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- PDB-3mb3: Crystal Structure of the second bromodomain of Pleckstrin homolog... -

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Basic information

Entry
Database: PDB / ID: 3mb3
TitleCrystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP)
ComponentsPH-interacting protein
KeywordsSIGNALING PROTEIN / PHIP / Pleckstrin homology domain interacting protein / DCAF14 / ndrp / DDB1 and CUL4 associated factor 14 / SGC / Structural Genomics Consortium / Bromodomain / Phosphoprotein / WD repeat
Function / homology
Function and homology information


regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein phosphorylation / lysine-acetylated histone binding / insulin receptor binding / insulin receptor signaling pathway ...regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein phosphorylation / lysine-acetylated histone binding / insulin receptor binding / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / WD40 repeat, conserved site ...Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1-methylpyrrolidin-2-one / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / 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
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Sep 6, 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: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2302
Polymers16,1311
Non-polymers991
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.090, 92.090, 76.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PH-interacting protein / PHIP / IRS-1 PH domain-binding protein / WD repeat-containing protein 11


Mass: 16131.264 Da / Num. of mol.: 1 / Fragment: UNP residues 1302-1434
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHIP, WDR11 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q8WWQ0
#2: Chemical ChemComp-MB3 / 1-methylpyrrolidin-2-one / N-Methyl-2-pyrrolidone


Mass: 99.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 11% PEG3350 4% glycerol,0.1M acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorDate: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.25→39.88 Å / Num. all: 18066 / Num. obs: 18012 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 9.2
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2 / Num. unique all: 2602 / Rsym value: 0.53 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.88 Å
Translation2.5 Å39.88 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

3hmh

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 2.25→39.88 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.803 / SU B: 12.537 / SU ML: 0.127 / SU R Cruickshank DPI: 0.134 / SU Rfree: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 914 5.1 %RANDOM
Rwork0.206 ---
all0.208 18065 --
obs0.208 17988 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 144.07 Å2 / Biso mean: 55.905 Å2 / Biso min: 25.23 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å21.69 Å20 Å2
2--3.37 Å20 Å2
3----5.06 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 7 85 1033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022971
X-RAY DIFFRACTIONr_bond_other_d0.0020.02672
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9851312
X-RAY DIFFRACTIONr_angle_other_deg1.9463.0011629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07224.16748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67815173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.709157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02198
X-RAY DIFFRACTIONr_mcbond_it4.493584
X-RAY DIFFRACTIONr_mcbond_other1.3063226
X-RAY DIFFRACTIONr_mcangle_it6.4285948
X-RAY DIFFRACTIONr_scbond_it11.0018387
X-RAY DIFFRACTIONr_scangle_it14.06511364
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 80 -
Rwork0.356 1231 -
all-1311 -
obs--99.39 %
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)
15.33590.61821.17763.07360.0527.58110.11540.1014-0.85730.00770.06240.46970.5043-0.4725-0.17780.1679-0.05910.00090.10670.02540.20254.02848.6087-0.5033
25.7598-2.6526-1.17361.70490.58963.36270.0317-0.01330.15510.0602-0.0249-0.13170.00870.269-0.00680.2054-0.0158-0.01190.0368-0.01020.045912.59352.10352.0354
312.6561-14.184-8.58227.292312.152720.1553-0.38081.40460.89550.42660.56690.6056-1.234-1.3823-0.1860.37770.12430.04010.49570.2510.2407-2.337665.68810.5259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1316 - 1350
2X-RAY DIFFRACTION2A1351 - 1415
3X-RAY DIFFRACTION3A1416 - 1431

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