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- PDB-3pdm: Hibiscus Latent Singapore virus -

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Basic information

Entry
Database: PDB / ID: 3pdm
TitleHibiscus Latent Singapore virus
Components
  • Coat protein
  • RNA (5'-R(P*GP*AP*A)-3')
KeywordsVIRUS / HELICAL VIRUS / VIRUS-RNA COMPLEX
Function / homology
Function and homology information


helical viral capsid / structural molecule activity
Similarity search - Function
Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / Capsid protein
Similarity search - Component
Biological speciesHibiscus latent Singapore virus
MethodFIBER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTewary, S.K. / Wong, S.M. / Swaminathan, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of Hibiscus latent Singapore virus by fiber diffraction: A non-conserved His122 contributes to coat protein stability
Authors: Tewary, S.K. / Oda, T. / Kendall, A. / Bian, W. / Stubbs, G. / Wong, S.M. / Swaminathan, K.
History
DepositionOct 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA (5'-R(P*GP*AP*A)-3')
P: Coat protein


Theoretical massNumber of molelcules
Total (without water)19,0382
Polymers19,0382
Non-polymers00
Water0
1
R: RNA (5'-R(P*GP*AP*A)-3')
P: Coat protein
x 49


Theoretical massNumber of molelcules
Total (without water)932,85998
Polymers932,85998
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation48
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)1.000, 1.000, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 49 / Rise per n subunits: 1.439 Å / Rotation per n subunits: 22.041 °)
DetailsHLSV IS A ROD-SHAPED VIRUS 3000 ANGSTROMS LONG AND 180 ANGSTROMS IN DIAMETER, WITH A CENTRAL HOLE OF DIAMETER 40 ANGSTROMS. APPROXIMATELY 2150 IDENTICAL PROTEIN SUBUNITS OF MOLECULAR WEIGHT 17500 FORM A RIGHT-HANDED HELIX OF PITCH 23.5 ANGSTROMS AND LENGTH 70.5 ANGTROMS WITH 49 SUBUNITS IN THREE TURNS. A SINGLE STRAND OF RNA FOLLOWS THE BASIC HELIX BETWEEN THE PROTEIN SUBUNITS AT A DISTANCE OF 40 ANGSTROMS. THERE ARE THREE NUCLEOTIDES BOUND TO EACH PROTEIN SUBUNIT. THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = 1080.00/49 DEGREES RISE PER SUBUNIT (HEIGHT) = 70.5/49 ANGSTROMS COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.

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Components

#1: RNA chain RNA (5'-R(P*GP*AP*A)-3')


Mass: 958.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic RNA
#2: Protein Coat protein


Mass: 18079.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hibiscus latent Singapore virus / References: UniProt: Q8BE68

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growMethod: oriented sol / Details: Oriented sol

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 3486 / Num. obs: 3486 / % possible obs: 100 % / Observed criterion σ(F): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
X-PLORmodel building
X-PLORrefinement
WCENdata reduction
RADdata reduction
CORRdata reduction
WCENdata scaling
RADdata scaling
CORRdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS DETERMINED BY FIBER DIFFRACTION USING MOLECULAR REPLACEMENT WITH LAYER-LINE SPLITTING, SOLVENT FLATTENING REFINEMENT AND RESTRAINED LEAST SQUARES COORDINATE REFINEMENT. THE ...Details: THE STRUCTURE WAS DETERMINED BY FIBER DIFFRACTION USING MOLECULAR REPLACEMENT WITH LAYER-LINE SPLITTING, SOLVENT FLATTENING REFINEMENT AND RESTRAINED LEAST SQUARES COORDINATE REFINEMENT. THE STRUCTURE INCLUDES 162 OF THE 163 AMINO ACIDS AND THREE RNA NUCLEOTIDES MODELLED AS GAA BUT REPRESENTING THE ENTIRE NUCLEIC ACID CONTENT.
RfactorNum. reflection
Rwork0.096 -
obs0.096 3486
all-3486
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 64 0 0 1341

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