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- PDB-4bp7: Asymmetric structure of a virus-receptor complex -

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Basic information

Entry
Database: PDB / ID: 4bp7
TitleAsymmetric structure of a virus-receptor complex
ComponentsCOAT PROTEIN
KeywordsVIRUS / BACTERIOPHAGE
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Biological speciesENTEROBACTERIA PHAGE MS2 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 39 Å
AuthorsDent, K.C. / Thompson, R. / Barker, A.M. / Barr, J.N. / Hiscox, J.A. / Stockley, P.G. / Ranson, N.A.
CitationJournal: Structure / Year: 2013
Title: The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release.
Authors: Kyle C Dent / Rebecca Thompson / Amy M Barker / Julian A Hiscox / John N Barr / Peter G Stockley / Neil A Ranson /
Abstract: Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their ...Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their genomes, which are vital for infection. Here, we report an asymmetric structure of bacteriophage MS2, attached to its receptor, the F-pilus. Cryo-electron tomography and subtomographic averaging of such complexes result in a structure containing clear density for the packaged genome, implying that the conformation of the genome is the same in each virus particle. The data also suggest that the single-copy viral maturation protein breaks the symmetry of the capsid, occupying a position that would be filled by a coat protein dimer in an icosahedral shell. This capsomere can thus fulfill its known biological roles in receptor and genome binding and suggests an exit route for the genome during infection.
History
DepositionMay 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references / Other
SupersessionDec 10, 2014ID: 4BP4, 4BP5, 4BP6 / Details: superseding all the associated split entries
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-2365
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,472,924180
Polymers2,472,924180
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 ...
COAT PROTEIN / ENTEROBACTERIOPHAGE MS2


Mass: 13738.464 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Source: (natural) ENTEROBACTERIA PHAGE MS2 (virus) / References: UniProt: P03612

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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: MS2 BOUND TO F-PILUS / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE HOME MADE FREEZING DEVICE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12 / Date: Jan 1, 2012
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 23000 X / Calibrated magnification: 23000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 3000 nm
Specimen holderTilt angle max: 60 ° / Tilt angle min: -60 °
Image recordingFilm or detector model: GATAN ULTRASCAN 10000 (10k x 10k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1IMOD3D reconstruction
2PEET3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 39 Å / Num. of particles: 1500 / Nominal pixel size: 9.12 Å / Actual pixel size: 9.12 Å
Details: THREE COORDINATE FILES (4BP4, 4BP5, 4BP6) LINKED TO 1 EM STRUCTURE EMD-2365.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY
Atomic model buildingPDB-ID: 2MS2
RefinementHighest resolution: 39 Å
Refinement stepCycle: LAST / Highest resolution: 39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57900 0 0 0 57900

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