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- PDB-7rjk: Crystal structure of human Bromodomain containing protein 3 (BRD3... -

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Basic information

Entry
Database: PDB / ID: 7rjk
TitleCrystal structure of human Bromodomain containing protein 3 (BRD3) in complex with hnRNPK
Components
  • Bromodomain-containing protein 3
  • Heterogeneous nuclear ribonucleoprotein K
KeywordsSIGNALING PROTEIN / Brd3 / hnRNPK / acetyllysine
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / positive regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / histone H3K9me2/3 reader activity ...regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / positive regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / histone H3K9me2/3 reader activity / podosome / lncRNA binding / endodermal cell differentiation / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / protein localization to chromatin / : / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / HCMV Late Events / cell projection / molecular condensate scaffold activity / mRNA splicing, via spliceosome / cytoplasmic stress granule / histone binding / cadherin binding / chromatin remodeling / ribonucleoprotein complex / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / mRNA binding / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
ROK, N-terminal / ROKNT (NUC014) domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. ...ROK, N-terminal / ROKNT (NUC014) domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / K Homology domain / K homology RNA-binding domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein K / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsFedorov, E. / Islam, K. / Ghosh, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123234 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130752 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM118303 United States
CitationJournal: Biorxiv / Year: 2021
Title: Uncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization
Authors: Wagner, S. / Fedorov, E. / Sudhamalla, B. / Jnawali, H.N. / Debiec, R. / Ghosh, A. / Islam, K.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: Heterogeneous nuclear ribonucleoprotein K
D: Heterogeneous nuclear ribonucleoprotein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,84110
Polymers31,3704
Non-polymers4706
Water4,630257
1
A: Bromodomain-containing protein 3
C: Heterogeneous nuclear ribonucleoprotein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8094
Polymers15,6852
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-13 kcal/mol
Surface area7550 Å2
MethodPISA
2
B: Bromodomain-containing protein 3
D: Heterogeneous nuclear ribonucleoprotein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0316
Polymers15,6852
Non-polymers3464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-19 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.658, 49.658, 255.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-347-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 14586.843 Da / Num. of mol.: 2 / Fragment: UNP residues 24-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: Q15059
#2: Protein/peptide Heterogeneous nuclear ribonucleoprotein K / hnRNP K / Transformation up-regulated nuclear protein / TUNP


Mass: 1098.317 Da / Num. of mol.: 2 / Fragment: UNP residues 57-66 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61978

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Non-polymers , 4 types, 263 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium/sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.85→24.83 Å / Num. obs: 28702 / % possible obs: 100 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.025 / Rrim(I) all: 0.125 / Net I/σ(I): 20.9 / Num. measured all: 735477 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.8923.10.5673896716840.9740.1220.586.6100
9.06-24.8319.80.0663263200.9990.0130.06132.596.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6QJU

6qju


Resolution: 1.85→24.83 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1430 5 %
Rwork0.1729 27160 -
obs0.1751 28590 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.18 Å2 / Biso mean: 18.2007 Å2 / Biso min: 5.9 Å2
Refinement stepCycle: final / Resolution: 1.85→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 28 258 2434
Biso mean--51.86 24.31 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.920.3241300.290826412771
1.92-1.990.22041320.188126502782
1.99-2.080.21521420.169926562798
2.08-2.190.21911300.167926642794
2.19-2.330.19031520.165626572809
2.33-2.510.22671390.165427132852
2.51-2.760.23081420.173427102852
2.76-3.160.20861480.185927072855
3.16-3.980.221630.160627672930
3.98-24.830.19631520.157529953147
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)
12.19431.62071.02372.45851.99771.6875-0.019-0.10780.20730.0582-0.19680.1922-0.04190.04070.20730.1913-0.0203-0.0240.13110.01660.14142.365338.3658-16.3711
23.2742.417-1.42112.5119-1.67742.3177-0.09930.0660.2048-0.08820.12430.2346-0.0778-0.1987-0.03780.0940.0215-0.030.1041-0.01270.1321-11.083227.2-20.5666
30.5128-0.44420.56450.4427-0.68811.4776-0.1767-0.645-0.29940.2590.47510.239-0.1622-0.6136-0.15370.15950.07640.0320.29320.06440.1174-8.752420.0556-3.0208
40.90640.459-0.50192.6659-0.88921.0994-0.0207-0.12150.13360.0887-0.025-0.0516-0.139-0.03430.04940.08960.0028-0.03090.1008-0.03160.09811.000228.8531-11.8364
52.2513-0.64530.91822.0580.61583.0181-0.0874-0.0472-0.33080.02050.00720.2310.1842-0.25660.10520.0887-0.00740.03440.1228-0.01320.1006-3.346410.8983-9.1781
64.49222.4095-1.47515.0834-2.35154.71310.10240.05670.264-0.14420.03610.1418-0.25570.2271-0.12340.08670.0185-0.01710.096-0.04140.0887-1.844923.9854-24.8511
72.86030.94221.75743.27331.90872.5131-0.05260.09310.0908-0.05710.03610.0107-0.12480.10990.03630.0519-0.0030.03520.10020.01420.06119.180414.9808-36.2163
80.32620.0999-0.25140.4133-0.1681.51380.0226-0.0274-0.0705-0.0124-0.0049-0.0190.12250.0642-0.02160.05710.0016-0.00440.0723-0.00170.092812.24238.8286-24.1016
90.52550.2186-0.18151.0706-0.61972.62130.0751-0.0626-0.035-0.04070.03560.0418-0.05040.0559-0.08860.06060.00230.0080.0815-0.01190.10265.431413.7117-20.8445
101.87331.1387-0.07113.45681.7512.299-0.0091-0.2405-0.04880.48530.142-0.29060.09890.3696-0.09090.11170.0201-0.01530.14810.01130.084810.74269.601-7.2823
111.0535-1.09131.39714.187-3.77954.3578-0.0883-0.11610.07490.1339-0.0512-0.2611-0.24390.09180.08930.0743-0.0070.00610.0935-0.02120.100112.171720.8992-17.5404
125.89980.4962-0.78991.77310.06350.93010.09190.7390.1248-0.8426-0.53190.6501-0.5973-0.3120.27310.34710.0593-0.04920.2161-0.04390.20636.236128.9661-32.6749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 24:42)A24 - 42
2X-RAY DIFFRACTION2(chain A and resid 43:55)A43 - 55
3X-RAY DIFFRACTION3(chain A and resid 56:73)A56 - 73
4X-RAY DIFFRACTION4(chain A and resid 74:112)A74 - 112
5X-RAY DIFFRACTION5(chain A and resid 113:122)A113 - 122
6X-RAY DIFFRACTION6(chain A and resid 123:144)A123 - 144
7X-RAY DIFFRACTION7(chain B and resid 23:48)B23 - 48
8X-RAY DIFFRACTION8(chain B and resid 49:101)B49 - 101
9X-RAY DIFFRACTION9(chain B and resid 102:114)B102 - 114
10X-RAY DIFFRACTION10(chain B and resid 115:121)B115 - 121
11X-RAY DIFFRACTION11(chain B and resid 122:136)B122 - 136
12X-RAY DIFFRACTION12(chain B and resid 137:143)B137 - 143

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