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- PDB-4bac: prototype foamy virus strand transfer complexes on product DNA -

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Basic information

Entry
Database: PDB / ID: 4bac
Titleprototype foamy virus strand transfer complexes on product DNA
Components
  • 5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3'
  • 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3'
  • DNA (38-MER)
  • INTEGRASE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / 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 ...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 / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Special / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase domain 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 CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.263 Å
AuthorsYin, Z. / Lapkouski, M. / Yang, W. / Craigie, R.
CitationJournal: Protein Sci. / Year: 2012
Title: Assembly of Prototype Foamy Virus Strand Transfer Complexes on Product DNA Bypassing Catalysis of Integration.
Authors: Yin, Z. / Lapkouski, M. / Yang, W. / Craigie, R.
History
DepositionSep 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references / Other / Structure summary
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_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: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3'
D: DNA (38-MER)
E: 5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1418
Polymers112,0275
Non-polymers1143
Water543
1
A: INTEGRASE
B: INTEGRASE
C: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3'
D: DNA (38-MER)
E: 5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3'
hetero molecules

A: INTEGRASE
B: INTEGRASE
C: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*TP*GP*TP*AP)-3'
D: DNA (38-MER)
E: 5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,28116
Polymers224,05310
Non-polymers2286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area31220 Å2
ΔGint-200.4 kcal/mol
Surface area64960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.617, 160.617, 125.092
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 INTEGRASE / / IN / P42IN


Mass: 44658.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN SPUMARETROVIRUS / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H

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DNA chain , 3 types, 3 molecules CDE

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


Mass: 5864.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain DNA (38-MER)


Mass: 11573.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*AP*GP*GP*AP*GP*CP*CP*AP*AP*GP*AP*CP*GP*GP *AP*TP*CP)-3'


Mass: 5270.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 6 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.88 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: CRYSTALS WERE GROWN THROUGH REVERSE VAPOR DIFFUSION IN HANGING DROPS AT 23 C BY MIXING 1 UL IN-DNA COMPLEX SOLUTION (20 MM HEPES, PH 7.5, 500 MM NACL, 5 MM MGCL2, 2 MM TCEP AND 8% (W/V) ...Details: CRYSTALS WERE GROWN THROUGH REVERSE VAPOR DIFFUSION IN HANGING DROPS AT 23 C BY MIXING 1 UL IN-DNA COMPLEX SOLUTION (20 MM HEPES, PH 7.5, 500 MM NACL, 5 MM MGCL2, 2 MM TCEP AND 8% (W/V) GLYCEROL) WITH 1 UL RESERVOIR SOLUTION (50 MM NA CACODYLATE, PH 6.5, 100 MM MGCL2, 1 MM COCL3 AND 6% (V/V) ETHANOL).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: DOUBLE CRYSTAL - SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.26→30 Å / Num. obs: 25740 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 75.3 Å2 / Rsym value: 0.11 / Net I/σ(I): 14.6
Reflection shellResolution: 3.26→3.32 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L2R

3l2r


Resolution: 3.263→29.141 Å / SU ML: 0.34 / σ(F): 0.13 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 1223 5.1 %
Rwork0.1847 --
obs0.1868 24101 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.773 Å2 / ksol: 0.257 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.9139 Å20 Å20 Å2
2--9.9139 Å20 Å2
3----19.8278 Å2
Refinement stepCycle: LAST / Resolution: 3.263→29.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 1305 3 3 5689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095960
X-RAY DIFFRACTIONf_angle_d1.3138390
X-RAY DIFFRACTIONf_dihedral_angle_d21.722298
X-RAY DIFFRACTIONf_chiral_restr0.073951
X-RAY DIFFRACTIONf_plane_restr0.007847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2626-3.3930.35551310.29352306X-RAY DIFFRACTION86
3.393-3.54720.28091150.24272365X-RAY DIFFRACTION88
3.5472-3.73390.28171300.21492447X-RAY DIFFRACTION91
3.7339-3.96730.26721320.19912477X-RAY DIFFRACTION91
3.9673-4.27270.18651610.16372540X-RAY DIFFRACTION95
4.2727-4.70110.18811320.13832637X-RAY DIFFRACTION96
4.7011-5.37760.17711430.14772644X-RAY DIFFRACTION96
5.3776-6.76130.19931420.16552691X-RAY DIFFRACTION96
6.7613-29.14260.20891370.17022771X-RAY DIFFRACTION95

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