[English] 日本語
Yorodumi
- EMDB-75608: C3 Hexon Map of Phage Goslar -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75608
TitleC3 Hexon Map of Phage Goslar
Map data
Sample
  • Virus: Goslarvirus
    • Protein or peptide: Major capsid protein
KeywordsMCP / Capsid / Phage / VIRAL PROTEIN
Function / homology: / Bacteriophage PhiKZ major capsid protein gp120 / Major capsid protein
Function and homology information
Biological speciesGoslarvirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsBasu D / Gu Y / Corbett KD
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: To Be Published
Title: C3 Hexon Map of Phage Goslar
Authors: Basu D
History
DepositionFeb 16, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75608.png

Downloads & links

-
Map

FileDownload / File: emd_75608.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 480 pix.
= 672. Å		1.4 Å/pix.
x 480 pix.
= 672. Å		1.4 Å/pix.
x 480 pix.
= 672. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.153
Minimum - Maximum-0.2694458 - 0.6233426
Average (Standard dev.)0.0028066935 (±0.033696722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 672.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_75608_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_75608_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Goslarvirus

EntireName: Goslarvirus
Components
  • Virus: Goslarvirus
    • Protein or peptide: Major capsid protein

-
Supramolecule #1: Goslarvirus

SupramoleculeName: Goslarvirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2733105 / Sci species name: Goslarvirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Goslarvirus
Molecular weightTheoretical: 83.400391 KDa
SequenceString: MNDKTLLSQQ VAATRQFLTA NGSKPADKGL ENTFLSMESA SKVDFKSMDK LVNEMDVKSF SSDIRKAEEP VLTLLGFETT TPEEKQRIE EQLFTMNAQQ ARAAALIMLA HGNPVEYAKQ ARSMNISTTP SGREVDSSNF VMMAADSCGC ESEELVQLSY D QKELRDMM ...String:
MNDKTLLSQQ VAATRQFLTA NGSKPADKGL ENTFLSMESA SKVDFKSMDK LVNEMDVKSF SSDIRKAEEP VLTLLGFETT TPEEKQRIE EQLFTMNAQQ ARAAALIMLA HGNPVEYAKQ ARSMNISTTP SGREVDSSNF VMMAADSCGC ESEELVQLSY D QKELRDMM PYSVVFNVKA SRLSRMGNEL YNTIVLAPNQ IGYDVSFRRP LVFNHLRRNA DGTPADWVRR PLLDAFMYND VL SNDVTDL HPIYRADDAN AQYFVDKAIV APRDIEIKGV TYKTSYLAVD KLIDMIGIAE DDSILANGYS DNTDALDAQI TLT KILVEI KSTKHSKTSY VPFDVSGLIT NGFQKSLEGD FRKMTLAFDT HSIFVDENTK DVKGAKAEAL QDIIDAKSAA QLAI EVYGS SNVEKAGLRV NGANAELYRL VDQDNIEQPR KSEEFKQLAE DLSFKLVGYE LRIRRNNSNR RERGKHLDFN MKQER YAIG LLAPFSIPRP LDWEENAADL DVLIQAANAR FDNLMVEKLF SYKDALKAVA TSRFRQFGDI QIEGFGRYLI RPWFEE INL DLEKSVQGTT TAERRAEVSA AIMNVIREMA YRMYSESGYQ PALQLLSSNA DEKPRCVVAT DNYIPQFLQT DGDFRTV GV SFNFVVVDNP NVMLRDKIFV TLSRGIQGSP DPLTFGMFLY VPELVSVAQV TRNGQVSKET MVQPRCRFVN NCPLLGLI N VVNLRKVYTE NIKLPVQTN

UniProtKB: Major capsid protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 102070
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-11bt:
C3 Hexon Map of Phage Goslar

+
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