A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein 3: gp_16 (Minor Capsid Protein) 2: gp_16 (Minor Capsid Protein) 1: gp_16 (Minor Capsid Protein) Y: HNH endonuclease Z: HNH endonuclease 6: gp_16 (Minor Capsid Protein) 5: gp_16 (Minor Capsid Protein) 4: gp_16 (Minor Capsid Protein) 7: gp_16 (Minor Capsid Protein)
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein 3: gp_16 (Minor Capsid Protein) 2: gp_16 (Minor Capsid Protein) 1: gp_16 (Minor Capsid Protein) Y: HNH endonuclease Z: HNH endonuclease 6: gp_16 (Minor Capsid Protein) 5: gp_16 (Minor Capsid Protein) 4: gp_16 (Minor Capsid Protein) 7: gp_16 (Minor Capsid Protein)
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein 3: gp_16 (Minor Capsid Protein) 2: gp_16 (Minor Capsid Protein) 1: gp_16 (Minor Capsid Protein) Y: HNH endonuclease Z: HNH endonuclease 6: gp_16 (Minor Capsid Protein) 5: gp_16 (Minor Capsid Protein) 4: gp_16 (Minor Capsid Protein) 7: gp_16 (Minor Capsid Protein)
x 5
icosahedral pentamer
2.14 MDa, 80 polymers
Theoretical mass
Number of molelcules
Total (without water)
2,137,201
80
Polymers
2,137,201
80
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
4
4
A: Major capsid protein B: Major capsid protein C: Major capsid protein D: Major capsid protein E: Major capsid protein F: Major capsid protein G: Major capsid protein 3: gp_16 (Minor Capsid Protein) 2: gp_16 (Minor Capsid Protein) 1: gp_16 (Minor Capsid Protein) Y: HNH endonuclease Z: HNH endonuclease 6: gp_16 (Minor Capsid Protein) 5: gp_16 (Minor Capsid Protein) 4: gp_16 (Minor Capsid Protein) 7: gp_16 (Minor Capsid Protein)
x 6
icosahedral 23 hexamer
2.56 MDa, 96 polymers
Theoretical mass
Number of molelcules
Total (without water)
2,564,641
96
Polymers
2,564,641
96
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
5
5
Idetical with deposited unit in distinct coordinate
icosahedral asymmetric unit, std point frame
Type
Name
Symmetry operation
Number
transform to point frame
1
Symmetry
Point symmetry: (Schoenflies symbol: I (icosahedral))
-
Components
#1: Protein
Majorcapsidprotein
Mass: 45525.645 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Adjutor (virus) / References: UniProt: B2ZNR4
#2: Protein
gp_16 (MinorCapsidProtein)
Mass: 13766.352 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Adjutor (virus) / References: UniProt: B2ZNR3
#3: Protein
HNHendonuclease
Mass: 6198.103 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacterium phage Adjutor (virus) / References: UniProt: B2ZNQ1
-
Experimental details
-
Experiment
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6664
-
Processing
EM software
ID
Name
Version
Category
Details
4
CTFFIND
4.1
CTFcorrection
Forinitialestimation
5
RELION
3.1.0
CTFcorrection
CTFRefinement
8
Coot
0.9.8.1
modelfitting
10
PHENIX
1.20.1
modelrefinement
11
ISOLDE
1.3
modelrefinement
12
RELION
3.1.0
initialEulerassignment
13
RELION
3.1.0
finalEulerassignment
14
RELION
3.1.0
classification
15
RELION
3.1.0
3Dreconstruction
CTF correction
Details: Standard CTF correction inside RELION's reconstruction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
Point symmetry: I (icosahedral)
3D reconstruction
Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44239 / Symmetry type: POINT
Atomic model building
Protocol: AB INITIO MODEL Details: Amino acid sequence built into the map for a single major capsid protein and refined with Phenix. Model then used for rest of asymmetric unit and refined with Phenix. Final step involved using Isolde.
+
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