[English] 日本語
Yorodumi
- EMDB-1904: Labeling and Localization of the Herpes Simplex Virus Capsid Prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1904
TitleLabeling and Localization of the Herpes Simplex Virus Capsid Protein UL25 and Its Interaction with the Two Triplexes Closest to the Penton.
Map dataSurface rendered view of HSV-1 C-capsid where protein UL25 has been genetically tagged with GFP at amino acid 50.
Sample
  • Sample: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at amino acid 50.
  • Virus: Human herpesvirus 1 strain KOS
KeywordsHSV-1 / capsid / UL25 / cryo-EM
Biological speciesHuman herpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 13.7 Å
AuthorsConway JF / Cockrell SK / Copeland AM / Newcomb WW / Brown JC / Homa FL
CitationJournal: J Mol Biol / Year: 2010
Title: Labeling and localization of the herpes simplex virus capsid protein UL25 and its interaction with the two triplexes closest to the penton.
Authors: James F Conway / Shelley K Cockrell / Anna Maria Copeland / William W Newcomb / Jay C Brown / Fred L Homa /
Abstract: The herpes simplex virus type 1 UL25 protein is one of seven viral proteins that are required for DNA cleavage and packaging. Together with UL17, UL25 forms part of an elongated molecule referred to ...The herpes simplex virus type 1 UL25 protein is one of seven viral proteins that are required for DNA cleavage and packaging. Together with UL17, UL25 forms part of an elongated molecule referred to as the C-capsid-specific component (CCSC). Five copies of the CCSC are located at each of the capsid vertices on DNA-containing capsids. To study the conformation of UL25 as it is folded on the capsid surface, we identified the sequence recognized by a UL25-specific monoclonal antibody and localized the epitope on the capsid surface by immunogold electron microscopy. The epitope mapped to amino acids 99-111 adjacent to the region of the protein (amino acids 1-50) that is required for capsid binding. In addition, cryo-EM reconstructions of C-capsids in which the green fluorescent protein (GFP) was fused within the N-terminus of UL25 localized the point of contact between UL25 and GFP. The result confirmed the modeled location of the UL25 protein in the CCSC density as the region that is distal to the penton with the N-terminus of UL25 making contact with the triplex one removed from the penton. Immunofluorescence experiments at early times during infection demonstrated that UL25-GFP was present on capsids located within the cytoplasm and adjacent to the nucleus. These results support the view that UL25 is present on incoming capsids with the capsid-binding domain of UL25 located on the surface of the mature DNA-containing capsid.
History
DepositionJun 7, 2011-
Header (metadata) releaseOct 3, 2012-
Map releaseOct 3, 2012-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1904.png

Downloads & links

-
Map

FileDownload / File: emd_1904.map.gz / Format: CCP4 / Size: 985.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendered view of HSV-1 C-capsid where protein UL25 has been genetically tagged with GFP at amino acid 50.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.12 Å/pix.
x 642 pix.
= 1361.04 Å		2.12 Å/pix.
x 642 pix.
= 1361.04 Å		2.12 Å/pix.
x 642 pix.
= 1361.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-3.73272991 - 4.35211754
Average (Standard dev.)-0.00000001 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions642642642
Spacing642642642
CellA=B=C: 1361.0399 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.122.122.12
M x/y/z642642642
origin x/y/z0.0000.0000.000
length x/y/z1361.0401361.0401361.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS642642642
D min/max/mean-3.7334.352-0.000

-
Supplemental data

-
Sample components

-
Entire : HSV-1 C-capsid with protein UL25 genetically labeled with GFP at ...

EntireName: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at amino acid 50.
Components
  • Sample: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at amino acid 50.
  • Virus: Human herpesvirus 1 strain KOS

-
Supramolecule #1000: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at ...

SupramoleculeName: HSV-1 C-capsid with protein UL25 genetically labeled with GFP at amino acid 50.
type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Human herpesvirus 1 strain KOS

SupramoleculeName: Human herpesvirus 1 strain KOS / type: virus / ID: 1 / Name.synonym: HSV-1 / NCBI-ID: 10306 / Sci species name: Human herpesvirus 1 strain KOS / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: HSV-1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 1250 Å / T number (triangulation number): 16

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 500 mM NaCl, 10 mM Tris, 1 mM EDTA
VitrificationCryogen name: OTHER / Instrument: FEI VITROBOT MARK III
Details: Vitrification instrument: Vitrobot mark III. Cryogen was an equal mix of ethane-propane.

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 29000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Phase flip each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM

+
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