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- PDB-3rcw: Crystal Structure of the bromodomain of human BRD1 -

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Basic information

Entry
Database: PDB / ID: 3rcw
TitleCrystal Structure of the bromodomain of human BRD1
ComponentsBromodomain-containing protein 1
KeywordsTRANSCRIPTION / Bromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


unmodified histone reader activity / histone H3-K14 acetyltransferase complex / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / histone reader activity / Regulation of TP53 Activity through Acetylation ...unmodified histone reader activity / histone H3-K14 acetyltransferase complex / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / histone reader activity / Regulation of TP53 Activity through Acetylation / positive regulation of erythrocyte differentiation / HATs acetylate histones / perikaryon / nuclear speck / chromatin remodeling / dendrite / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / zinc ion binding / nucleus
Similarity search - Function
BRPF2, ePHD domain / BRPF2, PHD domain / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif ...BRPF2, ePHD domain / BRPF2, PHD domain / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 1-methylpyrrolidin-2-one / Bromodomain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsFilippakopoulos, P. / Keates, T. / Picaud, S. / Felletar, I. / Pike, A.C.W. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Keates, T. / Picaud, S. / Felletar, I. / Pike, A.C.W. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 1
B: Bromodomain-containing protein 1
C: Bromodomain-containing protein 1
D: Bromodomain-containing protein 1
E: Bromodomain-containing protein 1
F: Bromodomain-containing protein 1
G: Bromodomain-containing protein 1
H: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,64513
Polymers125,3048
Non-polymers3415
Water2,990166
1
A: Bromodomain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)15,6631
Polymers15,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)15,6631
Polymers15,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7622
Polymers15,6631
Non-polymers991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7222
Polymers15,6631
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bromodomain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)15,6631
Polymers15,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7252
Polymers15,6631
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7252
Polymers15,6631
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7222
Polymers15,6631
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.137, 51.245, 130.626
Angle α, β, γ (deg.)100.610, 90.750, 93.890
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bromodomain-containing protein 1 / BR140-like protein / Bromodomain and PHD finger-containing protein 2


Mass: 15662.945 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1, BRL, BRPF2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: O95696
#2: Chemical ChemComp-MB3 / 1-methylpyrrolidin-2-one


Mass: 99.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 32.5% PEG3350, 5% EtGly, 0.1M Acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 2 % / Av σ(I) over netI: 11.3 / Number: 106585 / Rsym value: 0.057 / D res high: 2.21 Å / D res low: 19.892 Å / Num. obs: 53142 / % possible obs: 96.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
2.212.3396.810.4180.4182.1
2.332.4796.710.2690.2692
2.472.6497.110.190.192
2.642.8596.910.1320.1322.1
2.853.1396.710.0850.0851.9
3.133.4996.910.0550.0552.1
3.494.0396.910.0360.0362
4.034.9497.510.0290.0292
4.946.9996.510.0310.0311.9
6.9919.8992.310.0240.0242
ReflectionResolution: 2.21→19.892 Å / Num. all: 54956 / Num. obs: 53142 / % possible obs: 96.7 % / Redundancy: 2 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.21-2.332.10.4181.91595577680.41896.8
2.33-2.4720.2692.91464873630.26996.7
2.47-2.6420.194.11376969040.1997.1
2.64-2.852.10.1325.81330864890.13296.9
2.85-3.131.90.0858.91138058730.08596.7
3.13-3.492.10.05513.41098053280.05596.9
3.49-4.0320.03619.4927047360.03696.9
4.03-4.9420.02922.9816040180.02997.5
4.94-6.991.90.03121.1593330570.03196.5
6.99-19.89220.02422.8318216060.02492.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.89 Å
Translation2.5 Å19.89 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 3HME, 2MB3, 2OSS, 2OIO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

3hme

2mb3

2oss

2oio
PDB Unreleased entry

2grc

2oo1

3dai

3d7c

3dwy


Resolution: 2.21→19.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2751 / WRfactor Rwork: 0.2061 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7911 / SU B: 16.215 / SU ML: 0.196 / SU R Cruickshank DPI: 0.2746 / SU Rfree: 0.2372 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 1999 3.8 %RANDOM
Rwork0.2061 ---
all0.2087 54860 --
obs0.2087 53137 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 108.4 Å2 / Biso mean: 41.3436 Å2 / Biso min: 11.44 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å2-0.7 Å20.95 Å2
2---1.75 Å2-1.3 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.21→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7216 0 23 166 7405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227388
X-RAY DIFFRACTIONr_bond_other_d0.0010.025050
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9749994
X-RAY DIFFRACTIONr_angle_other_deg0.902312247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245905
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91523.826379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.296151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0041569
X-RAY DIFFRACTIONr_chiral_restr0.0740.21123
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021515
X-RAY DIFFRACTIONr_mcbond_it4.44234550
X-RAY DIFFRACTIONr_mcbond_other1.46331804
X-RAY DIFFRACTIONr_mcangle_it6.23857314
X-RAY DIFFRACTIONr_scbond_it10.25882838
X-RAY DIFFRACTIONr_scangle_it12.608112677
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 140 -
Rwork0.298 3765 -
all-3905 -
obs--96.95 %
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)
11.32810.8993-0.78131.533-0.55080.4112-0.0170.1336-0.1737-0.0942-0.0157-0.1373-0.0351-0.07890.03270.0690.00280.02530.074-0.03790.08070.442910.406186.1506
2-0.20540.06490.06481.8453-1.03931.55080.01710.0195-0.02550.1589-0.01990.0841-0.1729-0.03090.00270.10260.0010.03640.0683-0.02930.07827.3383-11.665678.3165
30.69220.7938-0.48041.59970.23570.7374-0.05670.0792-0.05340.0239-0.0601-0.0439-0.0619-0.13710.11680.08290.0735-0.03020.1304-0.00530.02963.5877-13.2509129.6753
4-0.0767-0.0990.08731.22650.79021.91210.0269-0.00090.0395-0.13280.015-0.04550.02130.1051-0.04190.05330.00310.02640.1046-0.00220.078419.169319.314260.0304
5-0.417-0.2970.29191.09580.43091.3929-0.00020.18420.25390.2126-0.2028-0.06260.5263-0.09160.2030.19-0.03860.03050.1146-0.01410.0234-16.69255.365625.9458
61.2727-1.96290.73062.856-0.53480.7044-0.05810.1010.18380.2165-0.0963-0.1411-0.02380.03380.15450.0652-0.0167-0.0350.05750.02470.09921.2786-17.170218.6729
71.2715-0.8037-0.0171.08720.01330.5149-0.0333-0.0760.09610.04660.06780.02370.0899-0.0342-0.03450.0767-0.02810.02390.074-0.03490.0836-9.4011-20.6135105.4405
8-0.27420.71941.27182.89422.72777.68390.0165-0.0185-0.1305-0.20690.3571-0.1311-0.58790.0049-0.37360.08680.0092-0.01820.0969-0.03260.00680.9064-23.973343.8433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A562 - 678
2X-RAY DIFFRACTION2B563 - 680
3X-RAY DIFFRACTION3C565 - 675
4X-RAY DIFFRACTION4D564 - 675
5X-RAY DIFFRACTION5E563 - 678
6X-RAY DIFFRACTION6F564 - 676
7X-RAY DIFFRACTION7G564 - 675
8X-RAY DIFFRACTION8H566 - 673

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