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- PDB-3tir: Pseudo-atomic model of the Rous Sarcoma Virus capsid hexamer -

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Basic information

Entry
Database: PDB / ID: 3tir
TitlePseudo-atomic model of the Rous Sarcoma Virus capsid hexamer
ComponentsRous Sarcoma Virus Capsid Protein p27
KeywordsVIRAL PROTEIN / viral capsid protein
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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 speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsBailey, G.B. / Hyun, J.K. / Mitra, A.K. / Kingston, R.L.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: A structural model for the generation of continuous curvature on the surface of a retroviral capsid.
Authors: Bailey, G.D. / Hyun, J.K. / Mitra, A.K. / Kingston, R.L.
History
DepositionAug 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rous Sarcoma Virus Capsid Protein p27


Theoretical massNumber of molelcules
Total (without water)24,4721
Polymers24,4721
Non-polymers00
Water00
1
A: Rous Sarcoma Virus Capsid Protein p27
x 6


Theoretical massNumber of molelcules
Total (without water)146,8336
Polymers146,8336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area11340 Å2
ΔGint-69 kcal/mol
Surface area63550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.559, 92.559, 49.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Rous Sarcoma Virus Capsid Protein p27 / Capsid protein p27


Mass: 24472.230 Da / Num. of mol.: 1 / Fragment: UNP resides 240-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Strain: Prague C / Gene: CA, gag-pro-pol / Plasmid: pTXB1 [NEB] / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta(DE3) / References: UniProt: P03354

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 291.15 K / pH: 10.3
Details: 2-7 %(w/v) PEG 8000 0.2M CAPS/KOH, pH 10.3, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2009 / Details: RIGAKU VARIMAX HF CONFOCAL
RadiationMonochromator: RIGAKU VARIMAX HF CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 4.1→34 Å / Num. obs: 1996 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 5.6
Reflection shellResolution: 4.1→4.22 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1EM9 AND 3G1I.

1em9

3g1i


Resolution: 4.1→33.96 Å / Cor.coef. Fo:Fc: 0.795 / Cor.coef. Fo:Fc free: 0.804 / SU B: 340.734 / SU ML: 1.853
Isotropic thermal model: Rigid-Body refinement using the TLS model.
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.559 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.391 117 5.9 %RANDOM
Rwork0.394 ---
all-1996 --
obs-1879 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 185.01 Å2
Baniso -1Baniso -2Baniso -3
1--11.63 Å2-5.82 Å20 Å2
2---11.63 Å20 Å2
3---17.45 Å2
Refinement stepCycle: LAST / Resolution: 4.1→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 0 0 1694
LS refinement shellResolution: 4.1→4.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 10 -
Rwork0.451 144 -
obs--100 %
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)
110.1813.58480.92097.2811-2.864516.2043-0.62711.29290.144-1.3421-0.1927-2.15930.3916-0.32640.81981.20160.2590.35361.46120.02761.7538-1.266725.77178.8726
216.014710.6232-10.715370.0258-12.93827.7530.6961-2.4521-0.54950.913-1.6118-5.8341-0.29721.41610.91571.496-0.5962-0.16031.8180.12610.753728.208430.049628.7197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 147
2X-RAY DIFFRACTION2A152 - 226

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