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- PDB-6ek5: Near-atomic resolution structure of a plant geminivirus determine... -

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Basic information

Entry
Database: PDB / ID: 6ek5
TitleNear-atomic resolution structure of a plant geminivirus determined by electron cryo-microscopy.
ComponentsCapsid protein
KeywordsVIRUS / African cassava mosaic virus / Geminivirus / ACMV
Function / homology
Function and homology information


T=1 icosahedral viral capsid / viral penetration into host nucleus / symbiont entry into host cell / host cell nucleus / structural molecule activity / DNA binding / metal ion binding
Similarity search - Function
Geminivirus AR1 coat protein / Geminivirus AR1/BR1 coat protein / Geminivirus coat protein/nuclear export factor BR1 family
Similarity search - Domain/homology
Biological speciesAfrican cassava mosaic virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGrimm, C. / Bottcher, B. / Hipp, K. / Jeske, H.
CitationJournal: Structure / Year: 2017
Title: Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.
Authors: Katharina Hipp / Clemens Grimm / Holger Jeske / Bettina Böttcher /
Abstract: African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its ...African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved.
History
DepositionSep 25, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionOct 11, 2017ID: 5MJF
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Other / Category: pdbx_database_related / pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.2Nov 20, 2019Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 27, 2019Group: Database references / Category: pdbx_database_related
Revision 1.4Feb 19, 2020Group: Database references / Category: database_2 / pdbx_database_related / Item: _database_2.database_code
Revision 1.5Mar 11, 2020Group: Database references / Category: pdbx_database_related
Revision 1.6Jul 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _em_admin.title / _pdbx_database_related.details

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Structure visualization

Movie
  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
N: Capsid protein
O: Capsid protein
P: Capsid protein
Q: Capsid protein
R: Capsid protein
S: Capsid protein
T: Capsid protein
U: Capsid protein
V: Capsid protein
W: Capsid protein
X: Capsid protein
Y: Capsid protein
Z: Capsid protein
BA: Capsid protein
BB: Capsid protein
BC: Capsid protein
BD: Capsid protein
a: Capsid protein
b: Capsid protein
c: Capsid protein
d: Capsid protein
e: Capsid protein
f: Capsid protein
g: Capsid protein
h: Capsid protein
i: Capsid protein
j: Capsid protein
m: Capsid protein
n: Capsid protein
o: Capsid protein
p: Capsid protein
q: Capsid protein
r: Capsid protein
s: Capsid protein
t: Capsid protein
u: Capsid protein
x: Capsid protein
y: Capsid protein
z: Capsid protein
3: Capsid protein
1: Capsid protein
2: Capsid protein
k: Capsid protein
w: Capsid protein
l: Capsid protein
v: Capsid protein
BE: Capsid protein
BF: Capsid protein
BG: Capsid protein
BJ: Capsid protein
BP: Capsid protein
BS: Capsid protein
BT: Capsid protein
BU: Capsid protein
BX: Capsid protein
BY: Capsid protein
BZ: Capsid protein
Ba: Capsid protein
Bb: Capsid protein
Bc: Capsid protein
Bd: Capsid protein
BK: Capsid protein
BL: Capsid protein
BM: Capsid protein
BN: Capsid protein
BO: Capsid protein
Be: Capsid protein
Bf: Capsid protein
Bg: Capsid protein
Bh: Capsid protein
Bi: Capsid protein
Bj: Capsid protein
Bm: Capsid protein
Bn: Capsid protein
Bo: Capsid protein
Bp: Capsid protein
Bq: Capsid protein
Br: Capsid protein
Bs: Capsid protein
Bt: Capsid protein
Bu: Capsid protein
Bx: Capsid protein
By: Capsid protein
Bz: Capsid protein
B3: Capsid protein
B1: Capsid protein
B2: Capsid protein
Bw: Capsid protein
BH: Capsid protein
BQ: Capsid protein
BV: Capsid protein
Bk: Capsid protein
Bv: Capsid protein
BI: Capsid protein
BR: Capsid protein
BW: Capsid protein
Bl: Capsid protein


Theoretical massNumber of molelcules
Total (without water)2,650,438110
Polymers2,650,438110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area280740 Å2
ΔGint-142 kcal/mol
Surface area929010 Å2
MethodPISA

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Components

#1: Protein ...
Capsid protein / Coat protein / CP


Mass: 24094.891 Da / Num. of mol.: 110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African cassava mosaic virus / Strain: isolate West Kenyan 844 / Gene: AR1, AV1 / Production host: African cassava mosaic virus / References: UniProt: P03561

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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: African cassava mosaic virus - [West Kenya 844] / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 3.3 MDa / Experimental value: NO
Source (natural)Organism: African cassava mosaic virus - [West Kenya 844]
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Manihot esculenta
Buffer solutionpH: 8
Buffer componentConc.: 0.1 M / Name: Sodium Borate / Formula: Na2B4O7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R1.2/1.3 + 2nm C. Glow discharged for 30-60 s with 25-28 MicroAmp (Quorum Tec Mini Sputter coater SC7620) and used within 1 hour
Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Samples (3 ?l) were applied to the glow discharged grids, incubated for 60 s on the grid, blotted and plunge frozen in liquid ethane using a Vitrobot IV (FEI, Eindhoven, The Netherlands) at ...Details: Samples (3 ?l) were applied to the glow discharged grids, incubated for 60 s on the grid, blotted and plunge frozen in liquid ethane using a Vitrobot IV (FEI, Eindhoven, The Netherlands) at 4?C with 100% humidity and blotting from both sides for 3 s with blot force 7

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 94000 X / Calibrated defocus min: 780 nm / Calibrated defocus max: 5600 nm / Cs: 0.01 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 934
Details: data acquisition with a cs-corrected FEI Titan Krios on a Falcon II direct detector at 300 kV. Data was acquired at a primary magnification of 94,000 (calibrated pixel size of 1.57 A) and ...Details: data acquisition with a cs-corrected FEI Titan Krios on a Falcon II direct detector at 300 kV. Data was acquired at a primary magnification of 94,000 (calibrated pixel size of 1.57 A) and with a total dose of 25 e/A2 in 17 frames. In total 1,108 movies were recorded of which 934 movies were used for further processing. The movie frames were averaged after motion correction and dose weightin
EM imaging opticsSpherical aberration corrector: Krios - cs-corrector
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 17 / Used frames/image: 1-17

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Processing

EM software
IDNameVersionCategory
1RELION1.4particle selection
4RELION1.4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
Image processingDetails: Images were motion correted and weighted for dose damage; the CTF was determined with CTFFIND 3
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 141141
Details: For the initial analysis, ca. 2,000 particle images were selected manually with e2boxer and extracted and normalized with relion 1.4 followed by 2D-classification and ctf-correction. Three ...Details: For the initial analysis, ca. 2,000 particle images were selected manually with e2boxer and extracted and normalized with relion 1.4 followed by 2D-classification and ctf-correction. Three characteristic class averages that resolved the two parts of the twin particle (side views and intermediate views) were selected as references for template-dependent automatic particle picking in Relion. Particle images were extracted at the determined coordinates with a box size of 300 x 300 Px and normalized for their grey value distribution followed by 2D-classification. Some of the 2D-classes showed disconnected twin particles or single capsids. These classes probably represented either adjacent capsids from different twin particles or incorrectly centered particles and were excluded from the subsequent analysis. 141141 particles is the number of automatically selected particles; 69685 were retained for he subsequent processing
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24451 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 139 / Protocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 4.2 Å

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