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- PDB-4e7l: PFV integrase Strand Transfer Complex (STC-Mn*) following reactio... -

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Basic information

Entry
Database: PDB / ID: 4e7l
TitlePFV integrase Strand Transfer Complex (STC-Mn*) following reaction in crystallo, at 3.0 A resolution.
Components
  • DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*G)-3')
  • DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
  • DNA (5'-D(P*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3')
  • Pro-Pol polyprotein
KeywordsRECOMBINATION/DNA / protein-DNA complex / tetramer / HHCC motif / endonuclease / metal-binding / multifunctional enzyme / nuclease / nucleotidyltransferase / nucleus / transferase / virion / DNA-binding / zinc-binding / viral protein / recombination / viral protein-DNA complex / RECOMBINATION-DNA complex
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain ...Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Arc Repressor Mutant, subunit A / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Endonuclease III; domain 1 / SH3 type barrels. - #140 / Helix non-globular / Ribonuclease H-like superfamily/Ribonuclease H / Special / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0001 Å
AuthorsMaertens, G.N. / Cherepanov, P.
CitationJournal: Embo J. / Year: 2012
Title: 3'-Processing and strand transfer catalysed by retroviral integrase in crystallo.
Authors: Hare, S. / Maertens, G.N. / Cherepanov, P.
History
DepositionMar 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Pro-Pol polyprotein
B: Pro-Pol polyprotein
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
t: DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*G)-3')
T: DNA (5'-D(P*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,45211
Polymers109,1266
Non-polymers3265
Water00
1
A: Pro-Pol polyprotein
B: Pro-Pol polyprotein
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
t: DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*G)-3')
T: DNA (5'-D(P*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3')
hetero molecules

A: Pro-Pol polyprotein
B: Pro-Pol polyprotein
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
t: DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*G)-3')
T: DNA (5'-D(P*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,90422
Polymers218,25112
Non-polymers65310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area29550 Å2
ΔGint-144 kcal/mol
Surface area54260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.078, 159.078, 126.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pro-Pol polyprotein / Pr125Pol / Protease/Reverse transcriptase/ribonuclease H / p87Pro-RT-RNaseH / Protease/Reverse ...Pr125Pol / Protease/Reverse transcriptase/ribonuclease H / p87Pro-RT-RNaseH / Protease/Reverse transcriptase / p65Pro-RT / Ribonuclease H / RNase H / Integrase / IN / p42In


Mass: 44456.695 Da / Num. of mol.: 2 / Fragment: UNP Residues 752-1143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Strain: HSRV2 / Gene: pol / Plasmid: pSSH6P-PFV-INFL / Production host: Escherichia coli (E. coli) / Strain (production host): PC2
References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases

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DNA chain , 4 types, 4 molecules CDtT

#2: DNA chain DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')


Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')


Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others)
#4: DNA chain DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*G)-3')


Mass: 3977.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others)
#5: DNA chain DNA (5'-D(P*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3')


Mass: 5204.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic DNA (others)

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Non-polymers , 3 types, 5 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.68 Å3/Da / Density % sol: 66.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 34% PEG-400, 180MM LI2SO4,2.5MM EDTA, 100MM TRIS-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 32641 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OS0

3os0


Resolution: 3.0001→37.947 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1625 4.98 %RANDOM
Rwork0.2281 ---
obs0.2299 32612 98.47 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.179 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.2164 Å20 Å2-0 Å2
2--10.2164 Å2-0 Å2
3----20.4329 Å2
Refinement stepCycle: LAST / Resolution: 3.0001→37.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 1065 9 0 5236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085481
X-RAY DIFFRACTIONf_angle_d1.2777703
X-RAY DIFFRACTIONf_dihedral_angle_d19.552081
X-RAY DIFFRACTIONf_chiral_restr0.07874
X-RAY DIFFRACTIONf_plane_restr0.006796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.08830.2971150.29392513X-RAY DIFFRACTION97
3.0883-3.18790.34721220.30712559X-RAY DIFFRACTION98
3.1879-3.30180.38151290.28622533X-RAY DIFFRACTION99
3.3018-3.43390.27821450.25852520X-RAY DIFFRACTION98
3.4339-3.59010.331360.26042551X-RAY DIFFRACTION99
3.5901-3.77920.31061200.23892582X-RAY DIFFRACTION99
3.7792-4.01580.25891400.22152559X-RAY DIFFRACTION99
4.0158-4.32540.23981600.19542560X-RAY DIFFRACTION99
4.3254-4.760.22381460.18632570X-RAY DIFFRACTION99
4.76-5.4470.2321500.19982605X-RAY DIFFRACTION99
5.447-6.8560.25581200.2212671X-RAY DIFFRACTION99
6.856-37.95030.23111420.22342764X-RAY DIFFRACTION98

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