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- PDB-4ctf: The limits of structural plasticity in a picornavirus capsid reve... -

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Basic information

Entry
Database: PDB / ID: 4ctf
TitleThe limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle
Components
  • (P1) x 2
  • EQUINE RHINITIS A VIRUS
  • VP1
KeywordsVIRUS / PICORNAVIRUS / CAPSID STRUCTURE / CAPSID EXPANSION / UNCOATING
Function / homology
Function and homology information


icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / cytoplasm
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Picornavirus coat protein / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEQUINE RHINITIS A VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17 Å
AuthorsBakker, S.E. / Groppelli, E. / Pearson, A.R. / Stockley, P.G. / Rowlands, D.J. / Ranson, N.A.
CitationJournal: J Virol / Year: 2014
Title: Limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle.
Authors: Saskia E Bakker / Elisabetta Groppelli / Arwen R Pearson / Peter G Stockley / David J Rowlands / Neil A Ranson /
Abstract: The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these ...The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these genomes are introduced into cells to initiate infection remains poorly understood. The structures of presumed uncoating intermediate particles of several picornaviruses show limited expansion and some increased porosity compared to the mature virions. Here, we present the cryo-electron microscopy structure of native equine rhinitis A virus (ERAV), together with the structure of a massively expanded ERAV particle, each at ∼17-Å resolution. The expanded structure has large pores on the particle 3-fold axes and has lost the RNA genome and the capsid protein VP4. The expanded structure thus illustrates both the limits of structural plasticity in such capsids and a plausible route by which genomic RNA might exit.
IMPORTANCE: Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the ...IMPORTANCE: Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the capsid to initiate a new round of infection. We describe here the structure of a unique, massively expanded state of equine rhinitis A virus that provides insight into how this exit might occur.
History
DepositionMar 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Other
SupersessionDec 10, 2014ID: 4CWG, 4CWH, 4CWI, 4CWJ, 4CWK, 4CWL / Details: supersedes the associated split entries
Revision 1.2Dec 10, 2014Group: Other
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5May 8, 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 / struct_sheet
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 / _struct_sheet.number_strands

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A0: VP1
A1: VP1
A2: VP1
A3: VP1
A4: VP1
A5: VP1
A6: VP1
A7: VP1
A8: VP1
A9: VP1
AA: VP1
AB: VP1
AC: VP1
AD: VP1
AE: VP1
AF: VP1
AG: VP1
AH: VP1
AI: VP1
AJ: VP1
AK: VP1
AL: VP1
AM: VP1
AN: VP1
AO: VP1
AP: VP1
AQ: VP1
AR: VP1
AS: VP1
AT: VP1
AU: VP1
AV: VP1
AW: VP1
AX: VP1
AY: VP1
AZ: VP1
Aa: VP1
Ab: VP1
Ac: VP1
Ad: VP1
Ae: VP1
Af: VP1
Ag: VP1
Ah: VP1
Ai: VP1
Aj: VP1
Ak: VP1
Al: VP1
Am: VP1
An: VP1
Ao: VP1
BA: VP1
BB: VP1
BC: VP1
BD: VP1
BE: VP1
BF: VP1
BG: VP1
BH: VP1
BI: VP1
C0: EQUINE RHINITIS A VIRUS
C1: EQUINE RHINITIS A VIRUS
C2: EQUINE RHINITIS A VIRUS
C3: EQUINE RHINITIS A VIRUS
C4: EQUINE RHINITIS A VIRUS
C5: EQUINE RHINITIS A VIRUS
C6: EQUINE RHINITIS A VIRUS
C7: EQUINE RHINITIS A VIRUS
C8: EQUINE RHINITIS A VIRUS
C9: EQUINE RHINITIS A VIRUS
CA: EQUINE RHINITIS A VIRUS
CB: EQUINE RHINITIS A VIRUS
CC: EQUINE RHINITIS A VIRUS
CD: EQUINE RHINITIS A VIRUS
CE: EQUINE RHINITIS A VIRUS
CF: EQUINE RHINITIS A VIRUS
CG: EQUINE RHINITIS A VIRUS
CH: EQUINE RHINITIS A VIRUS
CI: EQUINE RHINITIS A VIRUS
CJ: EQUINE RHINITIS A VIRUS
CK: EQUINE RHINITIS A VIRUS
CL: EQUINE RHINITIS A VIRUS
CM: EQUINE RHINITIS A VIRUS
CN: EQUINE RHINITIS A VIRUS
CO: EQUINE RHINITIS A VIRUS
CP: EQUINE RHINITIS A VIRUS
CQ: EQUINE RHINITIS A VIRUS
CR: EQUINE RHINITIS A VIRUS
CS: EQUINE RHINITIS A VIRUS
CT: EQUINE RHINITIS A VIRUS
CU: EQUINE RHINITIS A VIRUS
CV: EQUINE RHINITIS A VIRUS
CW: EQUINE RHINITIS A VIRUS
CX: EQUINE RHINITIS A VIRUS
CY: EQUINE RHINITIS A VIRUS
CZ: EQUINE RHINITIS A VIRUS
Ca: EQUINE RHINITIS A VIRUS
Cb: EQUINE RHINITIS A VIRUS
Cc: EQUINE RHINITIS A VIRUS
Cd: EQUINE RHINITIS A VIRUS
Ce: EQUINE RHINITIS A VIRUS
Cf: EQUINE RHINITIS A VIRUS
Cg: EQUINE RHINITIS A VIRUS
Ch: EQUINE RHINITIS A VIRUS
Ci: EQUINE RHINITIS A VIRUS
Cj: EQUINE RHINITIS A VIRUS
Ck: EQUINE RHINITIS A VIRUS
Cl: EQUINE RHINITIS A VIRUS
Cm: EQUINE RHINITIS A VIRUS
Cn: EQUINE RHINITIS A VIRUS
Co: EQUINE RHINITIS A VIRUS
Cp: EQUINE RHINITIS A VIRUS
Cq: EQUINE RHINITIS A VIRUS
Cr: EQUINE RHINITIS A VIRUS
Cs: EQUINE RHINITIS A VIRUS
Ct: EQUINE RHINITIS A VIRUS
Cu: EQUINE RHINITIS A VIRUS
Cv: EQUINE RHINITIS A VIRUS
Cw: EQUINE RHINITIS A VIRUS
Cx: EQUINE RHINITIS A VIRUS
D0: P1
D1: P1
D2: P1
D3: P1
D4: P1
D5: P1
D6: P1
D7: P1
D8: P1
D9: P1
DA: P1
DB: P1
DC: P1
DD: P1
DE: P1
DF: P1
DG: P1
DH: P1
DI: P1
DJ: P1
DK: P1
DL: P1
DM: P1
DN: P1
DO: P1
DP: P1
DQ: P1
DR: P1
DS: P1
DT: P1
DU: P1
DV: P1
DW: P1
DX: P1
DY: P1
DZ: P1
Da: P1
Db: P1
Dc: P1
Dd: P1
De: P1
Df: P1
Dg: P1
Dh: P1
Di: P1
Dj: P1
Dk: P1
Dl: P1
Dm: P1
Dn: P1
Do: P1
Dp: P1
Dq: P1
Dr: P1
Ds: P1
EA: P1
EB: P1
EC: P1
ED: P1
EE: P1
F0: P1
F1: P1
F2: P1
F3: P1
F4: P1
F5: P1
F6: P1
F7: P1
F8: P1
F9: P1
FA: P1
FB: P1
FC: P1
FD: P1
FE: P1
FF: P1
FG: P1
FH: P1
FI: P1
FJ: P1
FK: P1
FL: P1
FM: P1
FN: P1
FO: P1
FP: P1
FQ: P1
FR: P1
FS: P1
FT: P1
FU: P1
FV: P1
FW: P1
FX: P1
FY: P1
FZ: P1
Fa: P1
Fb: P1
Fc: P1
Fd: P1
Fe: P1
Ff: P1
Fg: P1
Fh: P1
Fi: P1
Fj: P1
Fk: P1
Fl: P1
Fm: P1
Fn: P1
Fo: P1
Fp: P1
Fq: P1
Fr: P1
Fs: P1
Ft: P1
Fu: P1
Fv: P1
Fw: P1
Fx: P1


Theoretical massNumber of molelcules
Total (without water)5,102,611240
Polymers5,102,611240
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
VP1 / EQUINE RHINITIS A VIRUS


Mass: 27296.846 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Details: OHIO HELA CELLS / Source: (natural) EQUINE RHINITIS A VIRUS / References: UniProt: A2TJ51
#2: Protein ...
EQUINE RHINITIS A VIRUS


Mass: 25297.660 Da / Num. of mol.: 60 / Fragment: RESIDUES 81-310 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / References: UniProt: Q91B42
#3: Protein ...
P1


Mass: 24338.451 Da / Num. of mol.: 60 / Fragment: RESIDUES 311-536 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / References: UniProt: Q91B37
#4: Protein ...
P1


Mass: 8110.563 Da / Num. of mol.: 60 / Fragment: RESIDUES 1-80 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / References: UniProt: Q91B42, UniProt: B9VV85*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: EQUINE RHINITIS A VIRUS / Type: VIRUS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 87209 X / Cs: 2 mm
Image recordingElectron dose: 15 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 25
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: PHASE FLIPPING, EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 17 Å / Num. of particles: 260 / Nominal pixel size: 1.71 Å / Actual pixel size: 1.71 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2WFF

2wff


Accession code: 2WFF / Source name: PDB / Type: experimental model
RefinementHighest resolution: 17 Å
Refinement stepCycle: LAST / Highest resolution: 17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms98379 0 0 0 98379

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