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- PDB-5mjf: Near-atomic resolution structure of a plant geminivirus determine... -

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Basic information

Entry
Database: PDB / ID: 5mjf
TitleNear-atomic resolution structure of a plant geminivirus determined by electron cryo-microscopy
DescriptorCapsid protein
KeywordsVIRUS / African cassava mosaic virus / Geminivirus / ACMV / Virus
Specimen sourceAfrican cassava mosaic virus (isolate West Kenyan 844) / virus / ACMV
MethodElectron microscopy (4.2 Å resolution / Particle / Single particle)
AuthorsGrimm, C. / Bottcher, B. / Hipp, K. / Jeske, H.
CitationStructure, 2017, 25, 1303-1309.e3

Structure, 2017, 25, 1303-1309.e3 StrPapers
Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.
Katharina Hipp / Clemens Grimm / Holger Jeske / Bettina Böttcher

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 1, 2016 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Aug 9, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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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
J: Capsid protein
P: Capsid protein
S: Capsid protein
T: Capsid protein
U: Capsid protein
X: Capsid protein
Y: Capsid protein
Z: Capsid protein
a: Capsid protein
b: Capsid protein
c: Capsid protein
d: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
N: Capsid protein
O: 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
H: Capsid protein
Q: Capsid protein
V: Capsid protein
w: Capsid protein
R: Capsid protein
I: Capsid protein
W: Capsid protein
l: Capsid protein
v: Capsid protein
BA: Capsid protein
BB: Capsid protein
BC: Capsid protein
BD: 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
Polyers2,650,438110
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)280740
ΔGint (kcal/M)-142
Surface area (Å2)929010
MethodPISA

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Components

#1: Polypeptide(L) ...
Capsid protein / Coat protein / CP


Mass: 24094.891 Da / Num. of mol.: 110
Source: (gene. exp.) African cassava mosaic virus (isolate West Kenyan 844) / virus
References: UniProt: P03561

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: African cassava mosaic virus - [West Kenya 844] / Type: VIRUS / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 3.3 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: African cassava mosaic virus - [West Kenya 844]
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Manihot esculenta
Buffer solutionpH: 8
Buffer componentConc.: 0.1 mg/ml / Units: 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 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins
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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 94000 / 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
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
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 934
EM imaging opticsSph aberration corrector: Krios - cs-corrector
Image scansDimension width: 4096 / Dimension height: 4096 / Movie frames/image: 17 / Used frames/image: 1-17

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Processing

EM software
IDNameVersionCategoryImage processing IDFitting ID
1Relion1.4PARTICLE SELECTION1
4Relion1.4CTF CORRECTION1
7CootMODEL FITTING1
9Relion1.4INITIAL EULER ASSIGNMENT1
10Relion1.4FINAL EULER ASSIGNMENT1
11Relion1.4CLASSIFICATION1
12Relion1.4RECONSTRUCTION1
13phenix.real_space_refineMODEL REFINEMENT1
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 selectionDetails: 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
Number of particles selected: 141141
SymmetryPoint symmetry: D5
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 24451 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 139 / Ref protocol: FLEXIBLE FIT / Ref space: REAL

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