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- PDB-3g21: Crystal structure of the C-terminal domain of the Rous Sarcoma Vi... -

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Basic information

Entry
Database: PDB / ID: 3g21
TitleCrystal structure of the C-terminal domain of the Rous Sarcoma Virus capsid protein: Low pH
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / ALPHA-HELICAL BUNDLE / CAPSID PROTEIN / VIRION / RETROVIRUS
Function / homology
Function and homology information


host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / aspartic-type endopeptidase activity / structural constituent of virion / nucleic acid binding / viral translational frameshifting / host cell plasma membrane ...host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / aspartic-type endopeptidase activity / structural constituent of virion / nucleic acid binding / viral translational frameshifting / host cell plasma membrane / proteolysis / zinc ion binding / membrane
Similarity search - Function
Retroviral Gag polyprotein, M / Retroviral M domain / Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease ...Retroviral Gag polyprotein, M / Retroviral M domain / Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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. / Aspartic peptidase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Gag polyprotein
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsKingston, R.L.
CitationJournal: Structure / Year: 2009
Title: Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly
Authors: Bailey, G.D. / Hyun, J.K. / Mitra, A.K. / Kingston, R.L.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5372
Polymers8,4751
Non-polymers621
Water1,49583
1
A: Gag polyprotein
hetero molecules

A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0734
Polymers16,9492
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1480 Å2
ΔGint-2 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.179, 32.179, 113.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Gag polyprotein / Capsid protein


Mass: 8474.636 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 389-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Strain: Prague C Strain / Gene: gag / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: P03322, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 0.20M Succinic acid/KOH, pH4.3, 13-18% PEG8000, 0.75M Magnesium Nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.85503 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 28, 2008
RadiationMonochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85503 Å / Relative weight: 1
ReflectionResolution: 0.9→27 Å / Num. all: 46299 / Num. obs: 46299 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 36.2
Reflection shellResolution: 0.9→0.93 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 7.2 / Num. unique all: 1546 / % possible all: 30

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Processing

Software
NameClassification
Blu-Icedata collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G1G

3g1g


Resolution: 0.9→27 Å / Num. parameters: 7348 / Num. restraintsaints: 10719
Isotropic thermal model: Restrained Anisotropic Thermal Parameters
Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.142 2306 -RANDOM
Rwork0.124 ---
obs0.124 43916 84.6 %-
all-43916 --
Solvent computationSolvent model: Moews and Kretsinger (Babinet scaling)
Refine analyzeNum. disordered residues: 42 / Occupancy sum hydrogen: 583.31 / Occupancy sum non hydrogen: 669.09
Refinement stepCycle: LAST / Resolution: 0.9→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 4 101 812
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0252
X-RAY DIFFRACTIONs_zero_chiral_vol0.114
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.164
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.078

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