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- PDB-5fh6: Crystal structure of the fifth bromodomain of human PB1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5fh6
TitleCrystal structure of the fifth bromodomain of human PB1 in complex with compound 10
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PBRM1 / BRG1-associated factor 180 / chromatin remodeling
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 / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / 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 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5XM / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTallant, C. / Sutherell, C.L. / Siejka, P. / Krojer, T. / Picaud, S. / Fonseca, M. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Tallant, C. / Sutherell, C.L. / Siejka, P. / Krojer, T. / Picaud, S. / Fonseca, M. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Ley, S.V. / Knapp, S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Identification and Development of 2,3-Dihydropyrrolo[1,2-a]quinazolin-5(1H)-one Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex.
Authors: Sutherell, C.L. / Tallant, C. / Monteiro, O.P. / Yapp, C. / Fuchs, J.E. / Fedorov, O. / Siejka, P. / Muller, S. / Knapp, S. / Brenton, J.D. / Brennan, P.E. / Ley, S.V.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)59,7258
Polymers58,5924
Non-polymers1,1334
Water23413
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9312
Polymers14,6481
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9312
Polymers14,6481
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9312
Polymers14,6481
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9312
Polymers14,6481
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.871, 136.416, 56.752
Angle α, β, γ (deg.)90.00, 92.33, 90.00
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: 14648.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Plasmid: pNIC28-Bsa4 / Details (production host): pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86U86
#2: Chemical
ChemComp-5XM / (3~{R})-3-(piperidin-1-ylmethyl)-2,3-dihydro-1~{H}-pyrrolo[1,2-a]quinazolin-5-one


Mass: 283.368 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 % / Description: Plates
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M LiSO4, 0.1 M bis-tris pH 6.5, 25% PEG 3350 / PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→29.73 Å / Num. all: 28108 / Num. obs: 28108 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 44.186 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.055 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 2.2 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1682refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q0O

4q0o


Resolution: 2.3→29.728 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.31 1401 4.99 %
Rwork0.2544 --
obs0.2573 28063 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 82 13 3743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133807
X-RAY DIFFRACTIONf_angle_d1.755121
X-RAY DIFFRACTIONf_dihedral_angle_d15.3341525
X-RAY DIFFRACTIONf_chiral_restr0.062549
X-RAY DIFFRACTIONf_plane_restr0.011642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2977-2.37980.38731230.36992499X-RAY DIFFRACTION93
2.3798-2.4750.42431450.35042695X-RAY DIFFRACTION100
2.475-2.58760.411420.33252651X-RAY DIFFRACTION100
2.5876-2.7240.37731240.32622683X-RAY DIFFRACTION100
2.724-2.89450.35521490.29972670X-RAY DIFFRACTION100
2.8945-3.11780.36921540.29032682X-RAY DIFFRACTION100
3.1178-3.43110.32391470.27172680X-RAY DIFFRACTION100
3.4311-3.92660.28581240.24352685X-RAY DIFFRACTION100
3.9266-4.94340.29791400.21362702X-RAY DIFFRACTION100
4.9434-29.73070.24711530.20662715X-RAY DIFFRACTION100
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.1810.1157-0.34224.22910.15133.1055-0.0187-0.0851-0.02560.9114-0.00970.09110.02530.18050.07440.5454-0.01580.02290.40360.01310.3428Chain A9.02319.129926.5685
21.3311-0.72450.30714.46020.29412.87720.09860.14330.1362-1.03290.0009-0.2953-0.55290.0963-0.00490.4607-0.09970.1030.35590.00030.3143Chain B-11.717144.389731.6547
30.9220.2738-0.2493.3476-2.01852.21540.06070.09680.12221.1154-0.1135-0.6824-0.8029-0.17810.08190.30580.0922-0.14440.4489-0.08330.6534Chain C-7.67248.490256.0121
42.47221.0392-0.38144.4365-0.3192.7398-0.30260.09950.2741-0.18230.41440.28370.1817-0.2211-0.06430.4074-0.0538-0.04950.47940.07860.3616Chain D13.093924.391659.859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain D and resid 625:731)
2X-RAY DIFFRACTION2(chain B and resid 621:731)
3X-RAY DIFFRACTION3(chain C and resid 623:731)
4X-RAY DIFFRACTION4(chain D and resid 625:731)

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