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- PDB-8uh4: Cryo-EM structure of Maize Streak Virus (MSV) - single head Gemin... -

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Basic information

Entry
Database: PDB / ID: 8uh4
TitleCryo-EM structure of Maize Streak Virus (MSV) - single head Geminivirus
Components
  • Capsid protein
  • genomic DNA
KeywordsVIRUS/DNA / geminivirus / single-head / maize / icosahedron / VIRUS-DNA complex
Function / homology
Function and homology information


T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Geminivirus MSV 27Kd coat protein / Geminivirus AR1/BR1 coat protein / Geminivirus coat protein/nuclear export factor BR1 family / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesMaize streak virus genotype A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsBennett, A.B. / McKenna, R. / Mietzsch, M. / Hull, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1563234 United States
CitationJournal: To Be Published
Title: The Two States of MSV Gemini Capsid Assembly
Authors: Bennett, A.D. / McKenna, R.
History
DepositionOct 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary / Category: em_admin / pdbx_entry_details / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
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
1: Capsid protein
2: Capsid protein
3: Capsid protein
4: Capsid protein
5: Capsid protein
6: Capsid protein
7: Capsid protein
8: Capsid protein
AA: genomic DNA
AB: genomic DNA
AC: genomic DNA
AD: genomic DNA
AE: genomic DNA
AF: genomic DNA
AG: genomic DNA
AH: genomic DNA
AI: genomic DNA
AJ: genomic DNA
AK: genomic DNA
AL: genomic DNA
AM: genomic DNA
AN: genomic DNA
AO: genomic DNA
AP: genomic DNA
AQ: genomic DNA
AR: genomic DNA
AS: genomic DNA
AT: genomic DNA
AU: genomic DNA
AV: genomic DNA
AW: genomic DNA
AX: genomic DNA
AY: genomic DNA
AZ: genomic DNA
Aa: genomic DNA
Ab: genomic DNA
Ac: genomic DNA
Ad: genomic DNA
Ae: genomic DNA
Af: genomic DNA
Ag: genomic DNA
Ah: genomic DNA
Ai: genomic DNA
Aj: genomic DNA
Ak: genomic DNA
Al: genomic DNA
Am: genomic DNA
An: genomic DNA
Ao: genomic DNA
Ap: genomic DNA
Aq: genomic DNA
Ar: genomic DNA
As: genomic DNA
At: genomic DNA
Au: genomic DNA
Av: genomic DNA
Aw: genomic DNA
Ax: genomic DNA
Ay: genomic DNA
Az: genomic DNA
A1: genomic DNA
A2: genomic DNA
A3: genomic DNA
A4: genomic DNA
A5: genomic DNA
A6: genomic DNA
A7: genomic DNA
A8: genomic DNA


Theoretical massNumber of molelcules
Total (without water)1,778,179120
Polymers1,778,179120
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Capsid protein


Mass: 26880.529 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maize streak virus genotype A (isolate Nigeria)
Strain: isolate Nigeria / Gene: V1 / Production host: Agrobacterium tumefaciens (bacteria) / References: UniProt: P06448
#2: Protein/peptide ...
genomic DNA


Mass: 2755.787 Da / Num. of mol.: 60 / Source method: obtained synthetically
Source: (synth.) Maize streak virus genotype A (isolate Nigeria)
Has protein modificationN

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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: Maize streak virus - [Nigeria] / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Maize streak virus genotype A (isolate Nigeria)
Source (recombinant)Organism: Agrobacterium tumefaciens (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Zea mays
Buffer solutionpH: 4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k)

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Processing

EM softwareName: Leginon / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43111 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008114120
ELECTRON MICROSCOPYf_angle_d0.743157320
ELECTRON MICROSCOPYf_dihedral_angle_d16.48284960
ELECTRON MICROSCOPYf_chiral_restr0.04617160
ELECTRON MICROSCOPYf_plane_restr0.00618360

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