymers6053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-13 kcal/mol
Surface area11790 Å2
MethodPISA
2
C: Bromodomain-containing protein 2
hetero molecules

C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1364
Polymers28,9442
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Buried area2480 Å2
ΔGint-35 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.083, 55.473, 67.792
Angle α, β, γ (deg.)90.00, 94.15, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 14471.866 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25440
#2: Chemical ChemComp-AC2 / 9-HYROXYETHOXYMETHYLGUANINE


Mass: 225.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: PEG MME 5000, 0.8M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20793 / % possible obs: 97 % / Redundancy: 4 % / Biso Wilson estimate: 29.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.118 / Net I/σ(I): 18.51
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2 / Num. unique obs: 884 / CC1/2: 0.78 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHENIX(1.18_3855: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6jke

6jke


Resolution: 2.2→28.39 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1039 5 %
Rwork0.1927 --
obs0.1951 20793 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→28.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2747 0 21 160 2928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082860
X-RAY DIFFRACTIONf_angle_d0.943871
X-RAY DIFFRACTIONf_dihedral_angle_d5.906398
X-RAY DIFFRACTIONf_chiral_restr0.05405
X-RAY DIFFRACTIONf_plane_restr0.006512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.39441180.35962476X-RAY DIFFRACTION86
2.32-2.460.25981540.23832757X-RAY DIFFRACTION96
2.46-2.650.28151570.20952870X-RAY DIFFRACTION99
2.65-2.920.28351430.21772878X-RAY DIFFRACTION99
2.92-3.340.2571570.20472885X-RAY DIFFRACTION99
3.34-4.20.21271550.16372923X-RAY DIFFRACTION100
4.21-28.390.20161550.15882965X-RAY DIFFRACTION99
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)
10.34680.01640.08150.2106-0.04760.08450.0561-0.5972-0.84960.18080.09371.2224-0.144-0.02280.00640.45290.12960.12140.64030.21980.66583.54785.436681.9125
20.3745-0.33430.05220.29190.17810.2104-0.11460.01450.0349-0.0332-0.08920.2921-0.0624-0.32240.00080.340.05540.05620.30990.02680.37326.078314.955270.3618
30.46330.6223-0.07190.8368-0.30330.41960.08020.4408-0.2353-0.5937-0.37860.5330.0077-0.31190.00010.41490.0009-0.04260.4186-0.04620.380111.26087.203255.7343
40.44790.16470.15760.36690.05060.0753-0.36810.2251-0.7675-0.206-0.05450.14930.97550.03010.00480.46850.0283-0.01060.3088-0.01470.452616.5841-0.605760.0546
50.1938-0.0125-0.14550.0630.07710.1352-0.4101-0.047-0.56170.38110.50070.98420.0883-0.9964-0.00120.28640.01470.15850.38640.02410.55073.24192.817369.6707
60.0468-0.1715-0.05790.86990.34030.1402-0.3818-0.7241-1.10851.58260.19731.13450.6082-0.3299-0.00590.66120.03620.36020.54680.16340.96713.8538-3.958576.7552
73.2512-2.260.5552.67690.55991.0213-0.3036-0.30330.0109-0.01430.16980.20920.19190.02670.00010.2828-0.00170.01180.2335-0.01280.307717.70026.064567.2384
80.7286-0.26820.17540.3918-0.06370.1398-0.1502-0.20030.08390.3202-0.07160.0988-0.70140.3406-0.00170.35420.03520.04990.3097-0.00380.314515.763414.672171.9366
90.1592-0.1549-0.21240.16860.21480.2568-0.1899-0.6112-1.15380.7203-0.54670.53280.7449-1.0104-0.01050.8924-0.08630.06560.61090.16780.56647.78022.941988.3981
101.19690.53460.5391.2564-0.42650.6807-0.0484-0.56630.11430.42060.1984-0.16460.04150.1216-0.00090.49730.055-0.05840.4091-0.0070.315929.00724.68385.522
110.4204-0.07750.1790.1294-0.00130.0880.34270.54350.3267-0.4055-1.0222-1.05740.09891.3284-0.00370.46040.09780.04020.60350.07110.593141.46819.884269.9934
121.924-0.0090.98592.3288-0.7672.1152-0.0576-0.23360.15820.17930.1031-0.183-0.4310.084100.354-0.0101-0.04990.2691-0.00420.373729.678813.200876.1591
130.39390.19470.32321.2659-0.54810.5062-0.14460.1569-0.3399-0.01140.04930.1950.2526-0.4117-0.00010.3619-0.0266-0.01360.27690.02750.345424.2651.067876.7017
140.0181-0.01160.02990.0836-0.07280.06380.7453-0.26340.69550.62740.19110.4932-0.2394-0.1609-0.00240.67860.08190.15230.7528-0.18270.639614.775811.782392.007
150.10420.11550.02840.1448-0.00890.0631-0.63630.20841.0980.3910.1736-0.2958-1.59050.2353-0.00080.61180.04150.0070.47630.10930.4914-7.172434.06390.132
160.01440.0888-0.01450.24060.1371-0.0448-0.36470.54640.1277-0.66640.47790.0608-0.10260.75570.01230.33610.07450.11540.5095-0.0030.36571.70320.900788.0092
170.0867-0.2744-0.04260.27040.08340.1511-0.1860.0978-0.71190.0160.049-0.33510.60880.05810.00060.63510.05690.03610.4592-0.070.4765-7.42966.700184.8052
180.01490.0268-0.06940.3270.08960.17730.05840.24540.1077-0.76910.16640.6490.2851-0.5254-0.00010.42620.0652-0.06390.4595-0.01960.379-14.74169.007490.9891
190.11130.0264-0.01210.14950.01910.0176-0.12480.61440.5854-1.45420.0960.16670.49340.0777-0.00130.4671-0.0091-0.00140.46450.06460.3626-9.848223.632784.0637
200.92880.7701-0.35420.51920.09452.109-0.0445-0.0670.0331-0.28460.24850.2278-0.1447-0.24220.00010.34550.0557-0.01010.42790.00550.2822-11.932720.922893.1602
210.23590.12510.04940.05560.04490.3139-0.18620.565-0.9976-0.6338-0.2163-0.69280.64820.27840.00350.54080.1375-0.03390.3559-0.0570.5957-1.14743.410197.8515
222.30851.4817-0.01881.0801-0.29852.0567-0.18890.180.25180.51880.2669-0.2634-0.11310.4914-0.00080.31770.00380.03590.47060.00050.3184-1.00322.173297.8297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 75 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 122 )
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 137 )
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 160 )
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 179 )
9X-RAY DIFFRACTION9chain 'A' and (resid 180 through 186 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 99 )
11X-RAY DIFFRACTION11chain 'B' and (resid 100 through 112 )
12X-RAY DIFFRACTION12chain 'B' and (resid 113 through 160 )
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 179 )
14X-RAY DIFFRACTION14chain 'B' and (resid 180 through 185 )
15X-RAY DIFFRACTION15chain 'C' and (resid 76 through 84 )
16X-RAY DIFFRACTION16chain 'C' and (resid 85 through 98 )
17X-RAY DIFFRACTION17chain 'C' and (resid 99 through 112 )
18X-RAY DIFFRACTION18chain 'C' and (resid 113 through 122 )
19X-RAY DIFFRACTION19chain 'C' and (resid 123 through 131 )
20X-RAY DIFFRACTION20chain 'C' and (resid 132 through 155 )
21X-RAY DIFFRACTION21chain 'C' and (resid 156 through 160 )
22X-RAY DIFFRACTION22chain 'C' and (resid 161 through 182 )

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