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

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Basic information

Entry
Database: PDB / ID: 4ctg
TitleThe limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle
Components(P1) x 3
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 capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
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
SupersessionDec 10, 2014ID: 4D14, 4D15, 4D16, 4D2A / Details: supersedes the associated split entries
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Dec 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]

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Assembly

Deposited unit
AA: P1
AB: P1
AC: P1
AD: P1
AE: P1
AF: P1
AG: P1
AH: P1
AI: P1
AJ: P1
AK: P1
AL: P1
AM: P1
AN: P1
AO: P1
AP: P1
AQ: P1
AR: P1
AS: P1
AT: P1
AU: P1
AV: P1
AW: P1
AX: P1
AY: P1
AZ: P1
A0: P1
A1: P1
A2: P1
A3: P1
A4: P1
A5: P1
A6: P1
A7: P1
A8: P1
A9: P1
Aa: P1
Ab: P1
Ac: P1
Ad: P1
Ae: P1
Af: P1
Ag: P1
Ah: P1
Ai: P1
Aj: P1
Ak: P1
Al: P1
Am: P1
An: P1
Ao: P1
BA: P1
BB: P1
BC: P1
BD: P1
BE: P1
BF: P1
BG: P1
BH: P1
BI: P1
BJ: P1
BK: P1
BL: P1
BM: P1
BN: P1
BR: P1
BO: P1
BS: P1
BP: P1
BQ: P1
BT: P1
BU: P1
BV: P1
BW: P1
BX: P1
BY: P1
BZ: P1
B0: P1
B1: P1
B2: P1
B3: P1
B4: P1
B5: P1
B6: P1
B7: P1
B8: P1
B9: P1
Ba: P1
Bb: P1
Bc: P1
Bd: P1
Be: P1
Bf: P1
Bg: P1
Bh: P1
Bi: P1
Bj: P1
Bk: P1
Bl: P1
Bm: P1
Bn: P1
Bo: P1
Bp: P1
Bq: P1
Br: P1
Bs: P1
Bt: P1
Bu: P1
Bv: P1
Bw: P1
Bx: P1
CA: P1
CB: P1
CC: P1
CD: P1
CE: P1
CF: P1
CG: P1
CH: P1
CI: P1
CJ: P1
CK: P1
CL: P1
CM: P1
CN: P1
CO: P1
CP: P1
CQ: P1
CR: P1
CS: P1
CT: P1
CU: P1
CV: P1
CW: P1
CX: P1
CY: P1
CZ: P1
C0: P1
C1: P1
C2: P1
C3: P1
C4: P1
C5: P1
C6: P1
C7: P1
C8: P1
C9: P1
Cc: P1
Cd: P1
Ce: P1
Cf: P1
Cg: P1
Ch: P1
Ci: P1
Cj: P1
Ck: P1
Cl: P1
Cm: P1
Cn: P1
Co: P1
Cp: P1
Cq: P1
Cr: P1
Cs: P1
Ct: P1
Cu: P1
Cv: P1
Cw: P1
Cx: P1
DA: P1
DB: P1
DC: P1
DD: P1
DE: P1
DF: P1
DG: P1
DH: P1
DI: P1
DJ: P1
DK: P1


Theoretical massNumber of molelcules
Total (without water)4,420,223180
Polymers4,420,223180
Non-polymers00
Water0
1


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

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Components

#1: Protein ...
P1


Mass: 27296.846 Da / Num. of mol.: 60 / Fragment: RESIDUES 537-782 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / References: UniProt: B9VV85
#2: Protein ...
P1


Mass: 22035.094 Da / Num. of mol.: 60 / Fragment: RESIDUES 111-310 / 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

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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 particle / Type: VIRUS
SpecimenEmbedding 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 FIELDBright-field microscopy / 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: 227 / 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

RefinementHighest resolution: 17 Å
Refinement stepCycle: LAST / Highest resolution: 17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms98328 0 0 0 98328

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