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- PDB-3hmf: Crystal Structure of the second Bromodomain of Human Poly-bromodo... -

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Basic information

Entry
Database: PDB / ID: 3hmf
TitleCrystal Structure of the second 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 / Bromodomain / Chromatin regulator / DNA-binding / Nucleus / Phosphoprotein / Transcription regulation / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / 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
DepositionMay 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 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_conn / 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4956
Polymers13,2311
Non-polymers2645
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein polybromo-1
hetero molecules

A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,99012
Polymers26,4632
Non-polymers52810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2810 Å2
ΔGint-159 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.810, 49.360, 33.610
Angle α, β, γ (deg.)90.000, 97.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-9-

HOH

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Components

#1: Protein Protein polybromo-1 / PB1 / hPB1 / Polybromo-1D / BRG1-associated factor 180 / BAF180


Mass: 13231.299 Da / Num. of mol.: 1 / Fragment: bromodomain, UNP residues 178-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PB1, PBRM1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q86U86
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.66 Å3/Da / Density % sol: 53.83 % / Mosaicity: 0.57 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.01M Zn_Cl, 15w/v PEG_6000, 10v/v ethylene_glycol, 5.5pH MES, 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: Jan 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.63→28.15 Å / Num. all: 17439 / Num. obs: 17021 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 18.4
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2357 / Rsym value: 0.274 / % possible all: 92.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.63 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.18 Å
Translation2.5 Å27.18 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 1.63→27.177 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.892 / SU ML: 1.3 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 821 4.93 %
Rwork0.171 --
all0.172 17489 -
obs0.172 16669 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.312 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 87.42 Å2 / Biso mean: 25.614 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1--2.601 Å20 Å21.609 Å2
2--7.902 Å20 Å2
3----5.301 Å2
Refinement stepCycle: LAST / Resolution: 1.63→27.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 8 200 1132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005963
X-RAY DIFFRACTIONf_angle_d0.8481301
X-RAY DIFFRACTIONf_chiral_restr0.057147
X-RAY DIFFRACTIONf_plane_restr0.004165
X-RAY DIFFRACTIONf_dihedral_angle_d15.175365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.63-1.7320.1931260.1782389251587
1.732-1.8660.1941280.1632561268992
1.866-2.0530.1791250.1542657278296
2.053-2.3510.1691460.1482688283498
2.351-2.9610.2021390.1632747288699
2.961-27.1810.1951570.17228062963100
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)
10.64130.50670.2681.34610.55651.20320.03660.0901-0.16070.0476-0.1002-0.10710.3239-0.18170.02630.1718-0.050.01280.0442-0.0270.107833.20296.69085.2207
20.3690.17520.00430.2106-0.4106-0.34510.1596-0.06280.05470.174-0.21250.1335-0.04050.04890.05090.1385-0.11220.03350.1975-0.05420.107917.61467.027611.3487
31.22050.6850.81620.54670.61731.78090.1623-0.1827-0.17120.139-0.1406-0.07030.4299-0.2232-0.02760.1634-0.0587-0.0030.04620.01550.08732.78797.249415.1039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 176:210)A176 - 210
2X-RAY DIFFRACTION2(CHAIN A AND RESID 211:241)A211 - 241
3X-RAY DIFFRACTION3(CHAIN A AND RESID 242:291)A242 - 291

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