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- PDB-9fkb: Tail of emppty Haloferax tailed virus 1 -

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Basic information

Entry
Database: PDB / ID: 9fkb
TitleTail of emppty Haloferax tailed virus 1
Components
  • Baseplate to tube adapter protein gp41
  • HK97 gp6-like/SPP1 gp15-like head-tail connector
  • SPP1 gp17-like tail completion protein
  • Tail tube protein
KeywordsVIRUS / Archeal virus / portal / tail
Function / homologyHK97 gp6-like/SPP1 gp15-like head-tail connector / Tail tube protein / SPP1 gp17-like tail completion protein / Uncharacterized protein
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 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
Authors: Zhang, D. / Daum, B. / Isupov, M.N. / McLaren, M. / Oksanen, H. / Quax, T.E.F. / Schwarzer, S. / Gold, V.A.M.
History
DepositionJun 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
PT: HK97 gp6-like/SPP1 gp15-like head-tail connector
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
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
Pa: SPP1 gp17-like tail completion protein
Pb: SPP1 gp17-like tail completion protein
Pc: SPP1 gp17-like tail completion protein
Pd: SPP1 gp17-like tail completion protein
Pe: SPP1 gp17-like tail completion protein
Pf: SPP1 gp17-like tail completion protein
B1: Tail tube protein
B2: Tail tube protein
B3: Tail tube protein
B4: Tail tube protein
B5: Tail tube protein
B6: Tail tube protein
AM: Tail tube protein
AN: Tail tube protein
AO: Tail tube protein
AP: Tail tube protein
AQ: Tail tube protein
AR: Tail tube protein
SB: Tail tube protein
SA: Tail tube protein
SC: Tail tube protein
SD: Tail tube protein
SE: Tail tube protein
SF: Tail tube protein
SG: Tail tube protein
SH: Tail tube protein
SI: Tail tube protein
SJ: Tail tube protein
SK: Tail tube protein
SL: Tail tube protein
SM: Tail tube protein
SN: Tail tube protein
SO: Tail tube protein
SP: Tail tube protein
SQ: Tail tube protein
SR: Tail tube protein
SS: Tail tube protein
ST: Tail tube protein
SU: Tail tube protein
SV: Tail tube protein
SW: Tail tube protein
SX: Tail tube protein
SY: Tail tube protein
SZ: Tail tube protein
Sa: Tail tube protein
Sb: Tail tube protein
Sc: Tail tube protein
Sd: Tail tube protein
Se: Tail tube protein
Sf: Tail tube protein
Sg: Tail tube protein
Sh: Tail tube protein
Si: Tail tube protein
Sj: Tail tube protein
Sk: Tail tube protein
Sl: Tail tube protein
Sm: Tail tube protein
Sn: Tail tube protein
So: Tail tube protein
Sp: Tail tube protein
Sq: Tail tube protein
Sr: Tail tube protein
Ss: Tail tube protein
St: Tail tube protein
Su: Tail tube protein
Sv: Tail tube protein
Sw: Tail tube protein
Sx: Tail tube protein
Sy: Tail tube protein
Sz: Tail tube protein
S1: Tail tube protein
S2: Tail tube protein
BA: Baseplate to tube adapter protein gp41
BB: Baseplate to tube adapter protein gp41
BC: Baseplate to tube adapter protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,517,06599
Polymers1,516,77387
Non-polymers29212
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

#1: 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
#2: Protein
SPP1 gp17-like tail completion protein


Mass: 17458.789 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6U9
#3: Protein ...
Tail tube protein


Mass: 17177.463 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6U0
#4: Protein Baseplate to tube adapter protein gp41


Mass: 30425.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6X8
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Haloferax tailed virus 1 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Haloferax tailed virus 1
Details of virusEmpty: YES / 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 softwareName: REFMAC / Version: 5.8.0267 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6580 / Symmetry type: POINT
RefinementResolution: 2.96→899.328 Å / Cor.coef. Fo:Fc: 0.48 / WRfactor Rwork: 0.639 / Average fsc overall: 0.2284 / Average fsc work: 0.2284 / ESU R: 0.08 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.6386 58741459 -
all0.639 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 39.998 Å2
Baniso -1Baniso -2Baniso -3
1-0.352 Å2-0.018 Å2-0.353 Å2
2---1.477 Å2-0.011 Å2
3---1.125 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.012108057
ELECTRON MICROSCOPYr_angle_refined_deg1.5181.643147462
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.127513677
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.73223.8285877
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.5011515990
ELECTRON MICROSCOPYr_dihedral_angle_4_deg21.85215516
ELECTRON MICROSCOPYr_chiral_restr0.1010.214538
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0285149
ELECTRON MICROSCOPYr_nbd_refined0.1920.281672
ELECTRON MICROSCOPYr_nbtor_refined0.2960.2149884
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1110.26912
ELECTRON MICROSCOPYr_metal_ion_refined0.0680.240
ELECTRON MICROSCOPYr_mcbond_it0454969
ELECTRON MICROSCOPYr_mcangle_it0668559
ELECTRON MICROSCOPYr_scbond_it0453088
ELECTRON MICROSCOPYr_scangle_it0678903
ELECTRON MICROSCOPYr_lrange_it075.206405979
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
2.96-3.0370.57743525010.57743525010.0710.577
3.037-3.120.5742357160.5742357160.0780.57
3.12-3.2110.56241215340.56241215340.0910.562
3.211-3.3090.55940010510.55940010510.1080.559
3.309-3.4180.5638783240.5638783240.1370.56
3.418-3.5380.56137497290.56137497290.1490.561
3.538-3.6710.55836218180.55836218180.1670.558
3.671-3.8210.55734796970.55734796970.1970.557
3.821-3.9910.55833420560.55833420560.2250.558
3.991-4.1860.55231907970.55231907970.2860.552
4.186-4.4120.5430362110.5430362110.3380.54
4.412-4.680.53828719310.53828719310.3740.538
4.68-5.0030.53426965510.53426965510.3940.534
5.003-5.4040.53825106350.53825106350.3780.538
5.404-5.920.5423096010.5423096010.3520.54
5.92-6.6190.55220890380.55220890380.3260.552
6.619-7.6420.54918414440.54918414440.3510.549
7.642-9.360.52815551430.52815551430.420.528
9.36-13.2360.49112009850.49112009850.5820.491
13.236-899.3280.6576566970.6576566970.4910.657

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