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- PDB-3hpg: Visna virus integrase (residues 1-219) in complex with LEDGF IBD:... -

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Basic information

Entry
Database: PDB / ID: 3hpg
TitleVisna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces
Components
  • Integrase
  • PC4 and SFRS1-interacting protein
KeywordsTRANSFERASE / PROTEIN-PROTEIN COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / MAGNESIUM / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / VIRAL NUCLEOPROTEIN / VIRION / ZINC / DNA-BINDING / HOST-VIRUS INTERACTION / TRANSCRIPTION / TRANSCRIPTION REGULATION / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / RECOMBINATION
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin / nuclear periphery / exoribonuclease H / exoribonuclease H activity / euchromatin / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral capsid / response to heat / response to oxidative stress / DNA recombination / DNA-binding transcription factor binding / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / transcription coactivator activity / chromatin remodeling / viral translational frameshifting / chromatin binding / symbiont entry into host cell / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Integrase, N-terminal zinc-binding domain / Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily ...Integrase, N-terminal zinc-binding domain / Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / gag protein p24 N-terminal domain / PWWP domain / PWWP domain profile. / PWWP domain / Ribonuclease H-like superfamily/Ribonuclease H / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMaedi visna virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsHare, S. / Labeja, A. / Cherepanov, P.
CitationJournal: Plos Pathog. / Year: 2009
Title: Structural basis for functional tetramerization of lentiviral integrase
Authors: Hare, S. / Di Nunzio, F. / Labeja, A. / Wang, J. / Engelman, A. / Cherepanov, P.
History
DepositionJun 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3May 28, 2025Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
E: Integrase
F: Integrase
G: PC4 and SFRS1-interacting protein
H: PC4 and SFRS1-interacting protein
I: PC4 and SFRS1-interacting protein
J: PC4 and SFRS1-interacting protein
K: PC4 and SFRS1-interacting protein
L: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,39118
Polymers216,99912
Non-polymers3926
Water00
1
A: Integrase
B: Integrase
E: Integrase
F: Integrase
G: PC4 and SFRS1-interacting protein
H: PC4 and SFRS1-interacting protein
K: PC4 and SFRS1-interacting protein
L: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,92712
Polymers144,6668
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-36 kcal/mol
Surface area21130 Å2
2
C: Integrase
D: Integrase
E: Integrase
F: Integrase
I: PC4 and SFRS1-interacting protein
J: PC4 and SFRS1-interacting protein
K: PC4 and SFRS1-interacting protein
L: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,92712
Polymers144,6668
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-36 kcal/mol
Surface area20430 Å2
3
C: Integrase
D: Integrase
I: PC4 and SFRS1-interacting protein
J: PC4 and SFRS1-interacting protein
hetero molecules

A: Integrase
B: Integrase
G: PC4 and SFRS1-interacting protein
H: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,92712
Polymers144,6668
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3200 Å2
ΔGint-38 kcal/mol
Surface area20580 Å2
Unit cell
Length a, b, c (Å)91.104, 148.904, 91.076
Angle α, β, γ (deg.)90.000, 113.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13G
23H
33I
43J
53K
63L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A, 1-43A1 - 43
211CHAIN B, 1-43B1 - 43
311CHAIN C, 1-43C1 - 43
411CHAIN D, 1-43D1 - 43
511CHAIN E, 1-43E1 - 43
611CHAIN F, 1-43F1 - 43
112CHAIN A, 60-141, 155-189, 197-212A60 - 141
122CHAIN A, 60-141, 155-189, 197-212A155 - 189
132CHAIN A, 60-141, 155-189, 197-212A197 - 212
212CHAIN B, 60-141, 155-189, 197-212B60 - 141
222CHAIN B, 60-141, 155-189, 197-212B155 - 189
232CHAIN B, 60-141, 155-189, 197-212B197 - 212
312CHAIN C, 60-141, 155-189, 197-212C60 - 141
322CHAIN C, 60-141, 155-189, 197-212C155 - 189
332CHAIN C, 60-141, 155-189, 197-212C197 - 212
412CHAIN D, 61-141, 155-189, 197-212D61 - 141
422CHAIN D, 61-141, 155-189, 197-212D155 - 189
432CHAIN D, 61-141, 155-189, 197-212D197 - 212
512CHAIN E, 60-141, 155-189, 197-212E60 - 141
522CHAIN E, 60-141, 155-189, 197-212E155 - 189
532CHAIN E, 60-141, 155-189, 197-212E197 - 212
612CHAIN F, 60-141, 155-189, 197-212F60 - 141
622CHAIN F, 60-141, 155-189, 197-212F155 - 189
632CHAIN F, 60-141, 155-189, 197-212F197 - 212
113CHAIN G, 320-423G320 - 423
213CHAIN H, 320-418H320 - 418
313CHAIN I, 320-418I320 - 418
413CHAIN J, 320-423J320 - 423
513CHAIN K, 320-426K320 - 426
613CHAIN L, 320-413L320 - 413

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Integrase / IN


Mass: 25090.455 Da / Num. of mol.: 6
Fragment: N-terminal and catalytic core domains, UNP residues 823-1039
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maedi visna virus / Strain: KV1772 / Gene: pol / Plasmid: pCDF-duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: P35956
#2: Protein
PC4 and SFRS1-interacting protein / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Dense fine speckles ...Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Dense fine speckles 70 kDa protein / DFS 70 / CLL-associated antigen KW-7


Mass: 11075.970 Da / Num. of mol.: 6 / Fragment: integrase binding domain, UNP residues 347-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DFS70, LEDGF, PSIP1, PSIP2 / Plasmid: pES / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: O75475
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
Has protein modificationN

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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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9696 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9696 Å / Relative weight: 1
ReflectionResolution: 3.28→40 Å / Num. all: 34448 / Num. obs: 34296 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 65.905 Å2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 3.28→3.46 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / Num. measured obs: 19335 / Num. unique obs: 5069 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B4J and 1K6Y

2b4j

1k6y


Resolution: 3.28→38.672 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.82 / SU ML: 0.44 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1718 5.04 %RANDOM
Rwork0.212 ---
obs0.214 34084 99.71 %-
all-34183 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.567 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 223.84 Å2 / Biso mean: 97.809 Å2 / Biso min: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.629 Å20 Å2-7.863 Å2
2--22.529 Å20 Å2
3----16.9 Å2
Refinement stepCycle: LAST / Resolution: 3.28→38.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12786 0 6 0 12792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113004
X-RAY DIFFRACTIONf_angle_d1.26117556
X-RAY DIFFRACTIONf_chiral_restr0.0842001
X-RAY DIFFRACTIONf_plane_restr0.0052248
X-RAY DIFFRACTIONf_dihedral_angle_d18.8234803
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A319X-RAY DIFFRACTIONPOSITIONAL0.048
12B319X-RAY DIFFRACTIONPOSITIONAL0.048
13C319X-RAY DIFFRACTIONPOSITIONAL0.05
14D319X-RAY DIFFRACTIONPOSITIONAL0.052
15E319X-RAY DIFFRACTIONPOSITIONAL0.044
16F313X-RAY DIFFRACTIONPOSITIONAL0.043
21A1068X-RAY DIFFRACTIONPOSITIONAL0.07
22B1068X-RAY DIFFRACTIONPOSITIONAL0.07
23C1068X-RAY DIFFRACTIONPOSITIONAL0.071
24D1056X-RAY DIFFRACTIONPOSITIONAL0.062
25E1068X-RAY DIFFRACTIONPOSITIONAL0.059
26F1068X-RAY DIFFRACTIONPOSITIONAL0.066
31G547X-RAY DIFFRACTIONPOSITIONAL0.043
32H547X-RAY DIFFRACTIONPOSITIONAL0.043
33I540X-RAY DIFFRACTIONPOSITIONAL0.038
34J604X-RAY DIFFRACTIONPOSITIONAL0.039
35K515X-RAY DIFFRACTIONPOSITIONAL0.039
36L500X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.28-3.3760.3591460.31627112857100
3.376-3.4850.2911340.28226712805100
3.485-3.610.3051300.24327072837100
3.61-3.7540.3071340.23826912825100
3.754-3.9250.2691440.21826712815100
3.925-4.1320.231420.19527232865100
4.132-4.390.2261440.1926742818100
4.39-4.7290.2381520.16926882840100
4.729-5.2030.1921470.17627072854100
5.203-5.9540.2641300.20527322862100
5.954-7.4930.2521490.21927142863100
7.493-38.6750.2161660.1862677284398
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)
12.7706-0.58930.60131.8531-0.60831.41910.0836-0.4532-0.247-0.1737-0.02710.0566-0.0109-0.0477-0.0880.5336-0.04760.01880.52480.11090.4494-3.42449.824132.7705
23.0939-0.5233-0.29590.93580.42571.52790.0299-0.0110.5756-0.3389-0.0632-0.19270.03-0.15440.01640.67270.0510.01570.2863-0.08620.604460.67546.096422.6373
34.33650.44071.28921.21170.47521.3166-0.08070.3874-0.1148-0.164-0.12830.0971-0.47520.05510.18790.69970.01760.01830.6442-0.08950.460326.542114.4044-4.2965
41.39962.74770.97030.97080.95270.0485-0.3690.21490.8214-0.37210.04780.8485-0.4015-0.02650.40340.8610.3361-0.21791.2767-0.2971.0291.35323.2858-6.4749
5-1.0553-0.06630.81283.03370.2674-0.20710.0523-0.38070.5395-0.9199-0.2609-0.20650.55360.24560.11630.71770.05760.27330.45640.17120.793-4.435140.592818.7116
6-1.67730.505-2.4158-0.07770.20930.395-0.0945-0.1578-0.6521-0.2833-0.26150.08070.1776-0.81280.00430.6944-0.031-0.19861.10870.14431.055864.19115.455520.7684
7-0.1487-0.6406-1.2624-0.0585-0.58081.125-0.27290.14430.04240.0992-0.11050.0291-0.01210.3580.30680.6684-0.1399-0.11250.772-0.04560.849850.872914.70017.573
80.1762-1.33110.69290.8151-1.09660.9461-0.5559-1.10470.29970.23390.48670.18880.4035-0.9711-0.05680.6566-0.1083-0.04071.1881-0.26051.056734.880238.752224.4858
9-1.4983-1.36680.73530.4751-0.27770.5725-0.1949-0.37370.4851-0.1009-0.2291-0.7799-0.30890.51530.17270.6058-0.12030.06270.99390.12281.01522.016518.24833.0562
100.8032-0.84850.42871.5923-0.45871.3862-0.17130.59070.18990.2284-0.046-0.3810.0706-0.03420.38270.7791-0.22840.00721.06490.12310.838719.370420.082359.9025
110.4096-0.4162-1.54751.1340.20564.6489-0.43420.6303-0.7117-0.026-0.35120.0634-0.116-1.21060.76860.8518-0.0616-0.03861.08940.00531.3647-28.6955-16.463938.6613
12-0.3216-0.27950.28413.04751.50622.8109-0.4339-0.0519-0.5702-0.04640.3595-0.07210.25551.07330.06550.84530.14760.19061.01030.18981.197388.644265.18059.7117
130.2939-0.092-0.14542.3259-0.53920.945-0.05230.1974-0.4936-0.01430.03781.05410.1914-0.39480.04080.7998-0.18560.05641.0928-0.2471.242232.290462.767340.2903
141.7667-0.5701-1.55490.54540.07522.6291-0.0831-1.0396-0.33510.22360.331-0.40110.17841.0425-0.41780.86890.0092-0.13591.2634-0.21621.037852.9287-10.3691-2.5567
150.77570.53280.11972.1781.25661.7412-0.34090.31430.0247-0.16810.15730.4415-0.08590.91030.32811.001-0.1318-0.23311.28970.18390.91834.563117.4563-32.2603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A, 50-212, chain B 50-212A50 - 212
2X-RAY DIFFRACTION1chain A, 50-212, chain B 50-212B50 - 212
3X-RAY DIFFRACTION2chain C, 50-212, chain D 50-212C50 - 212
4X-RAY DIFFRACTION2chain C, 50-212, chain D 50-212D50 - 212
5X-RAY DIFFRACTION3chain E, 50-212, chain F 50-212E50 - 212
6X-RAY DIFFRACTION3chain E, 50-212, chain F 50-212F50 - 212
7X-RAY DIFFRACTION4chain A, 4-49A4 - 49
8X-RAY DIFFRACTION5chain B, 4-49B4 - 49
9X-RAY DIFFRACTION6chain C, 4-49C4 - 49
10X-RAY DIFFRACTION7chain D, 2-49D2 - 49
11X-RAY DIFFRACTION8chain E, 2-49E2 - 49
12X-RAY DIFFRACTION9chain F, 2-49F2 - 49
13X-RAY DIFFRACTION10chain G, 348-423G348 - 423
14X-RAY DIFFRACTION11chain H, 347-418H347 - 418
15X-RAY DIFFRACTION12chain I, 348-418I348 - 418
16X-RAY DIFFRACTION13chain J, 347-423J347 - 423
17X-RAY DIFFRACTION14chain K, 347-426K347 - 426
18X-RAY DIFFRACTION15chain L, 348-413L348 - 413

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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