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- PDB-5llj: Maedi-Visna virus (MVV) integrase C-terminal domain (residues 220-276) -

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Basic information

Entry
Database: PDB / ID: 5llj
TitleMaedi-Visna virus (MVV) integrase C-terminal domain (residues 220-276)
ComponentsIntegrase
KeywordsVIRAL PROTEIN / integrase / visna/maedi virus / c-terminal domain
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral capsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / gag protein p24 N-terminal domain / 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 ...dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / gag protein p24 N-terminal domain / 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. / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / 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
Similarity search - Domain/homology
Biological speciesMaedi visna virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsPye, V.E. / Maskell, D.P. / Cherepanov, P.
CitationJournal: Science / Year: 2017
Title: A supramolecular assembly mediates lentiviral DNA integration.
Authors: Allison Ballandras-Colas / Daniel P Maskell / Erik Serrao / Julia Locke / Paolo Swuec / Stefán R Jónsson / Abhay Kotecha / Nicola J Cook / Valerie E Pye / Ian A Taylor / Valgerdur ...Authors: Allison Ballandras-Colas / Daniel P Maskell / Erik Serrao / Julia Locke / Paolo Swuec / Stefán R Jónsson / Abhay Kotecha / Nicola J Cook / Valerie E Pye / Ian A Taylor / Valgerdur Andrésdóttir / Alan N Engelman / Alessandro Costa / Peter Cherepanov /
Abstract: Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze insertion of viral DNA into cellular chromatin. Using cryo-electron microscopy, we now visualize the ...Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze insertion of viral DNA into cellular chromatin. Using cryo-electron microscopy, we now visualize the functional maedi-visna lentivirus intasome at 4.9 angstrom resolution. The intasome comprises a homo-hexadecamer of IN with a tetramer-of-tetramers architecture featuring eight structurally distinct types of IN protomers supporting two catalytically competent subunits. The conserved intasomal core, previously observed in simpler retroviral systems, is formed between two IN tetramers, with a pair of C-terminal domains from flanking tetramers completing the synaptic interface. Our results explain how HIV-1 IN, which self-associates into higher-order multimers, can form a functional intasome, reconcile the bulk of early HIV-1 IN biochemical and structural data, and provide a lentiviral platform for design of HIV-1 IN inhibitors.
History
DepositionJul 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4913
Polymers13,4562
Non-polymers351
Water2,558142
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-20 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.250, 64.250, 72.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Integrase


Mass: 6727.776 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maedi visna virus (strain KV1772) / Strain: KV1772 / Gene: pol / Production host: Escherichia coli (E. coli)
References: UniProt: P35956, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, dUTP diphosphatase, ...References: UniProt: P35956, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, dUTP diphosphatase, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.84 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M potassium sodium tartrate 0.1M BTP pH 7.5 20% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 1.78→48.04 Å / Num. all: 184115 / Num. obs: 15111 / % possible obs: 99.9 % / Redundancy: 12.2 % / Biso Wilson estimate: 31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.7
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.5 / Num. measured obs: 10797 / Num. unique all: 1088 / CC1/2: 0.52 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155:000)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ex4

1ex4


Resolution: 1.78→38.47 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.3 / Phase error: 23.2 / Details: Phenix.refine
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1424 5.14 %Random selection
Rwork0.1861 ---
obs0.1883 27721 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.19 Å2
Refinement stepCycle: LAST / Resolution: 1.78→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 1 142 1076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003970
X-RAY DIFFRACTIONf_angle_d0.6681312
X-RAY DIFFRACTIONf_dihedral_angle_d12.303575
X-RAY DIFFRACTIONf_chiral_restr0.054129
X-RAY DIFFRACTIONf_plane_restr0.005169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.84360.39921540.34892618X-RAY DIFFRACTION100
1.8436-1.91750.31171280.30762627X-RAY DIFFRACTION100
1.9175-2.00470.27991460.2392656X-RAY DIFFRACTION100
2.0047-2.11040.24581630.21182599X-RAY DIFFRACTION100
2.1104-2.24270.22851450.19612610X-RAY DIFFRACTION100
2.2427-2.41580.22821240.20212657X-RAY DIFFRACTION100
2.4158-2.65890.27041510.20742606X-RAY DIFFRACTION100
2.6589-3.04360.27441500.20062638X-RAY DIFFRACTION100
3.0436-3.83440.20931530.16422613X-RAY DIFFRACTION100
3.8344-48.05280.18791100.15292673X-RAY DIFFRACTION100
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)
10.30110.22270.18460.0757-0.17270.3726-0.2170.54010.6625-0.05980.4478-0.03730.0939-0.21480.00020.3445-0.00990.0970.28320.07010.34896.551818.378986.6929
20.04230.00730.03120.0208-0.03140.0523-0.013-0.21680.3009-0.15220.0820.2715-0.1695-0.48540.00130.42230.00280.03890.37150.01460.3445-6.675214.559599.1894
31.0728-0.410.42540.5991-0.5340.77250.06420.13570.15160.13960.0262-0.1459-0.2087-0.08560.03880.3618-0.01430.05550.23330.00860.2488.453815.783692.3892
40.38490.2367-0.05020.94050.23230.441-0.11180.2098-0.11070.19250.10250.0967-0.2520.0416-0.00170.3178-0.01130.0220.26620.04510.27414.69415.581587.5833
5-0.05350.28790.09440.43830.40490.46670.0419-0.15450.06310.0196-0.0807-0.1146-0.1927-0.018400.29720.04160.03730.3007-0.05380.26416.8746-0.4552104.0965
60.5380.06740.26930.2073-0.05090.09940.0274-0.00750.19530.0154-0.3147-0.27950.18230.1212-0.00630.28920.01820.01020.2565-0.01320.30416.95492.779395.479
70.0260.06150.11340.31790.74371.8338-0.5464-0.8706-1.23760.1174-0.00751.4281-0.06140.2428-0.24430.33670.04750.13810.20410.08180.65746.6166-2.306296.1558
80.35980.30020.29370.7532-0.20170.3978-0.24680.03510.1862-0.0420.2246-0.28180.00190.14120.00120.31890.0290.07170.2916-0.07940.339923.22291.255999.662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 220:227)
2X-RAY DIFFRACTION2(chain A and resid 228:236)
3X-RAY DIFFRACTION3(chain A and resid 237:259)
4X-RAY DIFFRACTION4(chain A and resid 260:276)
5X-RAY DIFFRACTION5(chain B and resid 220:237)
6X-RAY DIFFRACTION6(chain B and resid 238:254)
7X-RAY DIFFRACTION7(chain B and resid 255:261)
8X-RAY DIFFRACTION8(chain B and resid 262:276)

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