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- PDB-4q0n: Crystal Structure of the fifth bromodomain of Human Poly-bromodom... -

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Basic information

Entry
Database: PDB / ID: 4q0n
TitleCrystal Structure of the fifth bromodomain of Human Poly-bromodomain containing protein 1 (PB1) in complex with a hydroxyphenyl-propenone ligand
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PB1 / POLYBROMO 1 ISOFORM 1 / BAF180 / POLYBROMO-1D / PBRM1 / BRG1-ASSOCIATED FACTOR 180 / BROMODOMAIN / CHROMATIN REGULATOR / DNA-BINDING / NUCLEUS / TRANSCRIPTION REGULATION / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / 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 / RSC-type complex / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / 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 / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / kinetochore / nuclear matrix / RMTs methylate histone arginines / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / 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 domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-2XD / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Felletar, I. / Martin, S. / Monteiro, O. / Fedorov, O. / Chaikuad, A. / Yue, W. / von Delft, F. / Arrowsmith, C.H. ...Filippakopoulos, P. / Picaud, S. / Felletar, I. / Martin, S. / Monteiro, O. / Fedorov, O. / Chaikuad, A. / Yue, W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / 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) in complex with a hydroxyphenyl-propenone ligand
Authors: Filippakopoulos, P. / Picaud, S. / Felletar, I. / Martin, S. / Monteiro, O. / Fedorov, O. / Chaikuad, A. / Yue, W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. ...Authors: Filippakopoulos, P. / Picaud, S. / Felletar, I. / Martin, S. / Monteiro, O. / Fedorov, O. / Chaikuad, A. / Yue, W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: Protein polybromo-1
B: Protein polybromo-1
C: Protein polybromo-1
D: Protein polybromo-1
E: Protein polybromo-1
F: Protein polybromo-1
G: Protein polybromo-1
H: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,67025
Polymers136,9578
Non-polymers2,71317
Water9,818545
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4513
Polymers17,1201
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3892
Polymers17,1201
Non-polymers2691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4513
Polymers17,1201
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4513
Polymers17,1201
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5134
Polymers17,1201
Non-polymers3933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4513
Polymers17,1201
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5134
Polymers17,1201
Non-polymers3933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4513
Polymers17,1201
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.021, 136.722, 114.413
Angle α, β, γ (deg.)90.000, 91.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17119.678 Da / Num. of mol.: 8 / Fragment: UNP residues 645-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAF180, PB1, 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


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-2XD / (2E)-1-(2-hydroxyphenyl)-3-(2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)prop-2-en-1-one


Mass: 269.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H15N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.20M Na(malonate), 0.1M BTProp pH 6.5, 20.0% PEG 3350 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionRedundancy: 2.6 % / Number: 306966 / Rsym value: 0.052 / D res high: 1.78 Å / D res low: 29.687 Å / Num. obs: 119499 / % possible obs: 97
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
5.6329.6910.0260.0262.8
3.985.6310.0250.0252.5
3.253.9810.0280.0282.6
2.813.2510.0380.0382.7
2.522.8110.0560.0562.5
2.32.5210.0780.0782.6
2.132.310.1040.1042.6
1.992.1310.1790.1792.6
1.881.9910.3020.3022.5
1.781.8810.4840.4842.5
ReflectionResolution: 1.78→29.687 Å / Num. all: 123195 / Num. obs: 119499 / % possible obs: 97 % / Redundancy: 2.6 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.78-1.882.50.4841.542788173320.48496.6
1.88-1.992.50.3022.540870162910.30295.8
1.99-2.132.60.1794.241526157580.17998.8
2.13-2.32.60.1047.338204146180.10498.3
2.3-2.522.60.0789.634336133420.07897.5
2.52-2.812.50.05613.228484116190.05693.5
2.81-3.252.70.03818.428971108220.03899
3.25-3.982.60.02823.12392890660.02898.4
3.98-5.632.50.02523.61685767010.02593.5
5.63-29.6872.80.02614.41100239500.02698.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.89 Å
Translation3.5 Å19.89 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
DNAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MB4

3mb4


Resolution: 1.78→26.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2116 / WRfactor Rwork: 0.1718 / FOM work R set: 0.8551 / SU B: 4.789 / SU ML: 0.077 / SU R Cruickshank DPI: 0.099 / SU Rfree: 0.1024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 1938 1.6 %RANDOM
Rwork0.1756 ---
all0.1762 213233 --
obs0.1762 119437 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.32 Å2 / Biso mean: 29.313 Å2 / Biso min: 8.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0 Å20.3 Å2
2---0.45 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.78→26.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7380 0 196 545 8121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027833
X-RAY DIFFRACTIONr_bond_other_d0.0010.027495
X-RAY DIFFRACTIONr_angle_refined_deg1.5792.01710545
X-RAY DIFFRACTIONr_angle_other_deg0.86317258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0655909
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73823.689366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.107151485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0481563
X-RAY DIFFRACTIONr_chiral_restr0.0940.21121
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021774
X-RAY DIFFRACTIONr_mcbond_it5.0713.7633602
X-RAY DIFFRACTIONr_mcbond_other5.0553.7633593
X-RAY DIFFRACTIONr_mcangle_it5.796.9324484
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 146 -
Rwork0.291 8759 -
all-8905 -
obs--97.45 %
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)
10.1628-0.17570.00670.82190.02120.7683-0.0424-0.03220.0441-0.02540.05480.03380.16280.0486-0.01240.05670.0203-0.01950.03010.00130.06113.579453.255153.9424
20.4441-0.4089-0.430.6125-0.17451.8316-0.0940.01650.0094-0.0425-0.0313-0.04890.37250.01830.12530.1076-0.01380.01110.02240.01130.05968.706953.257287.7435
30.0898-0.1817-0.05910.65210.36571.0928-0.01810.0222-0.0317-0.10340.00990.0075-0.1603-0.01680.00830.095-0.02150.00210.0478-0.02020.05029.84718.4888.7452
40.0169-0.0070.03121.05520.49271.0283-0.01730.0120.0240.08360.0626-0.02850.17040.0209-0.04530.06460.0056-0.02580.04090.0160.0612.772656.732111.4608
50.02070.0925-0.07850.8389-0.03810.93140.0035-0.0001-0.0132-0.00030.0275-0.0067-0.16440.0504-0.03110.0579-0.0169-0.01280.0404-0.00810.072824.600877.812459.25
60.2449-0.14730.02660.6052-0.01080.89110.0124-0.03610.0791-0.1488-0.0236-0.03910.20860.0340.01120.11760.01510.00970.0164-0.00560.03899.237551.914330.0616
70.1821-0.17170.10720.461-0.04051.1523-0.02240.0068-0.05040.01790.0238-0.082-0.2181-0.0561-0.00140.05570.0136-0.00970.035-0.01280.077312.647113.0581113.2153
80.04430.02040.00760.32080.15740.9249-0.00050.0104-0.04930.03640.0071-0.0186-0.16170.0744-0.00660.0764-0.0197-0.01790.039-0.00340.063230.240378.251983.4013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A620 - 732
2X-RAY DIFFRACTION2B621 - 731
3X-RAY DIFFRACTION3C621 - 731
4X-RAY DIFFRACTION4D621 - 732
5X-RAY DIFFRACTION5E620 - 732
6X-RAY DIFFRACTION6F621 - 732
7X-RAY DIFFRACTION7G621 - 732
8X-RAY DIFFRACTION8H621 - 731

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