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- PDB-8qsy: Portal capsid interface of full Haloferax tailed virus 1. -

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Basic information

Entry
Database: PDB / ID: 8qsy
TitlePortal capsid interface of full Haloferax tailed virus 1.
Components
  • Capsid stabilization protein
  • HK97 gp5-like major capsid protein
  • HK97 gp6-like/SPP1 gp15-like head-tail connector
  • Hypothetical protein gp21
  • Portal protein
KeywordsVIRUS / Archaeal virus / portal / portal capsid interface / Mg ions
Function / homology: / Portal protein / Capsid stabilization protein / HK97 gp6-like/SPP1 gp15-like head-tail connector / HK97 gp5-like major capsid protein
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 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 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
JA: HK97 gp5-like major capsid protein
JB: HK97 gp5-like major capsid protein
JC: HK97 gp5-like major capsid protein
JD: HK97 gp5-like major capsid protein
JE: HK97 gp5-like major capsid protein
JF: HK97 gp5-like major capsid protein
JI: Capsid stabilization protein
JJ: Capsid stabilization protein
JK: Capsid stabilization protein
KA: HK97 gp5-like major capsid protein
KB: HK97 gp5-like major capsid protein
KC: HK97 gp5-like major capsid protein
KD: HK97 gp5-like major capsid protein
KE: HK97 gp5-like major capsid protein
KF: HK97 gp5-like major capsid protein
KI: Capsid stabilization protein
KJ: Capsid stabilization protein
KK: Capsid stabilization protein
LA: HK97 gp5-like major capsid protein
LB: HK97 gp5-like major capsid protein
LC: HK97 gp5-like major capsid protein
LD: HK97 gp5-like major capsid protein
LE: HK97 gp5-like major capsid protein
LF: HK97 gp5-like major capsid protein
LI: Capsid stabilization protein
LJ: Capsid stabilization protein
LK: Capsid stabilization protein
MA: HK97 gp5-like major capsid protein
MB: HK97 gp5-like major capsid protein
MC: HK97 gp5-like major capsid protein
MD: HK97 gp5-like major capsid protein
ME: HK97 gp5-like major capsid protein
MF: HK97 gp5-like major capsid protein
MI: Capsid stabilization protein
MJ: Capsid stabilization protein
MK: Capsid stabilization protein
NA: HK97 gp5-like major capsid protein
NB: HK97 gp5-like major capsid protein
NC: HK97 gp5-like major capsid protein
ND: HK97 gp5-like major capsid protein
NE: HK97 gp5-like major capsid protein
NF: HK97 gp5-like major capsid protein
NI: Capsid stabilization protein
NJ: Capsid stabilization protein
NK: Capsid stabilization protein
P5: Hypothetical protein gp21
P6: Hypothetical protein gp21
P7: Hypothetical protein gp21
P8: Hypothetical protein gp21
P9: Hypothetical protein gp21
PA: Portal protein
PB: Portal protein
PC: Portal protein
PD: Portal protein
PE: Portal protein
PF: Portal protein
PG: Portal protein
PH: Portal protein
PI: Portal protein
PJ: Portal protein
PK: Portal protein
PL: Portal protein
PM: HK97 gp6-like/SPP1 gp15-like head-tail connector
PN: HK97 gp6-like/SPP1 gp15-like head-tail connector
PO: HK97 gp6-like/SPP1 gp15-like head-tail connector
PP: HK97 gp6-like/SPP1 gp15-like head-tail connector
PQ: HK97 gp6-like/SPP1 gp15-like head-tail connector
PR: HK97 gp6-like/SPP1 gp15-like head-tail connector
PS: HK97 gp6-like/SPP1 gp15-like head-tail connector
PT: HK97 gp6-like/SPP1 gp15-like head-tail connector
PU: HK97 gp6-like/SPP1 gp15-like head-tail connector
PV: HK97 gp6-like/SPP1 gp15-like head-tail connector
PW: HK97 gp6-like/SPP1 gp15-like head-tail connector
PX: HK97 gp6-like/SPP1 gp15-like head-tail connector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,664,283274
Polymers2,659,17174
Non-polymers5,112200
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 74 molecules JAJBJCJDJEJFKAKBKCKDKEKFLALBLCLDLELFMAMBMCMDMEMFNANBNCNDNENF...

#1: Protein ...
HK97 gp5-like major capsid protein


Mass: 43544.406 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6T9
#2: Protein
Capsid stabilization protein


Mass: 13888.911 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6Q7
#3: Protein
Hypothetical protein gp21


Mass: 9860.767 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1
#4: Protein
Portal protein


Mass: 75680.906 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6Q2
#5: Protein
HK97 gp6-like/SPP1 gp15-like head-tail connector


Mass: 15585.868 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6S3

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Non-polymers , 2 types, 200 molecules

#6: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 183 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION

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Details

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 / 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 recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150TFS FALCON 4i (4k x 4k)
2154.6GATAN K3 (6k 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
Image processingDetails: Dataset produced as a combination of both FALCON 4i and K3 collections
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157388 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingType: in silico model
RefinementResolution: 2.68→412.192 Å / Cor.coef. Fo:Fc: 0.821 / WRfactor Rwork: 0.468 / SU B: 10.767 / SU ML: 0.217 / Average fsc overall: 0.5347 / Average fsc work: 0.5347 / ESU R: 0.175 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.4682 7619444 -
all0.468 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 65.653 Å2
Baniso -1Baniso -2Baniso -3
1--0.213 Å20.026 Å2-0.045 Å2
2---0.18 Å2-0.012 Å2
3---0.393 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.012139338
ELECTRON MICROSCOPYr_angle_refined_deg1.5811.641189393
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.611517653
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.35823.238587
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.9891522077
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.984151041
ELECTRON MICROSCOPYr_chiral_restr0.1040.218170
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.02110024
ELECTRON MICROSCOPYr_nbd_refined0.1980.2111044
ELECTRON MICROSCOPYr_nbtor_refined0.2890.2191830
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0770.29432
ELECTRON MICROSCOPYr_metal_ion_refined0.0590.2156
ELECTRON MICROSCOPYr_mcbond_it1.9946.35870852
ELECTRON MICROSCOPYr_mcangle_it3.4969.53688425
ELECTRON MICROSCOPYr_scbond_it2.7546.67468486
ELECTRON MICROSCOPYr_scangle_it4.6819.871100968
ELECTRON MICROSCOPYr_lrange_it9.291118.996549912
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
2.68-2.750.6115647460.6115647460.2610.611
2.75-2.8250.5755497520.5755497520.3060.575
2.825-2.9070.5495334180.5495334180.3540.549
2.907-2.9960.5265192060.5265192060.4130.526
2.996-3.0950.5135035500.5135035500.450.513
3.095-3.2030.4944863350.4944863350.5030.494
3.203-3.3240.4754695930.4754695930.5560.475
3.324-3.460.4594516980.4594516980.6080.459
3.46-3.6140.4464329150.4464329150.6450.446
3.614-3.790.4364139940.4364139940.6740.436
3.79-3.9950.433943470.433943470.6930.43
3.995-4.2370.4343717180.4343717180.6970.434
4.237-4.530.4353505570.4353505570.6990.435
4.53-4.8930.4363255640.4363255640.6950.436
4.893-5.360.4372993380.4372993380.6710.437
5.36-5.9920.4452707880.4452707880.6450.445
5.992-6.9190.4622392070.4622392070.6160.462
6.919-8.4740.4552015130.4552015130.6230.455
8.474-11.9810.4571558860.4571558860.6220.457
11.981-412.1920.577852940.577852940.4740.577

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