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

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Basic information

Entry
Database: PDB / ID: 7rjm
TitleCrystal structure of human Bromodomain containing protein 3 (BRD3) in complex with ILF3
Components
  • Bromodomain-containing protein 3
  • Interleukin enhancer-binding factor 3
KeywordsSIGNALING PROTEIN / Brd3 / ILF3 / acetyllysine
Function / homology
Function and homology information


Regulation of CDH11 gene transcription / mRNA 3'-UTR AU-rich region binding / lncRNA binding / negative regulation of viral genome replication / precatalytic spliceosome / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / PKR-mediated signaling ...Regulation of CDH11 gene transcription / mRNA 3'-UTR AU-rich region binding / lncRNA binding / negative regulation of viral genome replication / precatalytic spliceosome / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / PKR-mediated signaling / double-stranded RNA binding / virus receptor activity / defense response to virus / single-stranded RNA binding / negative regulation of translation / chromatin remodeling / ribonucleoprotein complex / protein phosphorylation / negative regulation of DNA-templated transcription / chromatin binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Interleukin enhancer-binding factor 3 / : / : / DZF C-terminal domain / DZF domain / DZF N-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...Interleukin enhancer-binding factor 3 / : / : / DZF C-terminal domain / DZF domain / DZF N-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Nucleotidyltransferase superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Interleukin enhancer-binding factor 3 / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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

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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: Interleukin enhancer-binding factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1194
Polymers30,0573
Non-polymers621
Water82946
1
A: Bromodomain-containing protein 3
C: Interleukin enhancer-binding factor 3


Theoretical massNumber of molelcules
Total (without water)15,4702
Polymers15,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-7 kcal/mol
Surface area7070 Å2
MethodPISA
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6492
Polymers14,5871
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint3 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.009, 59.009, 133.966
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 14586.843 Da / Num. of mol.: 2
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 Interleukin enhancer-binding factor 3 / Double-stranded RNA-binding protein 76 / DRBP76 / M-phase phosphoprotein 4 / MPP4 / Nuclear factor ...Double-stranded RNA-binding protein 76 / DRBP76 / M-phase phosphoprotein 4 / MPP4 / Nuclear factor associated with dsRNA / NFAR / Nuclear factor of activated T-cells 90 kDa / NF-AT-90 / Translational control protein 80 / TCP80


Mass: 883.088 Da / Num. of mol.: 1 / Fragment: UNP residues 99-106 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12906
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% w/v PEG3350, 0.1 M Bis-Tris, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2019 / Details: KB MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→51.103 Å / Num. all: 16445 / Num. obs: 16445 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.064 / Rsym value: 0.061 / Net I/av σ(I): 7.2 / Net I/σ(I): 19.5 / Num. measured all: 155473
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.219.90.5751.32321823430.1920.6070.5754.1100
2.21-2.359.60.3592.12149822300.1210.380.3596.1100
2.35-2.5110.20.2433.22131120930.080.2560.2438.8100
2.51-2.719.60.1455.21906719790.0490.1530.14513.4100
2.71-2.979.50.0977.31721518090.0330.1020.09719.299.9
2.97-3.329.40.0679.91560116590.0230.0710.06727.3100
3.32-3.838.70.04912.31266214610.0180.0530.04936100
3.83-4.79.20.04413.21163412690.0150.0470.04443100
4.7-6.648.40.04313.3855310130.0150.0460.04339100
6.64-24.61780.03913.347145890.0150.0410.03942.498

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.75 Å23.87 Å
Translation3.75 Å23.87 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6QJU

6qju


Resolution: 2.1→23.87 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 756 4.61 %
Rwork0.1918 15647 -
obs0.194 16403 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.11 Å2 / Biso mean: 55.249 Å2 / Biso min: 31.5 Å2
Refinement stepCycle: final / Resolution: 2.1→23.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 4 46 2016
Biso mean--52.57 45.59 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.260.26621300.226331003230
2.26-2.490.26031560.232830463202
2.49-2.850.27721510.220130903241
2.85-3.590.25611440.210831483292
3.59-23.870.21421750.165132633438
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)
16.24363.72422.08594.0705-0.89423.18570.0973-0.0585-1.72920.2421-1.16750.70611.9546-0.89150.85020.6057-0.08090.10630.4268-0.06510.7511-35.84553.697113.6823
26.2103-1.589-0.65122.30052.56743.08170.5383-0.6296-0.04450.72030.245-0.00730.6606-1.0051-0.93330.5399-0.0420.06830.36620.06570.3597-31.31826.743919.7715
33.90981.3384-0.10626.877-0.66424.66950.3705-0.3953-0.26750.9486-0.15470.20270.00850.4069-0.20030.47210.03490.01470.3853-0.02210.3549-25.763319.2825.2504
42.96160.32370.50272.181-0.52461.32210.05110.22750.28350.0777-0.12280.1705-0.231-0.09650.05710.3970.05970.06840.3967-0.00140.4053-31.253322.518614.0913
53.9272-0.34412.90281.29970.27444.0983-0.2030.10110.63480.7923-0.1671-0.4746-0.33060.58650.72430.4831-0.1044-0.04710.38490.00430.4757-16.662728.763716.0934
62.03352.84920.83545.10571.27612.923-0.0214-0.0328-0.08380.07010.00110.21080.07950.0768-0.01710.37920.0640.02320.29430.00120.4163-22.0119.472716.3756
72.5872-1.1484-1.01753.96530.74289.14550.2540.8947-1.83640.31820.04761.00540.2529-0.4503-0.33410.4376-0.1681-0.16030.49240.05490.5459-21.808119.8601-2.6781
85.3814-0.05730.19143.5659-0.34283.1902-0.32990.5870.88720.668-0.08640.0294-0.70930.83480.17760.4484-0.1664-0.00890.55970.14780.5362-14.851831.08182.7026
91.49290.2033-0.51415.0486-1.08842.43370.35180.5951-0.3165-0.1431-0.8857-0.77290.38091.25050.45180.41520.07670.06560.95520.10370.5466-2.043616.90381.7202
102.13370.7251-0.05114.2428-1.40481.67950.26170.5347-0.359-0.9001-0.20730.45380.68770.6009-0.07230.5310.0941-0.10350.5653-0.13780.4296-14.76889.29111.0062
112.5794-0.1162-0.08182.0136-1.23612.06750.11940.0329-0.26040.2413-0.17790.12880.04790.74250.09090.3921-0.0012-0.03780.5271-0.00570.3817-11.852613.36579.8755
122.96061.1004-0.22816.9424-1.09062.54660.180.4132-0.35250.4074-0.4694-1.0991-0.25761.01910.26570.4737-0.0917-0.08070.94720.08630.4182-1.96716.817411.687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 35:39)A35 - 39
2X-RAY DIFFRACTION2(chain A and resid 40:47)A40 - 47
3X-RAY DIFFRACTION3(chain A and resid 48:63)A48 - 63
4X-RAY DIFFRACTION4(chain A and resid 64:112)A64 - 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 23:29)B23 - 29
8X-RAY DIFFRACTION8(chain B and resid 30:39)B30 - 39
9X-RAY DIFFRACTION9(chain B and resid 40:61)B40 - 61
10X-RAY DIFFRACTION10(chain B and resid 62:94)B62 - 94
11X-RAY DIFFRACTION11(chain B and resid 95:120)B95 - 120
12X-RAY DIFFRACTION12(chain B and resid 121:142)B121 - 142

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