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

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Basic information

Entry
Database: PDB / ID: 7ksf
TitleCrystal structure of Prototype Foamy Virus Protease-Reverse Transcriptase (native)
ComponentsProtease/Reverse transcriptase/ribonuclease H
KeywordsVIRAL PROTEIN / Aspartyl protease / Hydrolase / Multifunctional enzyme / Transferase / reverse transcription / viral maturation
Function / homology
Function and homology information


ribonuclease H / DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity ...ribonuclease H / DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / host cell cytoplasm / host cell nucleus / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Foamy virus protease (FV PR) domain profile. / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease A9 / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Integrase zinc binding domain / Integrase zinc-binding domain / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H ...Foamy virus protease (FV PR) domain profile. / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease A9 / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Integrase zinc binding domain / Integrase zinc-binding domain / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H / Integrase core domain / Integrase catalytic domain profile. / Integrase, catalytic core / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / RNase H type-1 domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesEastern chimpanzee simian foamy virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: Protease/Reverse transcriptase/ribonuclease H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2132
Polymers85,1731
Non-polymers401
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)228.210, 52.540, 75.430
Angle α, β, γ (deg.)90.000, 90.090, 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 Protease/Reverse transcriptase/ribonuclease H / Pro-Pol polyprotein / Ribonuclease H / p42In / p65Pro-RT / p87Pro-RT-RNaseH


Mass: 85173.031 Da / Num. of mol.: 1 / Mutation: D26A
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.: 8 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.97601 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97601 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 19435 / % possible obs: 96.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 92.105 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.089 / Rrim(I) all: 0.157 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.532 / Mean I/σ(I) obs: 1 / Num. unique obs: 2867 / CC1/2: 0.334 / Rpim(I) all: 1.089 / Rrim(I) all: 1.888 / % possible all: 88.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KSE
Resolution: 2.9→50 Å / Cross valid method: FREE R-VALUE / σ(F): 43.83 / Phase error: 47.7899
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2572 992 5.11 %
Rwork0.2253 18432 -
obs0.2439 19424 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.42 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5901 0 1 8 5910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456051
X-RAY DIFFRACTIONf_angle_d0.71418243
X-RAY DIFFRACTIONf_chiral_restr0.047934
X-RAY DIFFRACTIONf_plane_restr0.00431047
X-RAY DIFFRACTIONf_dihedral_angle_d12.37312262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.050.35051170.3362389X-RAY DIFFRACTION84.15
3.05-3.240.41161170.34742481X-RAY DIFFRACTION86.9
3.24-3.490.36321360.33482621X-RAY DIFFRACTION91.42
3.49-3.850.35651420.30982669X-RAY DIFFRACTION93.13
3.85-4.40.32211420.26262737X-RAY DIFFRACTION94.74
4.4-5.550.26461620.21892718X-RAY DIFFRACTION94.28
5.55-500.18761550.17742838X-RAY DIFFRACTION94.32

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