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- PDB-3g1g: Crystal structure of the C-terminal domain from the Rous Sarcoma ... -

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Basic information

Entry
Database: PDB / ID: 3g1g
TitleCrystal structure of the C-terminal domain from the Rous Sarcoma Virus capsid protein: High 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 / nucleic acid binding / structural constituent of virion / aspartic-type endopeptidase activity / 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 / nucleic acid binding / structural constituent of virion / aspartic-type endopeptidase activity / viral translational frameshifting / host cell plasma membrane / proteolysis / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Retroviral Gag polyprotein, M / Retroviral M 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 ...Retrovirus capsid C-terminal domain / Retroviral Gag polyprotein, M / Retroviral M 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
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 29, 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 / 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: Gag polyprotein
B: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)19,0022
Polymers19,0022
Non-polymers00
Water1,09961
1
A: Gag polyprotein

B: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)19,0022
Polymers19,0022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
2
B: Gag polyprotein

A: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)19,0022
Polymers19,0022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)46.600, 72.200, 48.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Gag polyprotein / Capsid protein


Mass: 9500.799 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 390-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Strain: Prague C Strain / Gene: gag / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: P03322, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.3
Details: 0.2M Beta-Alanine/KOH, pH10.3, 10-25% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2005
RadiationMonochromator: Double Crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 11209 / Num. obs: 11209 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1101 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EOQ

1eoq


Resolution: 2.01→39.97 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.127 / SU ML: 0.142 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25703 555 5 %RANDOM
Rwork0.21673 ---
all0.21882 10630 --
obs0.21882 10630 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0 Å20 Å2
2--2.55 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.01→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 61 1243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9841648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70924.23152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95515202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6951510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.5769
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71321259
X-RAY DIFFRACTIONr_scbond_it2.5643440
X-RAY DIFFRACTIONr_scangle_it4.0084.5388
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 32 -
Rwork0.254 713 -
obs--91.64 %

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