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- PDB-5t3a: Maedi-Visna virus (MVV) integrase CCD-CTD (residues 60-275) -

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Basic information

Entry
Database: PDB / ID: 5t3a
TitleMaedi-Visna virus (MVV) integrase CCD-CTD (residues 60-275)
Componentsintegrase
KeywordsHYDROLASE / Visna virus integrase / catalytic core domain / c-terminal domain
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral capsid / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / 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 ...dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesVisna/maedi virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsCook, N.J. / Pye, V.E. / 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
DepositionAug 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9805
Polymers25,6071
Non-polymers3724
Water82946
1
A: integrase
hetero molecules

A: integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,95910
Polymers51,2152
Non-polymers7458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5230 Å2
ΔGint-39 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.050, 124.830, 62.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

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Components

#1: Protein integrase /


Mass: 25607.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Visna/maedi virus / Production host: Escherichia coli (E. coli) / References: UniProt: P35956
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Mes pH6.0, 15-100mM calcium acetate and 15-21% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.5→62.42 Å / Num. obs: 10859 / % possible obs: 99.7 % / Redundancy: 9.4 % / Biso Wilson estimate: 44.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.129 / Rsym value: 0.064 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.81 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HPG, 5LLJ

3hpg

5llj


Resolution: 2.501→62.415 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5
Details: Data were found to be anisotropic, 2.5A in a and c directions; 3.5A in b. Data were subjected to staraniso (global phasing; ian tickle et al) after processing and it is this file the model ...Details: Data were found to be anisotropic, 2.5A in a and c directions; 3.5A in b. Data were subjected to staraniso (global phasing; ian tickle et al) after processing and it is this file the model was refined against (and is uploaded). The model was refined using phenix and coot.
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 521 5.64 %random
Rwork0.1792 ---
obs0.1823 9236 84.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 62.4 Å2
Refinement stepCycle: LAST / Resolution: 2.501→62.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 24 46 1786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021792
X-RAY DIFFRACTIONf_angle_d0.5132425
X-RAY DIFFRACTIONf_dihedral_angle_d11.6791066
X-RAY DIFFRACTIONf_chiral_restr0.043258
X-RAY DIFFRACTIONf_plane_restr0.004309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5008-2.75250.26511150.21111493X-RAY DIFFRACTION60
2.7525-3.15080.28811200.22421990X-RAY DIFFRACTION79
3.1508-3.96960.24771600.19722534X-RAY DIFFRACTION99
3.9696-62.43440.21081260.15422698X-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)
10.54520.1965-0.14670.54130.03381.3672-0.15490.0845-0.121-0.0230.02790.00970.0172-0.357-0.08630.16770.0171-0.00580.2925-0.0140.2023-12.4839-34.20169.3469
20.5251-0.43990.11311.0577-0.20910.26950.03660.44690.04190.0373-0.1591-0.14250.05460.0519-0.06630.1848-0.02220.01720.36390.01510.16662.4554-29.61443.025
30.0094-0.0021-0.00140.00390.00180.00070.1854-0.19210.00090.13230.16240.2019-0.1248-0.14090.00020.91060.07830.03660.7224-0.15280.7483-9.5211-9.60921.2039
40.0513-0.03080.06830.0152-0.05050.17070.1609-0.3983-0.1937-0.1882-0.38110.078-0.12390.2146-00.83330.07040.0460.8894-0.0130.60527.6343-8.101738.0689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 60:153)
2X-RAY DIFFRACTION2(chain A and resid 154:207)
3X-RAY DIFFRACTION3(chain A and resid 208:220)
4X-RAY DIFFRACTION4(chain A and resid 221:276)

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