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- PDB-1uf2: The Atomic Structure of Rice dwarf Virus (RDV) -

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Basic information

Entry
Database: PDB / ID: 1uf2
TitleThe Atomic Structure of Rice dwarf Virus (RDV)
Components
  • Core protein P3
  • Outer capsid protein P8
  • Structural protein P7
KeywordsVIRUS / VIRUS COMPONENTS / Icosahedral virus
Function / homology
Function and homology information


: / viral outer capsid / host cell cytoplasmic vesicle / viral capsid / molecular adaptor activity / host cell cytoplasm / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding
Similarity search - Function
Phytoreovirus outer capsid P8 / Phytoreovirus S7 / Inner layer core protein VP3, Phytoreovirus / Phytoreovirus outer capsid protein P8 / Phytoreovirus S7 protein / Rice dwarf virus p3 / Jelly Rolls - #170 / Inner layer core protein VP3, Reovirus / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein ...Phytoreovirus outer capsid P8 / Phytoreovirus S7 / Inner layer core protein VP3, Phytoreovirus / Phytoreovirus outer capsid protein P8 / Phytoreovirus S7 protein / Rice dwarf virus p3 / Jelly Rolls - #170 / Inner layer core protein VP3, Reovirus / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein P8 / Outer capsid protein P3 / Protein P7
Similarity search - Component
Biological speciesRice dwarf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement Averaging / Resolution: 3.5 Å
AuthorsNakagawa, A. / Miyazaki, N. / Taka, J. / Naitow, H. / Ogawa, A. / Fujimoto, Z. / Mizuno, H. / Higashi, T. / Watanabe, Y. / Omura, T. ...Nakagawa, A. / Miyazaki, N. / Taka, J. / Naitow, H. / Ogawa, A. / Fujimoto, Z. / Mizuno, H. / Higashi, T. / Watanabe, Y. / Omura, T. / Cheng, R.H. / Tsukihara, T.
CitationJournal: Structure / Year: 2003
Title: The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins.
Authors: Nakagawa, A. / Miyazaki, N. / Taka, J. / Naitow, H. / Ogawa, A. / Fujimoto, Z. / Mizuno, H. / Higashi, T. / Watanabe, Y. / Omura, T. / Cheng, R.H. / Tsukihara, T.
History
DepositionMay 23, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core protein P3
B: Core protein P3
P: Outer capsid protein P8
C: Outer capsid protein P8
D: Outer capsid protein P8
Q: Outer capsid protein P8
E: Outer capsid protein P8
F: Outer capsid protein P8
R: Outer capsid protein P8
G: Outer capsid protein P8
H: Outer capsid protein P8
S: Outer capsid protein P8
I: Outer capsid protein P8
J: Outer capsid protein P8
T: Outer capsid protein P8
K: Structural protein P7


Theoretical massNumber of molelcules
Total (without water)889,08416
Polymers889,08416
Non-polymers00
Water00
1
A: Core protein P3
B: Core protein P3
P: Outer capsid protein P8
C: Outer capsid protein P8
D: Outer capsid protein P8
Q: Outer capsid protein P8
E: Outer capsid protein P8
F: Outer capsid protein P8
R: Outer capsid protein P8
G: Outer capsid protein P8
H: Outer capsid protein P8
S: Outer capsid protein P8
I: Outer capsid protein P8
J: Outer capsid protein P8
T: Outer capsid protein P8
K: Structural protein P7
x 60


Theoretical massNumber of molelcules
Total (without water)53,345,053960
Polymers53,345,053960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Core protein P3
B: Core protein P3
P: Outer capsid protein P8
C: Outer capsid protein P8
D: Outer capsid protein P8
Q: Outer capsid protein P8
E: Outer capsid protein P8
F: Outer capsid protein P8
R: Outer capsid protein P8
G: Outer capsid protein P8
H: Outer capsid protein P8
S: Outer capsid protein P8
I: Outer capsid protein P8
J: Outer capsid protein P8
T: Outer capsid protein P8
K: Structural protein P7
x 5


  • icosahedral pentamer
  • 4.45 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)4,445,42180
Polymers4,445,42180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Core protein P3
B: Core protein P3
P: Outer capsid protein P8
C: Outer capsid protein P8
D: Outer capsid protein P8
Q: Outer capsid protein P8
E: Outer capsid protein P8
F: Outer capsid protein P8
R: Outer capsid protein P8
G: Outer capsid protein P8
H: Outer capsid protein P8
S: Outer capsid protein P8
I: Outer capsid protein P8
J: Outer capsid protein P8
T: Outer capsid protein P8
K: Structural protein P7
x 6


  • icosahedral 23 hexamer
  • 5.33 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)5,334,50596
Polymers5,334,50596
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Core protein P3
B: Core protein P3
P: Outer capsid protein P8
C: Outer capsid protein P8
D: Outer capsid protein P8
Q: Outer capsid protein P8
E: Outer capsid protein P8
F: Outer capsid protein P8
R: Outer capsid protein P8
G: Outer capsid protein P8
H: Outer capsid protein P8
S: Outer capsid protein P8
I: Outer capsid protein P8
J: Outer capsid protein P8
T: Outer capsid protein P8
K: Structural protein P7
x 15


  • crystal asymmetric unit, crystal frame
  • 13.3 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)13,336,263240
Polymers13,336,263240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)770.000, 795.000, 814.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699)
3generate(-0.30901699, -0.80901699, -0.5), (-0.80901699, 0.5, -0.30901699), (0.5, 0.30901699, -0.80901699)
4generate(-0.30901699, -0.80901699, 0.5), (-0.80901699, 0.5, 0.30901699), (-0.5, -0.30901699, -0.80901699)
5generate(0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699)
6generate(0.30901699, -0.80901699, -0.5), (-0.80901699, -0.5, 0.30901699), (-0.5, 0.30901699, -0.80901699)
7generate(-1), (1), (-1)
8generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
9generate(0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5)
10generate(0.80901699, -0.5, -0.30901699), (-0.5, -0.30901699, -0.80901699), (0.30901699, 0.80901699, -0.5)
11generate(0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.80901699), (0.30901699, -0.80901699, -0.5)
12generate(-1), (1), (-1)
13generate(-0.80901699, -0.5, -0.30901699), (0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5)
14generate(-0.5, -0.30901699, 0.80901699), (-0.30901699, -0.80901699, -0.5), (0.80901699, -0.5, 0.30901699)
15generate(0.5, 0.30901699, 0.80901699), (-0.30901699, -0.80901699, 0.5), (0.80901699, -0.5, -0.30901699)

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Components

#1: Protein Core protein P3 / Core capsid protein


Mass: 114400.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Virus particle / Source: (natural) Rice dwarf virus / Genus: Phytoreovirus / Strain: O strain / References: UniProt: P22472
#2: Protein
Outer capsid protein P8 / Outer shell capsid protein


Mass: 46528.781 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Details: Virus particle / Source: (natural) Rice dwarf virus / Genus: Phytoreovirus / Strain: O strain / References: UniProt: P17379
#3: Protein Structural protein P7 / putative RNA-binding protein


Mass: 55409.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Virus particle / Source: (natural) Rice dwarf virus / Genus: Phytoreovirus / Strain: O strain / References: UniProt: P22473

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 86

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: His-Mg buffer, MgCl2, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Mizuno, H., (1991) J. Mol. Biol., 219, 665.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12851
22851
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-6B21
Detector
TypeIDDetectorDateDetails
WEISSENBERG1DIFFRACTOMETEROct 14, 1998Fused quartz mirror
WEISSENBERG2DIFFRACTOMETEROct 23, 1998Pt-coated quartz mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) asymmetrical cut monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) rotated-inclined monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→230 Å / Num. all: 3072898 / Num. obs: 3072898 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.186 / Net I/σ(I): 3.1
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 0.9 / Rsym value: 0.783 / % possible all: 91.5
Reflection
*PLUS
Num. obs: 3001937 / Num. measured all: 17806888

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
RAVEmodel building
CCP4model building
other jiffy programsmodel building
CNS1.1refinement
CCP4(SCALA)data scaling
RAVEphasing
CCP4phasing
RefinementMethod to determine structure: Molecular Replacement Averaging
Starting model: Cryo-electronmicrograph

Resolution: 3.5→228.74 Å / Rfactor Rfree error: 0.001 / Isotropic thermal model: Individual / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.306 138283 5 %random
Rwork0.303 ---
all0.303 3072895 --
obs0.303 2772912 90.1 %-
Solvent computationSolvent model: flat model / Bsol: 89.8 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.85 Å
Refinement stepCycle: LAST / Resolution: 3.5→228.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58130 0 0 0 58130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it3.192.5
Refine LS restraints NCSNCS model details: constraint
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 18986 4.9 %
Rwork0.388 365391 -
obs-365391 75.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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