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- PDB-8qpq: C1 turret to capsid interface of full Haloferax tailed virus 1 ad... -

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Basic information

Entry
Database: PDB / ID: 8qpq
TitleC1 turret to capsid interface of full Haloferax tailed virus 1 adjacent to the portal-capsid interface.
Components
  • HK97 gp5-like major capsid protein
  • Prokaryotic polysaccharide deacetylase
  • gp30
KeywordsVIRUS / Archaeal virus / turret / turret capsid interface / Mg ions
Function / homologyNodB homology domain / Polysaccharide deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / HK97 gp5-like major capsid protein / Prokaryotic polysaccharide deacetylase
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhang, D. / Daum, B. / Isupov, M.N. / McLaren, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: CryoEM structure of Haloferax tailed virus 1
Authors: Zhang, D. / Daum, B. / Isupov, M.N. / McLaren, M. / Oksanen, H. / Quax, T.E.F. / Schwarzer, S. / Gold, V.A.M. / Antson, A.
History
DepositionOct 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
TC: Prokaryotic polysaccharide deacetylase
TD: gp30
TE: gp30
TF: gp30
TG: gp30
TH: gp30
TI: gp30
TA: Prokaryotic polysaccharide deacetylase
TB: Prokaryotic polysaccharide deacetylase
LA: HK97 gp5-like major capsid protein
LB: HK97 gp5-like major capsid protein
LF: HK97 gp5-like major capsid protein
LE: HK97 gp5-like major capsid protein
LD: HK97 gp5-like major capsid protein
LC: HK97 gp5-like major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,43968
Polymers469,02715
Non-polymers1,41153
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11TC
21TC
32TC
42TC
53TC
63TC
74TC
84TC
95TC
105TC
116TC
126TC
137TC
147TC
158TC
168TC
179TC
189TC
1910TC
2010TC
2111TC
2211TC
2312TC
2412TC
2513TC
2613TC
2714TC
2814TC
2915TC
3015TC
3116TC
3216TC
3317TC
3417TC
3518TC
3618TC
3719TC
3819TC
3920TC
4020TC
4121TC
4221TC
4322TC
4422TC
4523TC
4623TC
4724TC
4824TC
4925TC
5025TC
5126TC
5226TC
5327TC
5427TC
5528TC
5628TC
5729TC
5829TC
5930TC
6030TC
6131TC
6231TC
6332TC
6432TC
6533TC
6633TC

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60
31Local NCS retraints between domains: 61 62
32Local NCS retraints between domains: 63 64
33Local NCS retraints between domains: 65 66

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Components

#1: Protein Prokaryotic polysaccharide deacetylase


Mass: 45242.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6W3
#2: Protein
gp30


Mass: 12005.731 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1
#3: Protein
HK97 gp5-like major capsid protein


Mass: 43544.406 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6T9
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Haloferax tailed virus 1 / Type: VIRUS / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Haloferax tailed virus 1
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Haloferax gibbonsii
Buffer solutionpH: 7
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 54.6 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPU5image acquisition
4RELION4.0-betaCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102012 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingType: in silico model
RefinementResolution: 2.7→299.776 Å / Cor.coef. Fo:Fc: 0.709 / WRfactor Rwork: 0.512 / SU B: 12.597 / SU ML: 0.255 / Average fsc overall: 0.4088 / Average fsc work: 0.4088 / ESU R: 0.14 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.512 2865333 -
all0.512 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 92.602 Å2
Baniso -1Baniso -2Baniso -3
1--0.162 Å20.239 Å2-0.079 Å2
2---0.199 Å2-0.021 Å2
3---0.361 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01228656
ELECTRON MICROSCOPYr_angle_refined_deg1.6191.63738989
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.26453668
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.43723.3271713
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.785154452
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.45615201
ELECTRON MICROSCOPYr_chiral_restr0.1130.23910
ELECTRON MICROSCOPYr_gen_planes_refined0.0110.0222542
ELECTRON MICROSCOPYr_nbd_refined0.1970.224282
ELECTRON MICROSCOPYr_nbtor_refined0.290.239140
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0860.22262
ELECTRON MICROSCOPYr_metal_ion_refined0.1190.266
ELECTRON MICROSCOPYr_mcbond_it2.7398.99414717
ELECTRON MICROSCOPYr_mcangle_it4.54513.50618370
ELECTRON MICROSCOPYr_scbond_it3.9729.40313939
ELECTRON MICROSCOPYr_scangle_it6.43513.93620619
ELECTRON MICROSCOPYr_lrange_it11.367176.002119341
ELECTRON MICROSCOPYr_ncsr_local_group_10.0930.0526690
ELECTRON MICROSCOPYr_ncsr_local_group_20.0930.0526770
ELECTRON MICROSCOPYr_ncsr_local_group_30.0680.056696
ELECTRON MICROSCOPYr_ncsr_local_group_40.0390.056752
ELECTRON MICROSCOPYr_ncsr_local_group_50.070.056672
ELECTRON MICROSCOPYr_ncsr_local_group_60.0390.056752
ELECTRON MICROSCOPYr_ncsr_local_group_70.0860.056582
ELECTRON MICROSCOPYr_ncsr_local_group_80.0610.056704
ELECTRON MICROSCOPYr_ncsr_local_group_90.0430.056752
ELECTRON MICROSCOPYr_ncsr_local_group_100.0630.056718
ELECTRON MICROSCOPYr_ncsr_local_group_110.0680.056680
ELECTRON MICROSCOPYr_ncsr_local_group_120.0650.056656
ELECTRON MICROSCOPYr_ncsr_local_group_130.0440.056742
ELECTRON MICROSCOPYr_ncsr_local_group_140.0830.056588
ELECTRON MICROSCOPYr_ncsr_local_group_150.0660.056672
ELECTRON MICROSCOPYr_ncsr_local_group_160.0680.056642
ELECTRON MICROSCOPYr_ncsr_local_group_170.0870.056566
ELECTRON MICROSCOPYr_ncsr_local_group_180.0870.0526890
ELECTRON MICROSCOPYr_ncsr_local_group_190.1410.0517382
ELECTRON MICROSCOPYr_ncsr_local_group_200.1440.0516432
ELECTRON MICROSCOPYr_ncsr_local_group_210.1390.0517330
ELECTRON MICROSCOPYr_ncsr_local_group_220.1330.0517500
ELECTRON MICROSCOPYr_ncsr_local_group_230.1370.0517448
ELECTRON MICROSCOPYr_ncsr_local_group_240.140.0516722
ELECTRON MICROSCOPYr_ncsr_local_group_250.1160.0517808
ELECTRON MICROSCOPYr_ncsr_local_group_260.1240.0517638
ELECTRON MICROSCOPYr_ncsr_local_group_270.1230.0517720
ELECTRON MICROSCOPYr_ncsr_local_group_280.1380.0516584
ELECTRON MICROSCOPYr_ncsr_local_group_290.1360.0516672
ELECTRON MICROSCOPYr_ncsr_local_group_300.1450.0516660
ELECTRON MICROSCOPYr_ncsr_local_group_310.1140.0517676
ELECTRON MICROSCOPYr_ncsr_local_group_320.1140.0517830
ELECTRON MICROSCOPYr_ncsr_local_group_330.1180.0517884
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.7-2.770.6052118370.6052118370.20.605
2.77-2.8460.582064170.582064170.2410.58
2.846-2.9290.5552010490.5552010490.2930.555
2.929-3.0190.5421950170.5421950170.3250.542
3.019-3.1180.5321899470.5321899470.3570.532
3.118-3.2270.5171825160.5171825160.3970.517
3.227-3.3490.511763690.511763690.4310.51
3.349-3.4860.5021703520.5021703520.4690.502
3.486-3.6410.4961627380.4961627380.4940.496
3.641-3.8180.4951558460.4951558460.5010.495
3.818-4.0250.4941478420.4941478420.5140.494
4.025-4.2690.4991406700.4991406700.5160.499
4.269-4.5640.4961314460.4961314460.5330.496
4.564-4.9290.4961227650.4961227650.5250.496
4.929-5.40.4951122510.4951122510.5010.495
5.4-6.0370.4981022740.4981022740.4740.498
6.037-6.970.505898360.505898360.460.505
6.97-8.5350.505757000.505757000.4610.505
8.535-12.0660.511585750.511585750.4510.511
12.066-299.7760.615321140.615321140.3710.615

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