[English] 日本語
Yorodumi
- EMDB-74418: Unknown entry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74418
TitleHuman cytomegalovirus UL52 3-mer
Map dataHCMV UL52 3-mer
Sample
  • Complex: UL52
    • Protein or peptide: HCMV UL52
KeywordsHuman cytomegalovirus / HCMV / viral genome packaging / packaging accessory factor / UL52 / VIRAL PROTEIN
Biological speciesHuman betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsBailey EJ / Devarkar SC / Xiong Y / Didychuk AL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP2 AI171113 United States
American Cancer SocietyPF-24-1322561-01-RMC United States
CitationJournal: Biorxiv / Year: 2026
Title: Conserved assembly architecture of the essential herpesvirus packaging accessory factor.
Authors: Bailey EJ / Devarkar SC / Szczepaniak R / Meissner LM / Chen X / Wu C / Weller SK / Xiong Y / Didychuk AL
History
DepositionDec 9, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74418.png

Downloads & links

-
Map

FileReleased
AnnotationHCMV UL52 3-mer
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0606
Minimum - Maximum-0.11157383 - 0.27745992
Average (Standard dev.)0.00023192272 (±0.006030281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_74418_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : UL52

EntireName: UL52
Components
  • Complex: UL52
    • Protein or peptide: HCMV UL52

-
Supramolecule #1: UL52

SupramoleculeName: UL52 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human betaherpesvirus 5

-
Macromolecule #1: HCMV UL52

MacromoleculeName: HCMV UL52 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGLEVLFQG PMNPSTHVSS NGPTTPPHGP HTTFLPPTSP APSTSSVAAA TLCSPQRQAV SRYSGWSTEY TQWHSDLTTE LLWHAHPRQV PMDEALAAAA AASYQVNPQH PANRYRHYEF QTLSLGTSEV DELLNCCAEE ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGLEVLFQG PMNPSTHVSS NGPTTPPHGP HTTFLPPTSP APSTSSVAAA TLCSPQRQAV SRYSGWSTEY TQWHSDLTTE LLWHAHPRQV PMDEALAAAA AASYQVNPQH PANRYRHYEF QTLSLGTSEV DELLNCCAEE TTCGGTQSTV LTNATNTTNC GGAVAGSSNA GPAGASAACD LDAELAGLET SAADFEQLRR LCAPLAIDTR CNLCAIISIC LKQDCDQSWL LEYSLLCFKC SYAPRAALST LIIMSEFTHL LQQHFSDLRI DDLFRHHVLT VFDFHLHFFI NRCFEKQVGD AVDNENVTLN HLAVVRAMVM GEDTVPYNKP RRHPQQKQKT NPYHVEVPQE LIDNFLEHSS PSRDRFVQLL FYMWAGTGVM STTPLTELTH TKFARLDALS TTSEREDARM MMEEEEDEEG GEKGGDDPGR HNGGGTSGGF SESTLKKNVG PIYLCPVPAF FTKNQTSTVC LLCELMACSY YDNVVLRELY RRVVSYCQNN VKMVDRIQLV LADLLRECTS PLGAAHEDVA RCGLEAPTSP GGDSDYHGLS GVDGALARPD PVFCHVLRQA GVTGIYKHFF CDPQCAGNIR VTNEAVLFGR LHPHHVQEVK LAICHDNYYI SRLPRRVWLC ITLFKAFQIT KRTYKGKVHL ADFMRDFTQL LESCDIKLVD PTYVIDKYV

UniProtKB: Packaging protein UL32 homolog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.55 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES pH 7.6
100.0 mMNaClsodium chloride
1.0 mMC4H10O2S2dithiothreitol (DTT)
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.015 kPa / Details: 11 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 118585
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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