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- PDB-8qsi: Portal protein of empty Haloferax tailed virus 1. -

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Basic information

Entry
Database: PDB / ID: 8qsi
TitlePortal protein of empty Haloferax tailed virus 1.
Components
  • HK97 gp6-like/SPP1 gp15-like head-tail connector
  • Portal protein
KeywordsVIRUS / Archaeal virus / portal / portal capsid interface / Mg ions
Function / homologyPortal protein / HK97 gp6-like/SPP1 gp15-like head-tail connector
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 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 10, 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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,095,49336
Polymers1,095,20124
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
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
#3: 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 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: #2, #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
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7163 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingType: in silico model
RefinementResolution: 2.75→2.75 Å / Cor.coef. Fo:Fc: 0.753 / WRfactor Rwork: 0.448 / SU B: 10.117 / SU ML: 0.175 / Average fsc overall: 0.4393 / Average fsc work: 0.4393 / ESU R: 0.096 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.4484 7971714 -
all0.448 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 75.425 Å2
Baniso -1Baniso -2Baniso -3
1--0.254 Å2-0.008 Å20.006 Å2
2---0.251 Å20.005 Å2
3---0.504 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01251648
ELECTRON MICROSCOPYr_angle_refined_deg1.6441.64270092
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.52656456
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.01323.743048
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.793158556
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.96315324
ELECTRON MICROSCOPYr_chiral_restr0.1120.26624
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0240224
ELECTRON MICROSCOPYr_nbd_refined0.1980.241784
ELECTRON MICROSCOPYr_nbtor_refined0.290.271554
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.070.22496
ELECTRON MICROSCOPYr_metal_ion_refined0.0420.248
ELECTRON MICROSCOPYr_mcbond_it3.817.23125932
ELECTRON MICROSCOPYr_mcangle_it6.94110.82432352
ELECTRON MICROSCOPYr_scbond_it5.0957.66925716
ELECTRON MICROSCOPYr_scangle_it9.0511.22937740
ELECTRON MICROSCOPYr_lrange_it17.342130.567200244
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
2.64-2.7090.5885893740.5885893740.1120.588
2.709-2.7830.5875755580.5875755580.1450.587
2.783-2.8640.5515599490.5515599490.1560.551
2.864-2.9520.545421660.545421660.1940.54
2.952-3.0480.5465257700.5465257700.2060.546
3.048-3.1550.5365097690.5365097690.2840.536
3.155-3.2750.5284916490.5284916490.3350.528
3.275-3.4080.5134715790.5134715790.4130.513
3.408-3.560.4924536270.4924536270.4970.492
3.56-3.7330.4724334250.4724334250.5720.472
3.733-3.9350.4384114860.4384114860.6620.438
3.935-4.1740.4143894720.4143894720.7270.414
4.174-4.4620.3913661060.3913661060.7660.391
4.462-4.820.3743412150.3743412150.80.374
4.82-5.280.3713131350.3713131350.7950.371
5.28-5.9030.3962837510.3962837510.7490.396
5.903-6.8160.4332494890.4332494890.6950.433
6.816-8.3470.4042112690.4042112690.7370.404
8.347-11.8020.3791630490.3791630490.7850.379
11.802-412.1920.521891740.521891740.5190.521

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