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- PDB-1p7n: Dimeric Rous Sarcoma virus Capsid protein structure with an upstr... -

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Basic information

Entry
Database: PDB / ID: 1p7n
TitleDimeric Rous Sarcoma virus Capsid protein structure with an upstream 25-amino acid residue extension of C-terminal of Gag p10 protein
ComponentsGAG POLYPROTEIN CAPSID PROTEIN P27
KeywordsVIRAL PROTEIN / Retrovirus / capsid protein / Gag Polyprotein / immature gag
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 / structural constituent of virion / nucleic acid binding / 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 / structural constituent of virion / nucleic acid binding / aspartic-type endopeptidase activity / viral translational frameshifting / host cell plasma membrane / proteolysis / zinc ion binding / membrane
Similarity search - Function
Retroviral Gag polyprotein, M / Retroviral M domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / 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 / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / 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: 2.6 Å
AuthorsNandhagopal, N. / Simpson, A.A. / Johnson, M.C. / Francisco, A.B. / Schatz, G.W. / Rossmann, M.G. / Vogt, V.M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Dimeric rous sarcoma virus capsid protein structure relevant to immature gag assembly
Authors: Nandhagopal, N. / Simpson, A.A. / Johnson, M.C. / Francisco, A.B. / Schatz, G.W. / Rossmann, M.G. / Vogt, V.M.
History
DepositionMay 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE The protein sequence contains the N-terminal domain of capsid protein P27 with an upstream ...SEQUENCE The protein sequence contains the N-terminal domain of capsid protein P27 with an upstream 25-amino acid extension C-terminal of GAG P10 PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAG POLYPROTEIN CAPSID PROTEIN P27


Theoretical massNumber of molelcules
Total (without water)18,7371
Polymers18,7371
Non-polymers00
Water00
1
A: GAG POLYPROTEIN CAPSID PROTEIN P27

A: GAG POLYPROTEIN CAPSID PROTEIN P27


Theoretical massNumber of molelcules
Total (without water)37,4732
Polymers37,4732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area3960 Å2
ΔGint-34 kcal/mol
Surface area17570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.870, 47.870, 170.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GAG POLYPROTEIN CAPSID PROTEIN P27


Mass: 18736.674 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03322

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM HEPES-sodium buffer and 0.8M potassium sodium tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
325 mM1dropNaCl
40.1 Msodium HEPES1reservoirpH7.5
50.8 Mpotassium sodium tartrate tetrahydrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 7911 / Num. obs: 6743 / % possible obs: 85.2 % / Redundancy: 8.3 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.329 / Num. unique all: 396 / % possible all: 51.4
Reflection
*PLUS
Redundancy: 3.18 %
Reflection shell
*PLUS
% possible obs: 51.4 % / Redundancy: 1.4 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EM9

1em9


Resolution: 2.6→26.5 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 558128.82 / Data cutoff high rms absF: 558128.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 331 5.7 %RANDOM
Rwork0.26 ---
obs0.26 5856 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5603 Å2 / ksol: 0.303224 e/Å3
Displacement parametersBiso mean: 56.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.81 Å20 Å20 Å2
2--10.17 Å20 Å2
3----20.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 0 0 1315
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it3.022
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 33 6 %
Rwork0.343 521 -
obs--52.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Highest resolution: 2.6 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.11
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.32
LS refinement shell
*PLUS
Rfactor Rfree: 0.366 / Rfactor Rwork: 0.337

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