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- PDB-5n2l: Crystal structure of the second bromodomain of human BRD2 in comp... -

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Basic information

Entry
Database: PDB / ID: 5n2l
TitleCrystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


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 / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...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 / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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 II / Brdt, bromodomain, repeat I / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8J2 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsTallant, C. / Slavish, P.J. / Siejka, P. / Bharatham, N. / Shadrick, W.R. / Chai, S. / Young, B.M. / Boyd, V.A. / Heroven, C. / Wiggers, H.J. ...Tallant, C. / Slavish, P.J. / Siejka, P. / Bharatham, N. / Shadrick, W.R. / Chai, S. / Young, B.M. / Boyd, V.A. / Heroven, C. / Wiggers, H.J. / Picaud, S. / Fedorov, O. / Krojer, T. / Chen, T. / Lee, R.E. / Guy, R.K. / Shelat, A.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue
Authors: Tallant, C. / Slavish, P.J. / Siejka, P. / Bharatham, N. / Shadrick, W.R. / Chai, S. / Young, B.M. / Boyd, V.A. / Heroven, C. / Wiggers, H.J. / Picaud, S. / Fedorov, O. / Krojer, T. / Chen, ...Authors: Tallant, C. / Slavish, P.J. / Siejka, P. / Bharatham, N. / Shadrick, W.R. / Chai, S. / Young, B.M. / Boyd, V.A. / Heroven, C. / Wiggers, H.J. / Picaud, S. / Fedorov, O. / Krojer, T. / Chen, T. / Lee, R.E. / Guy, R.K. / Shelat, A.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,02018
Polymers53,5024
Non-polymers2,51914
Water5,567309
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0195
Polymers13,3751
Non-polymers6444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0875
Polymers13,3751
Non-polymers7124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3815
Polymers13,3751
Non-polymers1,0054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5343
Polymers13,3751
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.244, 94.409, 38.585
Angle α, β, γ (deg.)90.00, 95.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-666-

HOH

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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.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-8J2 / propan-2-yl ~{N}-[(2~{S},4~{R})-6-(3-acetamidophenyl)-1-ethanoyl-2-methyl-3,4-dihydro-2~{H}-quinolin-4-yl]carbamate


Mass: 423.505 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H29N3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2 M ammonium sulfate, 0.1 M Bis-tris pH 5.5
PH range: 5.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.89→28.95 Å / Num. obs: 41476 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.519 Å2 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.131 / Net I/σ(I): 11.5
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 6 % / Rmerge(I) obs: 1.914 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2554 / Rpim(I) all: 1.286 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVV

2dvv


Resolution: 1.89→28.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.978 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23264 1999 4.8 %RANDOM
Rwork0.18136 ---
obs0.18375 39476 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.46 Å2
2---1.39 Å20 Å2
3---1.75 Å2
Refinement stepCycle: 1 / Resolution: 1.89→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 170 309 4065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193864
X-RAY DIFFRACTIONr_bond_other_d0.0010.023634
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9455213
X-RAY DIFFRACTIONr_angle_other_deg0.94638359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5175431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81723.439189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25115661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4251524
X-RAY DIFFRACTIONr_chiral_restr0.120.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02929
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 152 -
Rwork0.257 2775 -
obs--95.5 %
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)
10.3461-0.1667-0.19180.4516-0.36131.9069-0.03380.0186-0.01070.06940.09230.033-0.05650.0325-0.05850.07650.02010.02880.07720.00450.011727.96059.114314.5822
20.2642-0.4809-0.2260.98190.60162.0254-0.12190.0549-0.02040.092-0.15410.1361-0.02140.15830.2760.07790.0017-0.0520.06040.01170.16639.594630.427718.6372
30.223-0.44630.13091.54560.30120.66750.0118-0.0101-0.0034-0.08260.0686-0.01670.02360.0534-0.08040.06780.0125-0.00030.0612-0.00270.049741.721433.254622.8834
40.8552-0.62320.46350.5819-0.18361.0292-0.0714-0.08290.04030.0378-0.0026-0.0794-0.0105-0.14790.0740.03540.0115-0.00780.0767-0.0070.068960.413512.444221.4938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A346 - 454
2X-RAY DIFFRACTION2B346 - 454
3X-RAY DIFFRACTION3C348 - 454
4X-RAY DIFFRACTION4D347 - 454

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