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- PDB-3g0j: Crystal Structure of the fifth Bromodomain of Human Poly-bromodom... -

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Basic information

Entry
Database: PDB / ID: 3g0j
TitleCrystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PB1 / polybromo 1 isoform 1 / BAF180 / Polybromo-1D / PBRM1 / BRG1-associated factor 180 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group ...Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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
NITRATE ION / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsFilippakopoulos, P. / Keates, T. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)
Authors: Filippakopoulos, P. / Keates, T. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
History
DepositionJan 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Protein polybromo-1
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6067
Polymers29,2962
Non-polymers3105
Water4,738263
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7102
Polymers14,6481
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8965
Polymers14,6481
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.570, 57.370, 137.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARGAA623 - 65413 - 44
21METMETARGARGBB623 - 65413 - 44
12ASPASPPHEPHEAA673 - 70063 - 90
22ASPASPPHEPHEBB673 - 70063 - 90
13SERSERLEULEUAA711 - 731101 - 121
23SERSERLEULEUBB711 - 731101 - 121

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Protein polybromo-1 / hPB1 / Polybromo-1D / BRG1-associated factor 180 / BAF180


Mass: 14648.000 Da / Num. of mol.: 2 / Fragment: UNP residues 645-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q86U86
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Na_nitrate, 25% w/v PEG 3350, 5% v/v ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.78→30.831 Å / Num. all: 28619 / Num. obs: 28304 / % possible obs: 98.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 18.2
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 9 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4085 / Rsym value: 0.703 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.46 Å
Translation2.5 Å29.46 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC

3dwy

3dai

3d7c

2ouo

2oss

2oo1

2nxb

2grc


Resolution: 1.78→29.45 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.835 / SU B: 6.317 / SU ML: 0.087 / SU R Cruickshank DPI: 0.12 / SU Rfree: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1428 5.1 %RANDOM
Rwork0.19 ---
all0.193 ---
obs0.193 28246 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.02 Å2 / Biso mean: 15.392 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.78→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 20 263 2153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221947
X-RAY DIFFRACTIONr_bond_other_d0.0020.021383
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9912614
X-RAY DIFFRACTIONr_angle_other_deg0.92633373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1875226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46823.62691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47815383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.521516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02381
X-RAY DIFFRACTIONr_mcbond_it2.80831158
X-RAY DIFFRACTIONr_mcbond_other1.2663445
X-RAY DIFFRACTIONr_mcangle_it3.55751889
X-RAY DIFFRACTIONr_scbond_it5.218789
X-RAY DIFFRACTIONr_scangle_it6.66711725
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1462MEDIUM POSITIONAL0.530.5
1462MEDIUM THERMAL1.292
2393MEDIUM POSITIONAL0.420.5
2393MEDIUM THERMAL1.332
3269MEDIUM POSITIONAL0.310.5
3269MEDIUM THERMAL1.222
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 85 -
Rwork0.4 2018 -
all-2103 -
obs--99.95 %
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)
14.59821.7139-0.79263.3303-0.34570.1423-0.1172-0.19850.22430.08530.13910.67950.0616-0.002-0.02190.5183-0.04750.13390.52930.07470.5011-4.3-18.0105-10.037
22.10332.8864-1.45559.6457-4.49894.10960.1187-0.31140.1320.4935-0.05040.027-0.17280.0451-0.06840.0695-0.0115-0.00220.0773-0.02980.013510.4762-14.1286-6.881
32.38820.82611.87892.22991.40832.60490.0342-0.02220.08410.0493-0.0246-0.0114-0.07170.0323-0.00960.04870.00010.03560.05170.02170.04816.2188-6.7464-25.5926
43.13751.7043-2.36654.4954-3.12035.3140.0518-0.0333-0.04570.0967-0.0521-0.11710.01970.11380.00030.00560.0015-0.00570.0031-0.00160.006513.1566-13.8406-19.6787
51.73153.21952.10657.61155.1423.98750.1169-0.218-0.00540.5149-0.16110.10010.3734-0.090.04420.1319-0.0210.02970.10330.00630.02033.516913.8639-11.4481
66.72084.8137-1.156.2361-1.45922.60480.09310.0105-0.1642-0.0498-0.1044-0.08430.23130.00840.01130.09440.0097-0.01060.0052-0.00220.00885.91961.9681-24.6156
72.2933-0.1445-1.26050.72150.53854.6648-0.0405-0.0140.083-0.04630.0163-0.1133-0.12860.17080.02420.0207-0.00560.00950.00820.00610.03679.975415.7401-26.2971
85.1918-2.0489-2.14485.91264.77610.19960.0442-0.15050.080.0633-0.13810.3475-0.1643-0.370.09390.0191-0.0088-0.00150.04230.00810.0513-3.21639.4817-26.8291
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A615 - 621
2X-RAY DIFFRACTION2A622 - 641
3X-RAY DIFFRACTION3A642 - 671
4X-RAY DIFFRACTION4A672 - 731
5X-RAY DIFFRACTION5B621 - 642
6X-RAY DIFFRACTION6B643 - 658
7X-RAY DIFFRACTION7B659 - 707
8X-RAY DIFFRACTION8B708 - 731

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