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- PDB-2yem: Crystal Structure of the Second Bromodomain of Human Brd4 with th... -

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Basic information

Entry
Database: PDB / ID: 2yem
TitleCrystal Structure of the Second Bromodomain of Human Brd4 with the inhibitor GW841819X
ComponentsBROMODOMAIN-CONTAINING PROTEIN 4
KeywordsSIGNALING PROTEIN / HISTONE / EPIGENETIC READER
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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-WSH / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChung, C.W.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Discovery and Characterization of Small Molecule Inhibitors of the Bet Family Bromodomains.
Authors: Chung, C.W. / Coste, H. / White, J.H. / Mirguet, O. / Wilde, J. / Gosmini, R.L. / Delves, C. / Magny, S.M. / Woodward, R. / Hughes, S.A. / Boursier, E.V. / Flynn, H. / Bouillot, A.M. / ...Authors: Chung, C.W. / Coste, H. / White, J.H. / Mirguet, O. / Wilde, J. / Gosmini, R.L. / Delves, C. / Magny, S.M. / Woodward, R. / Hughes, S.A. / Boursier, E.V. / Flynn, H. / Bouillot, A.M. / Bamborough, P. / Brusq, J.M. / Gellibert, F.J. / Jones, E.J. / Riou, A.M. / Homes, P. / Martin, S.L. / Uings, I.J. / Toum, J. / Clement, C.A. / Boullay, A.B. / Grimley, R.L. / Blandel, F.M. / Prinjha, R.K. / Lee, K. / Kirilovsky, J. / Nicodeme, E.
History
DepositionMar 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Structure summary
Revision 1.2Aug 21, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BROMODOMAIN-CONTAINING PROTEIN 4
B: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9684
Polymers30,1212
Non-polymers8472
Water2,396133
1
A: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4842
Polymers15,0601
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4842
Polymers15,0601
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.674, 73.492, 74.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BROMODOMAIN-CONTAINING PROTEIN 4 / PROTEIN HUNK1


Mass: 15060.332 Da / Num. of mol.: 2 / Fragment: C-TERMINAL BROMODOMAIN, RESIDUES 333-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-WSH / BENZYL [(4R)-1-METHYL-6-PHENYL-4H-[1,2,4]TRIAZOLO[4,3-A][1,4]BENZODIAZEPIN-4-YL]CARBAMATE


Mass: 423.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H21N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.7 Å3/Da / Density % sol: 54.8 % / Description: NONE
Crystal growpH: 8.5 / Details: 2.5 M (NH4)2SO4, 0.1 M TRIS PH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9765
DetectorDate: Sep 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.3→73.49 Å / Num. obs: 14749 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 36.96 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OUO

1ouo


Resolution: 2.3→52.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.062 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22852 745 5.1 %RANDOM
Rwork0.18008 ---
obs0.18246 14004 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.493 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å20 Å20 Å2
2---0.9 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→52.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 64 133 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211966
X-RAY DIFFRACTIONr_bond_other_d0.0010.021386
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9752652
X-RAY DIFFRACTIONr_angle_other_deg0.8233363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5245231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14823.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89915354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.171511
X-RAY DIFFRACTIONr_chiral_restr0.0570.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
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_it0.72121136
X-RAY DIFFRACTIONr_mcbond_other0.092443
X-RAY DIFFRACTIONr_mcangle_it1.43541833
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7924830
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7566816
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 60 -
Rwork0.248 998 -
obs--98.05 %
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)
10.7726-0.13140.27663.50290.09243.1457-0.0615-0.05860.02490.01140.0895-0.0672-0.16830.1675-0.0280.0138-0.01090.00050.04390.00840.0833-4.76336.4512-24.0448
23.6045-1.29552.4162.8329-1.5474.928-0.11430.26790.046-0.18920.009-0.2127-0.07540.63170.10530.032-0.03760.02590.1269-0.02380.0375-1.99623.6294-45.0215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A349 - 458
2X-RAY DIFFRACTION2B349 - 459

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