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- PDB-7usi: BRD2-BD1 in complex with MDP5 -

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Basic information

Entry
Database: PDB / ID: 7usi
TitleBRD2-BD1 in complex with MDP5
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTON/INHIBITOR / Inhibitor / acetyllysine binding pocket / TRANSCRIPTON-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
Chem-O6O / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJayasinghe, T.D. / Ronning, D.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Control Release / Year: 2023
Title: Targeting BRD4 and PI3K signaling pathways for the treatment of medulloblastoma.
Authors: Sethi, B. / Kumar, V. / Jayasinghe, T.D. / Dong, Y. / Ronning, D.R. / Zhong, H.A. / Coulter, D.W. / Mahato, R.I.
History
DepositionApr 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
D: Bromodomain-containing protein 2
E: Bromodomain-containing protein 2
F: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,67463
Polymers81,0296
Non-polymers5,64557
Water1,33374
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,74214
Polymers13,5051
Non-polymers1,23713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,58613
Polymers13,5051
Non-polymers1,08212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3709
Polymers13,5051
Non-polymers8658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0465
Polymers13,5051
Non-polymers5414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,60914
Polymers13,5051
Non-polymers1,10513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3208
Polymers13,5051
Non-polymers8157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.810, 149.872, 63.819
Angle α, β, γ (deg.)90.000, 112.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 13504.795 Da / Num. of mol.: 6 / Fragment: BD1
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

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Non-polymers , 8 types, 131 molecules

#2: Chemical
ChemComp-O6O / (8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one


Mass: 365.379 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H19NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Sodium tartrate dibasic dihydrate pH 7.5 and 20 % w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→35.56 Å / Num. obs: 38336 / % possible obs: 99.69 % / Redundancy: 6.9 % / CC1/2: 0.978 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.048 / Net I/σ(I): 24.6
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 3871 / CC1/2: 0.834

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JKE

6jke


Resolution: 2.5→35.56 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1987 5.19 %
Rwork0.201 36319 -
obs0.2035 38306 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.32 Å2 / Biso mean: 55.3215 Å2 / Biso min: 30.42 Å2
Refinement stepCycle: final / Resolution: 2.5→35.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5537 0 369 74 5980
Biso mean--66.16 53.31 -
Num. residues----666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.560.30141400.24892560270097
2.56-2.630.34391400.248325592699100
2.63-2.710.3191410.21625972738100
2.71-2.790.20941400.21125912731100
2.79-2.890.2611450.211426272772100
2.89-3.010.34291370.241325682705100
3.01-3.150.341440.238125982742100
3.15-3.310.34121430.239225922735100
3.31-3.520.25461410.214226382779100
3.52-3.790.23391470.206226052752100
3.79-4.170.2471410.176725772718100
4.17-4.770.21051420.163426292771100
4.77-60.2021420.187625942736100
6.01-35.560.22091440.1952584272897

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