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

ID or keywords:

Entry

Database: PDB / ID: 7bbp

Title

Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac

Components

Histone H4
PH-interacting protein

Keywords

PROTEIN 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 / lysine-acetylated histone binding / insulin receptor binding / regulation of protein phosphorylation / structural constituent of chromatin ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

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. / Structural Genomics Consortium (SGC)

Citation

Journal: 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

Deposition	Dec 18, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: 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
Revision 1.2	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7bbp.cif.gz	120.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7bbp.ent.gz		Display	PDB format
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Validation report

Summary document	7bbp_validation.pdf.gz	489.7 KB	Display	wwPDB validaton report
Full document	7bbp_full_validation.pdf.gz	491.7 KB	Display
Data in XML	7bbp_validation.xml.gz	20.3 KB	Display
Data in CIF	7bbp_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bb/7bbp ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bbp	HTTPS FTP

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Related structure data

Related structure data	3mb3S S: Starting model for refinement
Similar structure data	3gld-2 4phq-2 5i7c-d 2jtn-d 3i9y-d 3gld-3 3b2m-2 4w80-d 6js9-d 1jth-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.5281/zenodo.4085070 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (4) #241 - Jan 2020 Twenty Years of Molecules similarity (4)

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

62.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: PH-interacting protein

DDD: PH-interacting protein

GGG: Histone H4

hetero molecules

defined by author
Evidence: gel filtration
31.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: PH-interacting protein

CCC: PH-interacting protein

FFF: Histone H4

hetero molecules

defined by author
31.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

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

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PHE	PHE	AAA	A	1316 - 1431	4 - 119
2	2	1	PHE	PHE	BBB	B	1316 - 1431	4 - 119
3	3	2	HIS	HIS	AAA	A	1316 - 1432	4 - 120
4	4	2	HIS	HIS	CCC	C	1316 - 1432	4 - 120
5	5	3	HIS	HIS	AAA	A	1316 - 1432	4 - 120
6	6	3	HIS	HIS	DDD	D	1316 - 1432	4 - 120
7	7	4	PHE	PHE	BBB	B	1316 - 1431	4 - 119
8	8	4	PHE	PHE	CCC	C	1316 - 1431	4 - 119
9	9	5	PHE	PHE	BBB	B	1316 - 1431	4 - 119
10	10	5	PHE	PHE	DDD	D	1316 - 1431	4 - 119
11	11	6	HIS	HIS	CCC	C	1316 - 1432	4 - 120
12	12	6	HIS	HIS	DDD	D	1316 - 1432	4 - 120

NCS ensembles :

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

#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 Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.87 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 20, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9282 Å / Relative weight: 1
Reflection	Resolution: 1.99→55.39 Å / Num. obs: 41404 / % possible obs: 99 % / Redundancy: 3.4 % / CC_1/2: 0.998 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.99→2.04 Å / Num. unique obs: 2999 / CC_1/2: 0.653

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3MB3

3mb3

Resolution: 1.99→55.39 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.2405	2016	4.87 %
R_work	0.2055	39378	-
all	0.207	-	-
obs	-	41394	98.858 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 38.966 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.279 Å²	-0 Å²	0.545 Å²
2-	-	1.134 Å²	-0 Å²
3-	-	-	-0.978 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→55.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4031	0	12	165	4208

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	4153
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3830
X-RAY DIFFRACTION	r_angle_refined_deg	1.456	1.651	5596
X-RAY DIFFRACTION	r_angle_other_deg	1.305	1.581	8865
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.272	5	488
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.139	21.452	248
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.492	15	732
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.872	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	523
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4642
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	986
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	732
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.159	0.2	3136
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	2014
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1882
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	161
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.127	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.133	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	3.269	3.857	1963
X-RAY DIFFRACTION	r_mcbond_other	3.229	3.852	1960
X-RAY DIFFRACTION	r_mcangle_it	4.63	5.753	2446
X-RAY DIFFRACTION	r_mcangle_other	4.634	5.754	2447
X-RAY DIFFRACTION	r_scbond_it	3.889	4.359	2190
X-RAY DIFFRACTION	r_scbond_other	3.888	4.36	2191
X-RAY DIFFRACTION	r_scangle_it	5.999	6.354	3150
X-RAY DIFFRACTION	r_scangle_other	5.998	6.355	3151
X-RAY DIFFRACTION	r_lrange_it	7.564	43.967	4577
X-RAY DIFFRACTION	r_lrange_other	7.575	43.938	4547
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	3818
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.083	0.05	3861
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.092	0.05	3819
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.092	0.05	3784
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.075	0.05	3839
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.092	0.05	3740

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.0825	0.05008
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.0825	0.05008
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.08314	0.05008
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.08314	0.05008
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.09219	0.05008
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.09219	0.05008
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.0917	0.05008
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.0917	0.05008
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.0755	0.05008
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.0755	0.05008
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.09198	0.05008
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.09198	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.99-2.042	0.345	136	0.304	2856	X-RAY DIFFRACTION	98.8437
2.042-2.097	0.298	133	0.292	2887	X-RAY DIFFRACTION	99.0489
2.097-2.158	0.32	155	0.275	2734	X-RAY DIFFRACTION	99.1421
2.158-2.225	0.287	147	0.247	2635	X-RAY DIFFRACTION	99.1447
2.225-2.298	0.262	134	0.236	2581	X-RAY DIFFRACTION	98.9792
2.298-2.378	0.323	122	0.237	2533	X-RAY DIFFRACTION	98.9564
2.378-2.468	0.261	120	0.232	2407	X-RAY DIFFRACTION	98.7495
2.468-2.568	0.293	123	0.225	2332	X-RAY DIFFRACTION	99.3123
2.568-2.682	0.253	105	0.213	2243	X-RAY DIFFRACTION	98.9882
2.682-2.813	0.22	113	0.198	2121	X-RAY DIFFRACTION	99.1567
2.813-2.965	0.247	119	0.202	2022	X-RAY DIFFRACTION	98.9829
2.965-3.145	0.241	106	0.217	1885	X-RAY DIFFRACTION	96.6505
3.145-3.361	0.276	88	0.216	1830	X-RAY DIFFRACTION	99.4298
3.361-3.63	0.23	79	0.201	1712	X-RAY DIFFRACTION	99.4448
3.63-3.976	0.185	72	0.182	1572	X-RAY DIFFRACTION	99.0361
3.976-4.444	0.195	77	0.168	1389	X-RAY DIFFRACTION	98.0602
4.444-5.128	0.182	61	0.155	1243	X-RAY DIFFRACTION	97.4589
5.128-6.273	0.244	64	0.187	1074	X-RAY DIFFRACTION	99.4755
6.273-8.842	0.192	41	0.176	833	X-RAY DIFFRACTION	98.2022
8.842-55.39	0.226	21	0.184	489	X-RAY DIFFRACTION	99.2218

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