PDB-5oym: HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor

ID or keywords:

Entry

Database: PDB / ID: 5oym

Title

HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor

Components

PC4 and SFRS1-interacting protein

Keywords

TRANSCRIPTION /

Integrase binding / transciptional co-activator / domain swap

Function / homology

Function and homology information

supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition /

heterochromatin ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Rabbitts, T.H. / Phillips, S.E.V. / Cruz-Migoni, A. / Carr, S.B. / Hannon, C.

Funding support

United Kingdom, 3items

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Cloning, purification and structure determination of the HIV integrase-binding domain of lens epithelium-derived growth factor.
Authors: Hannon, C. / Cruz-Migoni, A. / Platonova, O. / Owen, R.L. / Nettleship, J.E. / Miller, A. / Carr, S.B. / Harris, G. / Rabbitts, T.H. / Phillips, S.E.V.

History

Deposition	Sep 11, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 18, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 17, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5oym.cif.gz	164 KB	Display	PDBx/mmCIF format
PDB format	pdb5oym.ent.gz	129.7 KB	Display	PDB format
PDBx/mmJSON format	5oym.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oy/5oym ftp://data.pdbj.org/pub/pdb/validation_reports/oy/5oym	HTTPS FTP

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Related structure data

Related structure data	2b4jS S: Starting model for refinement
Similar structure data	6xrs-1 1sji-d 6nnv-d 2hdn-9 6oaw-d 5ddr-d 3gge-2 3zrt-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (6) #33 - Sep 2002 HIV Reverse Transcriptase similarity (6) #6 - Jun 2000 HIV-1 Protease similarity (6) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (4)

Deposited unit

H: PC4 and SFRS1-interacting protein

G: PC4 and SFRS1-interacting protein

A: PC4 and SFRS1-interacting protein

B: PC4 and SFRS1-interacting protein

C: PC4 and SFRS1-interacting protein

D: PC4 and SFRS1-interacting protein

E: PC4 and SFRS1-interacting protein

F: PC4 and SFRS1-interacting protein

95.2 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering, Monomeric in solution and octamer only observed in the crystal

Unit cell

Length a, b, c (Å)	71.181, 54.814, 117.996
Angle α, β, γ (deg.)	90.00, 91.23, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	H	345 - 403
2	1	1	5	G	345 - 403
3	1	1	5	A	345 - 403
4	1	1	5	B	345 - 403
5	1	1	5	C	345 - 403
6	1	1	5	D	345 - 403
7	1	1	5	E	345 - 403
8	1	1	5	F	345 - 403
1	1	2	3	H	404 - 407
2	1	2	3	B	404 - 407
3	1	2	3	D	404 - 407
4	1	2	3	E	404 - 407
1	1	3	5	A	404 - 407
2	1	3	5	C	404 - 407
3	1	3	5	F	404 - 407
4	1	3	5	G	404 - 407
1	1	4	5	H	408 - 431
2	1	4	5	G	408 - 431
3	1	4	5	A	408 - 431
4	1	4	5	B	408 - 431
5	1	4	5	C	408 - 431
6	1	4	5	D	408 - 431
7	1	4	5	E	408 - 431
8	1	4	5	F	408 - 431

NCS ensembles :

ID
1
2
3
4

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.870587, -0.351108, 0.344676), (-0.353817, -0.040035, -0.934457), (0.341895, -0.935479, -0.089374)	-32.6111, -38.19386, -26.8054
3	given	(0.981886, 0.008067, -0.189302), (0.013509, -0.999531, 0.027474), (-0.188992, -0.029534, -0.981534)	-5.78004, 7.08327, -61.26504
4	given	(-0.92059, 0.34861, -0.176027), (-0.175424, 0.033571, 0.98392), (0.348914, 0.936666, 0.03025)	-51.08638, 20.70631, -29.3428
5	given	(-0.984765, -0.015644, 0.173183), (-0.043927, -0.941263, -0.334806), (0.168248, -0.337313, 0.926236)	-28.51008, -4.48537, 1.74766
6	given	(0.922471, 0.259256, 0.286066), (0.187842, 0.34595, -0.919257), (-0.337288, 0.901723, 0.27043)	-5.95349, -29.94531, -33.84008
7	given	(-0.999854, 0.015897, -0.006287), (0.012749, 0.938396, 0.345327), (0.011389, 0.345197, -0.938461)	-33.79777, 10.16747, -57.99757
8	given	(0.862479, -0.247652, -0.441359), (0.347005, -0.345439, 0.871929), (-0.368398, -0.905174, -0.211998)	-26.84839, 27.53649, -42.46955

#1: Protein	PC4 and SFRS1-interacting protein / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 Mass: 11897.691 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / Variant (production host): DE3 / References: UniProt: O75475
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

PC4 and SFRS1-interacting protein / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...

Mass: 11897.691 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Production host:

Escherichia coli (E. coli) / Strain (production host): B834 / Variant (production host): DE3 / References: UniProt: O75475

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Sodium Fluoride, 0.1 M bis-Tris propane, pH 8.5 and 20 % w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9778 Å / Relative weight: 1
Reflection	Resolution: 2.05→54.81 Å / Num. obs: 55617 / % possible obs: 97.1 % / Redundancy: 2.4 % / B_iso Wilson estimate: 28.8 Å² / R_rim(I) all: 0.097 / Net I/σ(I): 8.6
Reflection shell	Resolution: 2.05→2.16 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8059 / CC_1/2: 0.51 / R_rim(I) all: 0.796 / % possible all: 97

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2b4j

2b4j

Resolution: 2.05→14.98 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.932 / SU B: 5.311 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23628	2800	5.1 %	RANDOM
R_work	0.1823	-	-	-
obs	0.18506	52601	96.29 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 37.998 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0 Å²	-0.01 Å²
2-	-	-0.01 Å²	-0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: 1 / Resolution: 2.05→14.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5606	0	0	445	6051

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	5736
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	5925
X-RAY DIFFRACTION	r_angle_refined_deg	1.877	1.967	7662
X-RAY DIFFRACTION	r_angle_other_deg	1.044	3	13627
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.298	5	703
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.905	24.773	264
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.821	15	1300
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.502	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	909
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6270
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1271
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.359	3.331	2770
X-RAY DIFFRACTION	r_mcbond_other	3.354	3.33	2769
X-RAY DIFFRACTION	r_mcangle_it	4.921	4.966	3457
X-RAY DIFFRACTION	r_mcangle_other	4.92	4.967	3458
X-RAY DIFFRACTION	r_scbond_it	4.714	4.036	2966
X-RAY DIFFRACTION	r_scbond_other	4.713	4.037	2967
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.24	5.774	4196
X-RAY DIFFRACTION	r_long_range_B_refined	9.207	40.854	6815
X-RAY DIFFRACTION	r_long_range_B_other	9.187	40.615	6705
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	H	340	medium positional	0.21	0.5
1	1	G	340	medium positional	0.18	0.5
1	1	A	340	medium positional	0.2	0.5
1	1	B	340	medium positional	0.16	0.5
1	1	C	340	medium positional	0.19	0.5
1	1	D	340	medium positional	0.14	0.5
1	1	E	340	medium positional	0.2	0.5
1	1	F	340	medium positional	0.15	0.5
3	3	A	24	medium positional	0.29	0.5
3	3	C	24	medium positional	0.23	0.5
3	3	F	24	medium positional	0.26	0.5
3	3	G	24	medium positional	0.19	0.5
4	4	H	114	medium positional	0.29	0.5
4	4	G	114	medium positional	0.29	0.5
4	4	A	114	medium positional	0.31	0.5
4	4	B	114	medium positional	0.82	0.5
4	4	C	114	medium positional	0.27	0.5
4	4	D	114	medium positional	0.76	0.5
4	4	E	114	medium positional	0.3	0.5
4	4	F	114	medium positional	0.26	0.5
1	1	H	566	loose positional	0.53	5
1	1	G	566	loose positional	0.5	5
1	1	A	566	loose positional	0.63	5
1	1	B	566	loose positional	0.56	5
1	1	C	566	loose positional	0.61	5
1	1	D	566	loose positional	0.56	5
1	1	E	566	loose positional	0.57	5
1	1	F	566	loose positional	0.51	5
2	2	H	66	loose positional	0.03	5
2	2	B	66	loose positional	0.03	5
2	2	D	66	loose positional	0.04	5
2	2	E	66	loose positional	0.02	5
3	3	H	66	loose positional	1.11	5
3	3	B	66	loose positional	1.23	5
3	3	D	66	loose positional	0.97	5
3	3	E	66	loose positional	1.03	5
4	4	H	194	loose positional	0.82	5
4	4	G	194	loose positional	1.09	5
4	4	A	194	loose positional	0.8	5
4	4	D	194	loose positional	1.97	5
4	4	C	194	loose positional	0.99	5
4	4	D	194	loose positional	1.87	5
4	4	E	194	loose positional	1.1	5
4	4	F	194	loose positional	1.09	5
2	2	A	24	tight thermal	13.2	0.5
2	2	C	24	tight thermal	6.53	0.5
2	2	F	24	tight thermal	3.92	0.5
2	2	G	24	tight thermal	13.92	0.5
1	1	H	340	medium thermal	4.36	2
1	1	G	340	medium thermal	5.01	2
1	1	A	340	medium thermal	2.36	2
1	1	B	340	medium thermal	2.97	2
1	1	C	340	medium thermal	3.49	2
1	1	D	340	medium thermal	5.46	2
1	1	E	340	medium thermal	12.61	2
1	1	F	340	medium thermal	6.58	2
3	3	H	24	medium thermal	4.49	2
3	3	B	24	medium thermal	9.76	2
3	3	D	24	medium thermal	3.87	2
3	3	E	24	medium thermal	9.18	2
4	4	H	114	medium thermal	3.61	2
4	4	G	114	medium thermal	3.88	2
4	4	A	114	medium thermal	3.04	2
4	4	B	114	medium thermal	8.15	2
4	4	C	114	medium thermal	5.28	2
4	4	D	114	medium thermal	4.38	2
4	4	E	114	medium thermal	5.95	2
4	4	F	114	medium thermal	15.85	2
1	1	H	566	loose thermal	5.99	10
1	1	G	566	loose thermal	6.46	10
1	1	A	566	loose thermal	4.73	10
1	1	B	566	loose thermal	4.67	10
1	1	C	566	loose thermal	4.45	10
1	1	D	566	loose thermal	7.39	10
1	1	E	566	loose thermal	13.42	10
1	1	F	566	loose thermal	7.98	10
2	2	H	66	loose thermal	7.41	10
2	2	G	66	loose thermal	9.72	10
2	2	A	66	loose thermal	7.89	10
2	2	B	66	loose thermal	13.34	10
3	3	C	66	loose thermal	4.98	10
3	3	D	66	loose thermal	10.66	10
3	3	E	66	loose thermal	3.67	10
3	3	F	66	loose thermal	9.43	10
4	4	H	194	loose thermal	5.74	10
4	4	G	194	loose thermal	5	10
4	4	A	194	loose thermal	3.65	10
4	4	B	194	loose thermal	12.01	10
4	4	C	194	loose thermal	7.92	10
4	4	D	194	loose thermal	6.2	10
4	4	E	194	loose thermal	8.27	10
4	4	F	194	loose thermal	15.67	10

LS refinement shell

Resolution: 2.05→2.102 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.322	200	-
R_work	0.297	3819	-
obs	-	-	95.85 %

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