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- PDB-7bbp: Crystal Structure of the second bromodomain of Pleckstrin homolog... -

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Basic information

Entry
Database: PDB / ID: 7bbp
TitleCrystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac
Components
  • Histone H4
  • PH-interacting protein
KeywordsPROTEIN BINDING / PHIP / PLECKSTRIN HOMOLOGY DOMAIN INTERACTING PROTEIN / bromodomain / Structural Genomics / Structural Genomics Consortium / SGC
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 / structural constituent of chromatin ...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 / structural constituent of chromatin / nucleosome / insulin receptor signaling pathway / regulation of cell shape / protein heterodimerization activity / 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 / DNA binding / nucleus
Similarity search - Function
Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain ...Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone-fold / 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
Similarity search - Domain/homology
ACETATE ION / Histone H4 / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsKrojer, T. / Talon, R. / Fairhead, M. / Szykowska, A. / Burgess-Brown, N.A. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac
Authors: Krojer, T. / Talon, R. / Fairhead, M. / Szykowska, A. / Burgess-Brown, N.A. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: PH-interacting protein
BBB: PH-interacting protein
CCC: PH-interacting protein
DDD: PH-interacting protein
FFF: Histone H4
GGG: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8079
Polymers62,6276
Non-polymers1803
Water2,972165
1
AAA: PH-interacting protein
DDD: PH-interacting protein
GGG: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3764
Polymers31,3133
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: PH-interacting protein
CCC: PH-interacting protein
FFF: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4325
Polymers31,3133
Non-polymers1182
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.210, 58.310, 77.120
Angle α, β, γ (deg.)90.000, 99.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

Beg auth comp-ID: TYR / Beg label comp-ID: TYR

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEAAAA1316 - 14314 - 119
221PHEPHEBBBB1316 - 14314 - 119
332HISHISAAAA1316 - 14324 - 120
442HISHISCCCC1316 - 14324 - 120
553HISHISAAAA1316 - 14324 - 120
663HISHISDDDD1316 - 14324 - 120
774PHEPHEBBBB1316 - 14314 - 119
884PHEPHECCCC1316 - 14314 - 119
995PHEPHEBBBB1316 - 14314 - 119
10105PHEPHEDDDD1316 - 14314 - 119
11116HISHISCCCC1316 - 14324 - 120
12126HISHISDDDD1316 - 14324 - 120

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
PH-interacting protein / PHIP / DDB1- and CUL4-associated factor 14 / IRS-1 PH domain-binding protein / WD repeat-containing protein 11


Mass: 15156.185 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHIP, DCAF14, WDR11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ0
#2: Protein/peptide Histone H4 /


Mass: 1001.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q0VAS5
#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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% 2-propanol -- 0.2M ammonium acetate -- 0.1M tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.99→55.39 Å / Num. obs: 41404 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 11.3
Reflection shellResolution: 1.99→2.04 Å / Num. unique obs: 2999 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MB3

3mb3


Resolution: 1.99→55.39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.021 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2405 2016 4.87 %
Rwork0.2055 39378 -
all0.207 --
obs-41394 98.858 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.279 Å2-0 Å20.545 Å2
2--1.134 Å2-0 Å2
3----0.978 Å2
Refinement stepCycle: LAST / Resolution: 1.99→55.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4031 0 12 165 4208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134153
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173830
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.6515596
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5818865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2725488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.13921.452248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49215732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8721534
X-RAY DIFFRACTIONr_chiral_restr0.0780.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02986
X-RAY DIFFRACTIONr_nbd_refined0.2030.2732
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1590.23136
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22014
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2161
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.213
X-RAY DIFFRACTIONr_nbd_other0.1870.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.25
X-RAY DIFFRACTIONr_mcbond_it3.2693.8571963
X-RAY DIFFRACTIONr_mcbond_other3.2293.8521960
X-RAY DIFFRACTIONr_mcangle_it4.635.7532446
X-RAY DIFFRACTIONr_mcangle_other4.6345.7542447
X-RAY DIFFRACTIONr_scbond_it3.8894.3592190
X-RAY DIFFRACTIONr_scbond_other3.8884.362191
X-RAY DIFFRACTIONr_scangle_it5.9996.3543150
X-RAY DIFFRACTIONr_scangle_other5.9986.3553151
X-RAY DIFFRACTIONr_lrange_it7.56443.9674577
X-RAY DIFFRACTIONr_lrange_other7.57543.9384547
X-RAY DIFFRACTIONr_ncsr_local_group_10.0830.053818
X-RAY DIFFRACTIONr_ncsr_local_group_20.0830.053861
X-RAY DIFFRACTIONr_ncsr_local_group_30.0920.053819
X-RAY DIFFRACTIONr_ncsr_local_group_40.0920.053784
X-RAY DIFFRACTIONr_ncsr_local_group_50.0750.053839
X-RAY DIFFRACTIONr_ncsr_local_group_60.0920.053740
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.08250.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.08250.05008
23AAAX-RAY DIFFRACTIONLocal ncs0.083140.05008
24CCCX-RAY DIFFRACTIONLocal ncs0.083140.05008
35AAAX-RAY DIFFRACTIONLocal ncs0.092190.05008
36DDDX-RAY DIFFRACTIONLocal ncs0.092190.05008
47BBBX-RAY DIFFRACTIONLocal ncs0.09170.05008
48CCCX-RAY DIFFRACTIONLocal ncs0.09170.05008
59BBBX-RAY DIFFRACTIONLocal ncs0.07550.05008
510DDDX-RAY DIFFRACTIONLocal ncs0.07550.05008
611CCCX-RAY DIFFRACTIONLocal ncs0.091980.05008
612DDDX-RAY DIFFRACTIONLocal ncs0.091980.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.0420.3451360.3042856X-RAY DIFFRACTION98.8437
2.042-2.0970.2981330.2922887X-RAY DIFFRACTION99.0489
2.097-2.1580.321550.2752734X-RAY DIFFRACTION99.1421
2.158-2.2250.2871470.2472635X-RAY DIFFRACTION99.1447
2.225-2.2980.2621340.2362581X-RAY DIFFRACTION98.9792
2.298-2.3780.3231220.2372533X-RAY DIFFRACTION98.9564
2.378-2.4680.2611200.2322407X-RAY DIFFRACTION98.7495
2.468-2.5680.2931230.2252332X-RAY DIFFRACTION99.3123
2.568-2.6820.2531050.2132243X-RAY DIFFRACTION98.9882
2.682-2.8130.221130.1982121X-RAY DIFFRACTION99.1567
2.813-2.9650.2471190.2022022X-RAY DIFFRACTION98.9829
2.965-3.1450.2411060.2171885X-RAY DIFFRACTION96.6505
3.145-3.3610.276880.2161830X-RAY DIFFRACTION99.4298
3.361-3.630.23790.2011712X-RAY DIFFRACTION99.4448
3.63-3.9760.185720.1821572X-RAY DIFFRACTION99.0361
3.976-4.4440.195770.1681389X-RAY DIFFRACTION98.0602
4.444-5.1280.182610.1551243X-RAY DIFFRACTION97.4589
5.128-6.2730.244640.1871074X-RAY DIFFRACTION99.4755
6.273-8.8420.192410.176833X-RAY DIFFRACTION98.2022
8.842-55.390.226210.184489X-RAY DIFFRACTION99.2218

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