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- PDB-6ajz: Joint nentron and X-ray structure of BRD4 in complex with colchicin -

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Basic information

Entry
Database: PDB / ID: 6ajz
TitleJoint nentron and X-ray structure of BRD4 in complex with colchicin
ComponentsBromodomain-containing protein 4BRD4
KeywordsTRANSCRIPTION / bromodomain / brd4 / inhibitor / isoliquiritigenin
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / 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 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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
DEUTERATED WATER / Chem-LOC / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / Resolution: 1.301 Å
AuthorsYokoyama, T. / Ostermann, A. / Schrader, T.E. / Nabeshima, Y. / Mizuguchi, M.
CitationJournal: Febs J. / Year: 2019
Title: Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Authors: Yokoyama, T. / Matsumoto, K. / Ostermann, A. / Schrader, T.E. / Nabeshima, Y. / Mizuguchi, M.
History
DepositionAug 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5833
Polymers16,1611
Non-polymers4222
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.763, 47.101, 79.052
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 / BRD4 / Protein HUNK1


Mass: 16160.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-LOC / N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide / COLCHICINE / Colchicine


Mass: 399.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiinflammatory*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.9M sodium formate, 17mM Tris, 83mM Tris-HCl in D2O

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
NUCLEAR REACTORFRM II BIODIFF23.99
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDMay 14, 2017
BIODIFF2IMAGE PLATEFeb 12, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
23.991
Reflection

Entry-ID: 6AJZ

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rpim(I) allDiffraction-IDNet I/σ(I)
1.3-40.53327996.56.10.022118.9
1.85-30.31103089.32.50.07127.8
Reflection shell
Resolution (Å)Rpim(I) allDiffraction-ID
1.3-1.350.1711
1.85-1.90.2942

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
HKL-2000data reduction
XSCALEdata scaling
SCALEPACKdata scaling
MOLREPphasing
Refinement

SU ML: 0.09 / Cross valid method: FREE R-VALUE / Phase error: 18.18 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
1.301-30.278X-RAY DIFFRACTION0.17870.1630.1638166333255596.551.38
1.847-30.278NEUTRON DIFFRACTION0.23460.20390.2054555110115.0489.34
Refinement stepCycle: LAST / Resolution: 1.301→30.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 30 110 1255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012682
X-RAY DIFFRACTIONf_angle_d1.4124717
X-RAY DIFFRACTIONf_dihedral_angle_d17.552833
X-RAY DIFFRACTIONf_chiral_restr0.32176
X-RAY DIFFRACTIONf_plane_restr0.007503
NEUTRON DIFFRACTIONf_bond_d0.012682
NEUTRON DIFFRACTIONf_angle_d1.4124717
NEUTRON DIFFRACTIONf_dihedral_angle_d17.552833
NEUTRON DIFFRACTIONf_chiral_restr0.32176
NEUTRON DIFFRACTIONf_plane_restr0.007503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.301-1.33930.25581330.25552529X-RAY DIFFRACTION95
1.3393-1.38250.22531340.22112546X-RAY DIFFRACTION95
1.3825-1.43190.20891350.19692565X-RAY DIFFRACTION95
1.4319-1.48930.26721350.20352573X-RAY DIFFRACTION96
1.4893-1.55710.26551380.21742616X-RAY DIFFRACTION96
1.5571-1.63910.19541360.1822589X-RAY DIFFRACTION97
1.6391-1.74180.22371390.17592639X-RAY DIFFRACTION97
1.7418-1.87630.21711390.17442642X-RAY DIFFRACTION98
1.8763-2.06510.1771410.15442677X-RAY DIFFRACTION98
2.0651-2.36380.1811420.14772698X-RAY DIFFRACTION98
2.3638-2.97770.18121440.15522735X-RAY DIFFRACTION99
2.9777-30.28570.12741470.1412783X-RAY DIFFRACTION95
1.8468-2.03260.28781340.21552415NEUTRON DIFFRACTION85
2.0326-2.32670.23731260.19422467NEUTRON DIFFRACTION86
2.3267-2.9310.2111450.19522697NEUTRON DIFFRACTION93
2.931-30.28160.22751500.20932877NEUTRON DIFFRACTION94

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