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- PDB-7kse: Crystal structure of Prototype Foamy Virus Protease-Reverse Trans... -

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Basic information

Entry
Database: PDB / ID: 7kse
TitleCrystal structure of Prototype Foamy Virus Protease-Reverse Transcriptase CSH mutant (selenomethionine-labeled)
ComponentsPeptidase A9/Reverse transcriptase/RNase H
KeywordsVIRAL PROTEIN / Aspartyl protease / Hydrolase / Multifunctional enzyme / Transferase / reverse transcription / viral maturation
Function / homology
Function and homology information


DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / proteolysis / RNA binding ...DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / proteolysis / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
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 / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H ...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 / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / 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 speciesEastern chimpanzee simian foamy virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsHarrison, J.J.E.K. / Das, K. / Ruiz, F.X. / Arnold, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM103368 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI027690 United States
CitationJournal: Viruses / Year: 2021
Title: Crystal Structure of a Retroviral Polyprotein: Prototype Foamy Virus Protease-Reverse Transcriptase (PR-RT).
Authors: Harrison, J.J.E.K. / Tuske, S. / Das, K. / Ruiz, F.X. / Bauman, J.D. / Boyer, P.L. / DeStefano, J.J. / Hughes, S.H. / Arnold, E.
History
DepositionNov 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase A9/Reverse transcriptase/RNase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8262
Polymers85,7861
Non-polymers401
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)240.375, 53.352, 74.922
Angle α, β, γ (deg.)90.000, 100.000, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Peptidase A9/Reverse transcriptase/RNase H / Pro-Pol polyprotein / Protease/Reverse transcriptase / Protease/Reverse transcriptase/ribonuclease ...Pro-Pol polyprotein / Protease/Reverse transcriptase / Protease/Reverse transcriptase/ribonuclease H / Ribonuclease H / p42In / p65Pro-RT / p87Pro-RT-RNaseH


Mass: 85785.664 Da / Num. of mol.: 1 / Mutation: D26A, C282S, H509D, S586K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern chimpanzee simian foamy virus / Gene: gag / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1Q1N9V8, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 57.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM KCl, 50 mM sodium cacodylate trihydrate pH 6.0, 12% PEG 8000, 1.0 mM spermine, 1.0 mM L-argininamide, 200 mM glycyglycine or glycylglycylglycine, 100 mM CaCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.97601
SYNCHROTRONSSRL BL9-220.97852
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 19, 2016
DECTRIS PILATUS 6M2PIXELMar 13, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.976011
20.978521
ReflectionResolution: 3→50 Å / Num. obs: 19100 / % possible obs: 99.7 % / Redundancy: 30.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.331 / Rpim(I) all: 0.061 / Rrim(I) all: 0.337 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.18 Å / Redundancy: 29.7 % / Rmerge(I) obs: 1.973 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2990 / CC1/2: 0.818 / Rpim(I) all: 0.367 / Rrim(I) all: 2.007 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3→50 Å / Cross valid method: FREE R-VALUE / σ(F): 351.39 / Phase error: 37.4882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3131 1086 5.69 %
Rwork0.278 17984 -
obs0.2909 19070 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.34 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 1 11 5908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00696045
X-RAY DIFFRACTIONf_angle_d1.38568236
X-RAY DIFFRACTIONf_chiral_restr0.0808934
X-RAY DIFFRACTIONf_plane_restr0.01161047
X-RAY DIFFRACTIONf_dihedral_angle_d14.93162260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.42391350.39082536X-RAY DIFFRACTION93.93
3.16-3.360.38971330.3632536X-RAY DIFFRACTION94.98
3.36-3.620.35411310.34352588X-RAY DIFFRACTION95.15
3.62-3.980.36641500.32162550X-RAY DIFFRACTION94.24
3.98-4.550.2981460.27552589X-RAY DIFFRACTION94.63
4.55-5.740.35281280.26172618X-RAY DIFFRACTION95.3
5.74-500.27041520.24482678X-RAY DIFFRACTION94.53

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