[English] 日本語
Yorodumi
- PDB-8qqn: Portal protein of full Haloferax tailed virus 1. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qqn
TitlePortal protein of full 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: 2.342 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 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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
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
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Haloferax tailed virus 1 / Type: VIRUS / Entity ID: #1-#2 / 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

-
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)

-
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: 2.342 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165198 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingType: in silico model
RefinementResolution: 2.342→2.342 Å / Cor.coef. Fo:Fc: 0.747 / WRfactor Rwork: 0.406 / SU B: 3.213 / SU ML: 0.068 / Average fsc overall: 0.5921 / Average fsc work: 0.5921 / ESU R: 0.065 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.4063 11158547 -
all0.406 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 81.974 Å2
Baniso -1Baniso -2Baniso -3
1--0.308 Å20.007 Å2-0.001 Å2
2---0.31 Å2-0.005 Å2
3---0.618 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.01251240
ELECTRON MICROSCOPYr_angle_refined_deg1.6431.64469576
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.98456396
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.54223.5863012
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.123158484
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.90815324
ELECTRON MICROSCOPYr_chiral_restr0.1160.26576
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0239792
ELECTRON MICROSCOPYr_nbd_refined0.1880.237776
ELECTRON MICROSCOPYr_nbtor_refined0.2850.269690
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.070.22620
ELECTRON MICROSCOPYr_metal_ion_refined0.0070.24
ELECTRON MICROSCOPYr_mcbond_it2.4258.02425692
ELECTRON MICROSCOPYr_mcangle_it4.32412.02332052
ELECTRON MICROSCOPYr_scbond_it3.1138.24325548
ELECTRON MICROSCOPYr_scangle_it5.38412.20237524
ELECTRON MICROSCOPYr_lrange_it10.485147.928197448
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
2.36-2.4210.6038263580.6038263580.2140.603
2.421-2.4880.598043690.598043690.2470.59
2.488-2.560.5757837080.5757837080.2890.575
2.56-2.6390.5577592690.5577592690.3550.557
2.639-2.7250.5277369350.5277369350.4510.527
2.725-2.8210.5067122810.5067122810.5490.506
2.821-2.9270.4686885300.4686885300.6110.468
2.927-3.0470.4386607950.4386607950.670.438
3.047-3.1820.4066339940.4066339940.7370.406
3.182-3.3380.3786065580.3786065580.7770.378
3.338-3.5180.3535774080.3535774080.8240.353
3.518-3.7310.3485449690.3485449690.8350.348
3.731-3.9890.335124430.335124430.8650.33
3.989-4.3090.334772560.334772560.8690.33
4.309-4.720.354384160.354384160.8530.35
4.72-5.2770.3283968880.3283968880.8590.328
5.277-6.0930.3643500250.3643500250.8070.364
6.093-7.4620.4162950040.4162950040.7510.416
7.462-10.5510.3942282520.3942282520.7590.394
10.551-412.1920.5331250110.5331250110.2240.533

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more