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- PDB-1ej6: Reovirus core -

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Basic information

Entry
Database: PDB / ID: 1ej6
TitleReovirus core
Components
  • LAMBDA1
  • LAMBDA2
  • SIGMA2
KeywordsVIRUS / icosahedral / non-equivalence / dsRNA virus / methylase / methyltransferase / guanylyltransferase / zinc finger / Icosahedral virus
Function / homology
Function and homology information


icosahedral viral capsid / viral inner capsid / viral outer capsid / 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / RNA helicase ...icosahedral viral capsid / viral inner capsid / viral outer capsid / 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / RNA helicase / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Inner capsid protein lambda-1 / Inner capsid protein lambda-1 / Helix Hairpins - #1520 / Reovirus core / Reovirus components fold / Reovirus components / Reovirus components fold / Reovirus components / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family ...Inner capsid protein lambda-1 / Inner capsid protein lambda-1 / Helix Hairpins - #1520 / Reovirus core / Reovirus components fold / Reovirus components / Reovirus components fold / Reovirus components / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / : / : / : / : / : / : / : / : / Reovirus core-spike protein lambda-2 (L2), 6th domain / Reovirus core-spike protein lambda-2 (L2), 7th domain / Reovirus core-spike protein lambda-2 (L2), ferredoxin-like domain / Reovirus core-spike protein lambda-2 (L2), GTase domain / Reovirus core-spike protein lambda-2 (L2), N-terminal / Reovirus core-spike protein lambda-2 (L2), methyltransferase-1 / Reovirus core-spike protein lambda-2 (L2), methyltransferase-2 / Reovirus core-spike lambda-2 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Inner capsid protein lambda-1/ VP3 / 3-Layer(bab) Sandwich / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Vaccinia Virus protein VP39 / Helix Hairpins / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Inner capsid protein sigma-2 / Outer capsid protein lambda-2 / Inner capsid protein sigma-2 / Inner capsid protein lambda-1
Similarity search - Component
Biological speciesReovirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.6 Å
AuthorsReinisch, K.M. / Nibert, M.L. / Harrison, S.C.
CitationJournal: Nature / Year: 2000
Title: Structure of the reovirus core at 3.6 A resolution.
Authors: Reinisch, K.M. / Nibert, M.L. / Harrison, S.C.
History
DepositionFeb 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: LAMBDA2
B: LAMBDA1
C: LAMBDA1
D: SIGMA2
E: SIGMA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,4916
Polymers522,4265
Non-polymers651
Water0
1
A: LAMBDA2
B: LAMBDA1
C: LAMBDA1
D: SIGMA2
E: SIGMA2
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)31,349,479360
Polymers31,345,554300
Non-polymers3,92560
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: LAMBDA2
B: LAMBDA1
C: LAMBDA1
D: SIGMA2
E: SIGMA2
hetero molecules
x 5


  • icosahedral pentamer
  • 2.61 MDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)2,612,45730
Polymers2,612,13025
Non-polymers3275
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: LAMBDA2
B: LAMBDA1
C: LAMBDA1
D: SIGMA2
E: SIGMA2
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 3.13 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)3,134,94836
Polymers3,134,55530
Non-polymers3926
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: LAMBDA2
B: LAMBDA1
C: LAMBDA1
D: SIGMA2
E: SIGMA2
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 2.61 MDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)2,612,45730
Polymers2,612,13025
Non-polymers3275
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)1255.000, 1255.000, 1255.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.80901699, 0.309017, -0.5), (0.309017, 0.50000001, 0.80901699), (0.5, -0.809017, 0.30901699)119.84184, -193.90817, 313.74998
3generate(0.5, 0.80901699, -0.30901699), (0.809017, -0.30901699, 0.5), (0.30901699, -0.5, -0.809017)1.0E-5, -2.0E-5, 627.49998
4generate(0.5, 0.80901699, 0.309017), (0.809017, -0.309017, -0.49999999), (-0.309017, 0.5, -0.80901699)-193.90815, 313.74997, 507.65816
5generate(0.809017, 0.30901699, 0.5), (0.309017, 0.5, -0.80901699), (-0.50000001, 0.80901699, 0.309017)-193.90816, 313.74999, 119.84185

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Components

#1: Protein LAMBDA2


Mass: 144098.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / Strain: REASSORTANT F18 / References: UniProt: P11079
#2: Protein LAMBDA1


Mass: 142008.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / Strain: REASSORTANT F18 / References: UniProt: P15024
#3: Protein SIGMA2


Mass: 47155.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Reovirus sp. / Strain: REASSORTANT F18 / References: UniProt: P03525, UniProt: P11314*PLUS
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 500

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.5 M1dropNaCl
30-0.3 M1dropNaOAc
450 mM1dropMgCl2
550 mMHEPES1drop
61 M1reservoirNaCl
70-0.6 M1reservoirNaOAc
8100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→65 Å / Num. all: 947106 / Num. obs: 928767 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 2.7
Reflection shellResolution: 3.47→3.71 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.53 / Num. unique all: 132212 / % possible all: 70
Reflection shell
*PLUS
% possible obs: 70 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CCP4model building
RAVEmodel building
CNSrefinement
CCP4(SCALA)data scaling
CCP4phasing
RAVEphasing
RefinementResolution: 3.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: positional refinement, torsion angle dynamics, individual B-factor refinement. strict 5-fold ncs restraints were maintained. NOTE: Portions of the sigma2 positioned on the ...Details: positional refinement, torsion angle dynamics, individual B-factor refinement. strict 5-fold ncs restraints were maintained. NOTE: Portions of the sigma2 positioned on the icosahedral/crystallographic 2-fold axis (for which we do not provide coordinates) were included in the refinement (occupancy 1/2 for each of two possible orientations) but were not refined. No portions at the interface with lambda1 were included.
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 1428 -random
Rwork0.2059 ---
all0.2081 833412 --
obs0.2081 831984 88.5 %-
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34486 0 1 0 34487

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