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- PDB-3hph: Closed tetramer of Visna virus integrase (residues 1-219) in comp... -

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Basic information

Entry
Database: PDB / ID: 3hph
TitleClosed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD
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 / 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 / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation ...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 / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 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 / nuclear periphery / euchromatin / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / viral capsid / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / response to heat / DNA-binding transcription factor binding / DNA recombination / response to oxidative stress / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / transcription coactivator activity / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / chromatin remodeling / symbiont entry into host cell / chromatin binding / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Integrase, N-terminal zinc-binding domain / 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 / TFIIS/LEDGF domain superfamily / dUTPase-like / dUTPase / dUTPase, trimeric ...Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Integrase, N-terminal zinc-binding domain / 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 / TFIIS/LEDGF domain superfamily / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / gag protein p24 N-terminal 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 / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / Aspartic peptidase domain 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
PHOSPHATE ION / 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: 2.64 Å
AuthorsHare, S. / Wang, J. / Cherepanov, P.
Citation
Journal: 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.
#1: Journal: To be Published
Title: Application of General Formulas for the Correction of a Lattice Translocation Defect in Crystals of a Lentiviral Integrase in Complex with LEDGF
Authors: Hare, S. / Cherepanov, P. / Wang, J.
History
DepositionJun 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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

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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: PC4 and SFRS1-interacting protein
F: PC4 and SFRS1-interacting protein
G: PC4 and SFRS1-interacting protein
H: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,23219
Polymers144,3178
Non-polymers91511
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.870, 83.150, 115.300
Angle α, β, γ (deg.)90.000, 101.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11F
21G
12A
22D
13B
23C
14B
24C
15A
25D
16H
26E
17A
27B
18D
28C
19F
29E
110G
210H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112F1 - 426
2112G1 - 420
1122A55 - 213
2122D55 - 214
1132B1 - 50
2132C1 - 50
1142B55 - 215
2142C55 - 216
1152A1 - 50
2152D1 - 50
1162H1 - 440
2162E1 - 440
1175A1 - 50
2175B1 - 50
1185D1 - 50
2185C1 - 50
1195F350 - 426
2195E350 - 440
11105G350 - 420
21105H350 - 440

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Integrase / / IN


Mass: 25090.455 Da / Num. of mol.: 4
Fragment: N-terminal and catalytic domains, UNP residues 923-1039
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: 10988.893 Da / Num. of mol.: 4 / Fragment: Integrase binding domain, UNP residues 348-435
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

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Non-polymers , 4 types, 121 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7-0.9M (NH4)2HPO4, 2.5% Jeffamine M600,100mM Bis-Tris propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.64→40 Å / Num. all: 56209 / Num. obs: 55918 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 50.579 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.1
Reflection shellResolution: 2.64→2.71 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 13611 / Num. unique all: 4115 / Num. unique obs: 4092 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HPG and 2B4J

3hpg

2b4j


Resolution: 2.64→39.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.224 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.81 / SU B: 23.978 / SU ML: 0.225 / SU R Cruickshank DPI: 0.425 / SU Rfree: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.425 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2827 5.1 %RANDOM
Rwork0.226 ---
obs0.228 55918 99.55 %-
all-56171 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.01 Å2 / Biso mean: 26.532 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å22.19 Å2
2---1.45 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.64→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8625 0 43 110 8778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228804
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.94911879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30851068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43125.086409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.727151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0031541
X-RAY DIFFRACTIONr_chiral_restr0.0940.21357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216462
X-RAY DIFFRACTIONr_mcbond_it0.8011.55393
X-RAY DIFFRACTIONr_mcangle_it1.56428684
X-RAY DIFFRACTIONr_scbond_it2.13533411
X-RAY DIFFRACTIONr_scangle_it3.7944.53195
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1F212TIGHT POSITIONAL0.020.05
1F212MEDIUM POSITIONAL0.020.5
1F212TIGHT THERMAL0.050.5
1F212MEDIUM THERMAL0.032
2A616TIGHT POSITIONAL0.030.05
2A612MEDIUM POSITIONAL0.040.5
2A616TIGHT THERMAL0.070.5
2A612MEDIUM THERMAL0.082
3B176TIGHT POSITIONAL0.020.05
3B155MEDIUM POSITIONAL0.020.5
3B176TIGHT THERMAL0.050.5
3B155MEDIUM THERMAL0.082
4B624TIGHT POSITIONAL0.040.05
4B614MEDIUM POSITIONAL0.040.5
4B624TIGHT THERMAL0.090.5
4B614MEDIUM THERMAL0.12
5A160TIGHT POSITIONAL0.020.05
5A151MEDIUM POSITIONAL0.020.5
5A160TIGHT THERMAL0.030.5
5A151MEDIUM THERMAL0.042
6H356TIGHT POSITIONAL0.030.05
6H374MEDIUM POSITIONAL0.040.5
6H356TIGHT THERMAL0.050.5
6H374MEDIUM THERMAL0.072
7A160MEDIUM POSITIONAL0.20.5
7A151LOOSE POSITIONAL0.785
7A160MEDIUM THERMAL2.422
7A151LOOSE THERMAL2.53
8D164MEDIUM POSITIONAL0.220.5
8D152LOOSE POSITIONAL0.795
8D164MEDIUM THERMAL2.392
8D152LOOSE THERMAL2.53
9F240MEDIUM POSITIONAL0.270.5
9F242LOOSE POSITIONAL0.485
9F240MEDIUM THERMAL4.442
9F242LOOSE THERMAL4.25
10G216MEDIUM POSITIONAL0.240.5
10G213LOOSE POSITIONAL0.495
10G216MEDIUM THERMAL4.642
10G213LOOSE THERMAL4.49
LS refinement shellResolution: 2.64→2.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 207 -
Rwork0.304 3860 -
all-4067 -
obs--99.44 %
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)
11.44720.0416-0.20391.35590.66391.35380.04220.1121-0.1195-0.0522-0.0141-0.0732-0.13150.0233-0.02810.1723-0.02920.00540.3475-0.00040.233528.899-0.9664.624
21.6231-0.585-0.09551.2231-0.11531.231-0.049-0.1096-0.20120.13700.0682-0.047-0.01830.04890.2443-0.0140.02740.35150.0440.1987-4.7150.91234.682
38.1797-4.4717-0.04429.7311-0.05635.8262-0.8323-0.1622-1.13940.7520.3272-0.48390.69160.21050.50510.44080.20170.05470.3785-0.06970.765640.704-25.0585.371
45.83430.43781.73266.3280.78156.3424-0.08630.4765-1.0240.2291-0.09820.3130.97870.33490.18450.30420.16710.11870.232-0.00890.377510.531-19.25324.923
55.3425-1.853-1.43297.41660.2438.09830.1879-0.25990.8502-0.2484-0.0621-0.0416-0.6585-0.4736-0.12580.2009-0.00170.01790.2197-0.14010.27417.06119.09518.612
62.35171.4659-1.897711.24874.31877.5310.3323-0.17210.58060.59350.2446-0.6693-0.96710.0551-0.5770.67360.08340.03990.3947-0.20190.4296-5.27225.09946.257
76.6147-3.79960.36454.84450.26528.25810.28770.1748-0.3142-0.006-0.1323-0.2090.50160.3676-0.15540.05120.0169-0.05330.1822-0.00450.122636.469-33.214-17.87
88.4648-5.62155.465517.222-0.60056.1946-0.3313-0.16430.35720.05760.09030.7604-1.2066-0.31870.2410.80680.01960.05490.07330.09590.456924.3733.9624.316
97.32974.53652.93114.6854.66156.43950.37180.205-1.2216-0.5120.1872-0.59560.61910.0576-0.5590.6142-0.05820.06850.10020.02920.8907-5.037-33.09631.589
106.5932-0.7944-0.03188.44645.58658.2098-0.0487-0.36420.2997-0.2709-0.31680.3491-0.8703-0.50680.36550.20510.0541-0.05150.2654-0.07950.0459-28.11533.21339.53
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 213
2X-RAY DIFFRACTION1B55 - 215
3X-RAY DIFFRACTION1E364 - 368
4X-RAY DIFFRACTION1F364 - 368
5X-RAY DIFFRACTION2C55 - 216
6X-RAY DIFFRACTION2D60 - 214
7X-RAY DIFFRACTION2G364 - 368
8X-RAY DIFFRACTION2H364 - 368
9X-RAY DIFFRACTION3A4 - 43
10X-RAY DIFFRACTION3A220
11X-RAY DIFFRACTION4B1 - 44
12X-RAY DIFFRACTION4B220
13X-RAY DIFFRACTION5C1 - 44
14X-RAY DIFFRACTION5C220
15X-RAY DIFFRACTION6D3 - 43
16X-RAY DIFFRACTION6D220
17X-RAY DIFFRACTION7E348 - 363
18X-RAY DIFFRACTION7E369 - 440
19X-RAY DIFFRACTION8F352 - 363
20X-RAY DIFFRACTION8F369 - 426
21X-RAY DIFFRACTION9G353 - 363
22X-RAY DIFFRACTION9G369 - 420
23X-RAY DIFFRACTION10H348 - 363
24X-RAY DIFFRACTION10H369 - 440

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