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- PDB-5e7d: Crystal Structure of the fifth bromodomain of human PB1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5e7d
TitleCrystal Structure of the fifth bromodomain of human PB1 in complex with a hydroxyphenyl ligand
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / Bromodomain / chemical probe / ligand / inhibitor / structural genomics consortium / SGC
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / 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 / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / 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
Chem-5KL / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsFilippakopoulos, P. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Owen, D. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal Structure of the fifth bromodomain of human PB1 in complex with a hydroxyphenyl ligand
Authors: Filippakopoulos, P. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Owen, D. / Knapp, S.
History
DepositionOct 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4199
Polymers58,5924
Non-polymers8275
Water4,179232
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8392
Polymers14,6481
Non-polymers1911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8392
Polymers14,6481
Non-polymers1911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8392
Polymers14,6481
Non-polymers1911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9013
Polymers14,6481
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.790, 135.664, 56.045
Angle α, β, γ (deg.)90.000, 90.600, 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 / PB1


Mass: 14648.000 Da / Num. of mol.: 4 / Fragment: UNP residues 645-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q86U86
#2: Chemical
ChemComp-5KL / (2E)-3-(dimethylamino)-1-(2-hydroxyphenyl)prop-2-en-1-one


Mass: 191.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13NO2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M Na2SO4 20w/v PEG_3350 10v/v ethylene_glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Number: 196359 / Rsym value: 0.069 / D res high: 1.866 Å / D res low: 23.819 Å / Num. obs: 44203 / % possible obs: 87.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
5.9123.8210.040.043.4
4.185.9110.0360.0363.5
3.414.1810.0370.0373.9
2.963.4110.0550.0554.6
2.642.9610.0660.0664.7
2.412.6410.1060.1064.9
2.242.4110.140.144.6
2.092.2410.2050.2054.8
1.972.0910.3490.3494.7
1.871.9710.6320.6323.8
ReflectionResolution: 1.866→23.819 Å / Num. all: 44203 / Num. obs: 44203 / % possible obs: 87.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.037 / Rrim(I) all: 0.079 / Rsym value: 0.069 / Net I/av σ(I): 6.492 / Net I/σ(I): 12.1 / Num. measured all: 196359
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.87-1.973.80.63212105156110.3690.632276.7
1.97-2.094.70.3492.22891361270.1780.3493.987.9
2.09-2.244.80.2053.73057764240.1050.2056.598.1
2.24-2.414.60.145.42375951290.0720.148.684.2
2.41-2.644.90.10672691655160.0530.10611.999.3
2.64-2.964.70.06610.52103544610.0340.06616.387.3
2.96-3.414.60.055122037144010.0290.05522.298.5
3.41-4.183.90.03715.51011926100.0210.03727.769.3
4.18-5.913.50.03611.8891525400.0220.03627.186.3
5.91-23.8193.40.049.5470313840.0240.0425.885.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.62 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.82 Å
Translation2.5 Å23.82 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMAC5.5.0110refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→23.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2411 / WRfactor Rwork: 0.1956 / FOM work R set: 0.7919 / SU B: 7.658 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1547 / SU Rfree: 0.1512 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1782 4.1 %RANDOM
Rwork0.2007 ---
obs0.2026 41808 86.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.17 Å2 / Biso mean: 27.133 Å2 / Biso min: 7.99 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å2-0.31 Å2
2---1.9 Å20 Å2
3----1.67 Å2
Refinement stepCycle: final / Resolution: 1.87→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 60 232 3920
Biso mean--30.8 33.68 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223764
X-RAY DIFFRACTIONr_bond_other_d0.0010.022585
X-RAY DIFFRACTIONr_angle_refined_deg1.36425069
X-RAY DIFFRACTIONr_angle_other_deg0.923.0016276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74124.205176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81615710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6251525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02725
X-RAY DIFFRACTIONr_mcbond_it3.62832235
X-RAY DIFFRACTIONr_mcbond_other1.1713869
X-RAY DIFFRACTIONr_mcangle_it5.27853631
X-RAY DIFFRACTIONr_scbond_it8.74281529
X-RAY DIFFRACTIONr_scangle_it10.896111437
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 130 -
Rwork0.407 3069 -
all-3199 -
obs--87.43 %
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)
10.80680.67010.0673.62332.80750.8978-0.021-0.11560.0015-0.0143-0.02160.03740.31680.07370.04260.2612-0.00150.00920.01030.02730.041711.72246.3855-0.7252
21.3892-1.31770.33481.3304-0.81130.8402-0.1047-0.04420.09360.14050.0722-0.03510.0137-0.04380.03240.0449-0.00140.00830.08360.00760.06877.097425.44766.9681
30.31370.32780.30341.54240.25551.4283-0.0167-0.0060.0769-0.0661-0.0385-0.0210.1410.05240.05520.0507-0.00020.0370.08310.02020.06213.889120.7315-0.0193
40.3573-2.3112-0.5546.36032.99831.288-0.04050.0059-0.0057-0.11360.05350.0452-0.22520.1054-0.0130.195-0.03140.01930.01660.01130.039132.499757.0309-0.499
50.89370.8844-1.09751.2594-0.47521.34180.03290.0862-0.0811-0.0108-0.0020.0602-0.1647-0.0669-0.03090.0179-0.00540.02110.11380.01570.075426.9238.3164-8.746
60.3723-0.221-0.25063.4710.46181.5711-0.04120.0184-0.05130.29070.0071-0.0775-0.09750.10320.03410.0513-0.00590.00220.07290.01030.052933.86443.3808-1.0849
70.33861.7095-1.30053.7468-1.25672.2531-0.0641-0.20830.04-0.16870.10680.2873-0.55750.1015-0.04270.25920.0117-0.03590.01220.0120.028625.458859.2224-24.9906
80.0406-0.19290.22941.2393-0.29111.3732-0.0563-0.0288-0.0866-0.20440.06590.105-0.18890.0894-0.00960.114-0.0271-0.00830.0633-0.00990.037428.116444.2945-27.0068
9-0.7521.10460.49159.9989-5.967213.68630.00470.00250.0567-0.13710.15830.4298-0.4337-0.4794-0.1630.11390.0523-0.16840.01140.07270.182416.042354.5292-29.6238
100.7443-0.15390.98432.0461-0.42242.99570.00520.154-0.00890.21930.0719-0.05940.15420.3456-0.0770.0790.03120.01380.1013-0.0190.03937.461618.3031-33.7119
111.4449-0.2935-1.22214.29030.79112.4755-0.1150.07170.26410.02610.2283-0.126-0.02490.3726-0.11330.0247-0.0355-0.05180.1561-0.00850.07612.896231.001-29.9105
120.7499-0.71610.88821.79390.51181.9479-0.1624-0.04990.10220.29560.09130.02460.0129-0.04880.07110.08980.01860.0180.06560.00240.03132.47924.9601-28.6845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A621 - 639
2X-RAY DIFFRACTION2A640 - 671
3X-RAY DIFFRACTION3A672 - 731
4X-RAY DIFFRACTION4B621 - 640
5X-RAY DIFFRACTION5B641 - 671
6X-RAY DIFFRACTION6B672 - 731
7X-RAY DIFFRACTION7C621 - 646
8X-RAY DIFFRACTION8C647 - 720
9X-RAY DIFFRACTION9C721 - 731
10X-RAY DIFFRACTION10D621 - 660
11X-RAY DIFFRACTION11D661 - 680
12X-RAY DIFFRACTION12D681 - 731

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