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- PDB-2cse: Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electro... -

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Basic information

Entry
Database: PDB / ID: 2cse
TitleFeatures of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution
Components
  • Minor core protein lambda 3
  • Sigma 2 protein
  • guanylyltransferase
  • major capsid surface protein sigma-3
  • major core protein lambda 1
  • major outer-capsid protein mu1
KeywordsVIRUS / cryoEM / image processing / reovirus / membrane penetration protein / Icosahedral virus
Function / homology
Function and homology information


icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / 7-methylguanosine mRNA capping ...icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / 7-methylguanosine mRNA capping / host cell mitochondrion / viral life cycle / viral genome replication / viral capsid / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / RNA helicase / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / structural molecule activity / GTP binding / host cell plasma membrane / ATP hydrolysis activity / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Mu1 membrane penetration protein, domain I / Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) ...Mu1 membrane penetration protein, domain I / Reovirus, outer capsid sigma 3 / Reovirus, outer capsid sigma-3 domain superfamily / Reovirus outer capsid protein, Sigma 3 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / 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 RNA-dependent RNA polymerase lambda 3 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Reovirus RNA-dependent RNA polymerase lambda 3 / Inner capsid protein lambda-1/ VP3 / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer capsid protein sigma-3 / RNA-directed RNA polymerase lambda-3 / Outer capsid protein mu-1 / Outer capsid protein lambda-2 / Inner capsid protein sigma-2 / RNA-directed RNA polymerase lambda-3 / Inner capsid protein lambda-1
Similarity search - Component
Biological speciesMammalian orthoreovirus 1
Mammalian orthoreovirus 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsZhang, X. / Ji, Y. / Zhang, L. / Harrison, S.C. / Marinescu, D.C. / Nibert, M.L. / Baker, T.S.
CitationJournal: Structure / Year: 2005
Title: Features of reovirus outer capsid protein mu1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Angstrom resolution.
Authors: Xing Zhang / Yongchang Ji / Lan Zhang / Stephen C Harrison / Dan C Marinescu / Max L Nibert / Timothy S Baker /
Abstract: Reovirus is a useful model for addressing the molecular basis of membrane penetration by one of the larger nonenveloped animal viruses. We now report the structure of the reovirus virion at ...Reovirus is a useful model for addressing the molecular basis of membrane penetration by one of the larger nonenveloped animal viruses. We now report the structure of the reovirus virion at approximately 7.0 A resolution as obtained by electron cryomicroscopy and three-dimensional image reconstruction. Several features of the myristoylated outer capsid protein mu1, not seen in a previous X-ray crystal structure of the mu1-sigma3 heterohexamer, are evident in the virion. These features appear to be important for stabilizing the outer capsid, regulating the conformational changes in mu1 that accompany perforation of target membranes, and contributing directly to membrane penetration during cell entry.
History
DepositionMay 21, 2005Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Other / Category: atom_sites / cell / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_a / _cell.length_b / _cell.length_c / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: major outer-capsid protein mu1
B: major outer-capsid protein mu1
C: major outer-capsid protein mu1
S: major capsid surface protein sigma-3
D: major capsid surface protein sigma-3
E: major capsid surface protein sigma-3
F: major capsid surface protein sigma-3
M: major capsid surface protein sigma-3
N: major capsid surface protein sigma-3
O: major capsid surface protein sigma-3
G: major capsid surface protein sigma-3
H: major capsid surface protein sigma-3
I: major capsid surface protein sigma-3
P: major outer-capsid protein mu1
Q: major outer-capsid protein mu1
R: major outer-capsid protein mu1
J: major outer-capsid protein mu1
K: major outer-capsid protein mu1
L: major outer-capsid protein mu1
T: major outer-capsid protein mu1
U: guanylyltransferase
V: major core protein lambda 1
W: major core protein lambda 1
X: Sigma 2 protein
Y: Sigma 2 protein
Z: Sigma 2 protein
1: Minor core protein lambda 3


Theoretical massNumber of molelcules
Total (without water)1,887,92627
Polymers1,887,92627
Non-polymers00
Water0
1
A: major outer-capsid protein mu1
B: major outer-capsid protein mu1
C: major outer-capsid protein mu1
S: major capsid surface protein sigma-3
D: major capsid surface protein sigma-3
E: major capsid surface protein sigma-3
F: major capsid surface protein sigma-3
M: major capsid surface protein sigma-3
N: major capsid surface protein sigma-3
O: major capsid surface protein sigma-3
G: major capsid surface protein sigma-3
H: major capsid surface protein sigma-3
I: major capsid surface protein sigma-3
P: major outer-capsid protein mu1
Q: major outer-capsid protein mu1
R: major outer-capsid protein mu1
J: major outer-capsid protein mu1
K: major outer-capsid protein mu1
L: major outer-capsid protein mu1
T: major outer-capsid protein mu1
U: guanylyltransferase
V: major core protein lambda 1
W: major core protein lambda 1
X: Sigma 2 protein
Y: Sigma 2 protein
Z: Sigma 2 protein
1: Minor core protein lambda 3
x 60


Theoretical massNumber of molelcules
Total (without water)113,275,5431620
Polymers113,275,5431620
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: major outer-capsid protein mu1
B: major outer-capsid protein mu1
C: major outer-capsid protein mu1
S: major capsid surface protein sigma-3
D: major capsid surface protein sigma-3
E: major capsid surface protein sigma-3
F: major capsid surface protein sigma-3
M: major capsid surface protein sigma-3
N: major capsid surface protein sigma-3
O: major capsid surface protein sigma-3
G: major capsid surface protein sigma-3
H: major capsid surface protein sigma-3
I: major capsid surface protein sigma-3
P: major outer-capsid protein mu1
Q: major outer-capsid protein mu1
R: major outer-capsid protein mu1
J: major outer-capsid protein mu1
K: major outer-capsid protein mu1
L: major outer-capsid protein mu1
T: major outer-capsid protein mu1
U: guanylyltransferase
V: major core protein lambda 1
W: major core protein lambda 1
X: Sigma 2 protein
Y: Sigma 2 protein
Z: Sigma 2 protein
1: Minor core protein lambda 3
x 5


  • icosahedral pentamer
  • 9.44 MDa, 135 polymers
Theoretical massNumber of molelcules
Total (without water)9,439,629135
Polymers9,439,629135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: major outer-capsid protein mu1
B: major outer-capsid protein mu1
C: major outer-capsid protein mu1
S: major capsid surface protein sigma-3
D: major capsid surface protein sigma-3
E: major capsid surface protein sigma-3
F: major capsid surface protein sigma-3
M: major capsid surface protein sigma-3
N: major capsid surface protein sigma-3
O: major capsid surface protein sigma-3
G: major capsid surface protein sigma-3
H: major capsid surface protein sigma-3
I: major capsid surface protein sigma-3
P: major outer-capsid protein mu1
Q: major outer-capsid protein mu1
R: major outer-capsid protein mu1
J: major outer-capsid protein mu1
K: major outer-capsid protein mu1
L: major outer-capsid protein mu1
T: major outer-capsid protein mu1
U: guanylyltransferase
V: major core protein lambda 1
W: major core protein lambda 1
X: Sigma 2 protein
Y: Sigma 2 protein
Z: Sigma 2 protein
1: Minor core protein lambda 3
x 6


  • icosahedral 23 hexamer
  • 11.3 MDa, 162 polymers
Theoretical massNumber of molelcules
Total (without water)11,327,554162
Polymers11,327,554162
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
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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Protein , 6 types, 27 molecules ABCPQRJKLTSDEFMNOGHIUVWXYZ1

#1: Protein
major outer-capsid protein mu1 / Coordinate model: Cα atoms only


Mass: 76346.336 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: P11077
#2: Protein
major capsid surface protein sigma-3 / Coordinate model: Cα atoms only


Mass: 41237.117 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: P07939
#3: Protein guanylyltransferase / / Coordinate model: Cα atoms only


Mass: 144098.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Dearing / References: UniProt: P11079
#4: Protein major core protein lambda 1 / Coordinate model: Cα atoms only


Mass: 142008.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: Q9WAB2
#5: Protein Sigma 2 protein / / Core protein / Coordinate model: Cα atoms only


Mass: 47155.211 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: P11314
#6: Protein Minor core protein lambda 3 / Coordinate model: Cα atoms only


Mass: 142510.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: P17376, UniProt: P0CK32*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HUMAN REOVIRUS VIRIONS (T3D) / Type: VIRUS / Details: The structure was monodisperse.
Details of virusHost category: MAMMALIAN
Buffer solutionName: 10 mM TRIS / pH: 7.5 / Details: 10 mM TRIS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: PLUNGED INTO ETHANE

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Electron microscopy imaging

EM imaging

Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELDBright-field microscopy / Specimen-ID: 1

IDAccelerating voltage (kV)Calibrated magnification (X)DateDetailsModelCs (mm)Nominal defocus max (nm)Nominal defocus min (nm)Nominal magnification (X)Temperature (K)Tilt angle max (°)Tilt angle min (°)
120045000Dec 10, 1997SAMPLES WERE MAINTAINED AT -176 CELSIUS DEGREE IN THE ELECTRON MICROSCOPES.FEI/PHILIPS CM200FEG232001300380009700
230047440Apr 18, 2002FEI/PHILIPS CM300FEG/T39200
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 54

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Processing

CTF correctionDetails: CTF correction of each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: PFT, OOR, POR / Resolution: 7 Å / Num. of particles: 7939 / Nominal pixel size: 2.3 Å / Actual pixel size: 2.21 Å / Magnification calibration: CROSS-CORRELATION / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11EJ6

1ej6

11EJ61PDBexperimental model
21JMU

1jmu

11JMU2PDBexperimental model
31N35

1n35

11N353PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms16111 0 0 0 16111

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