[English] 日本語
Yorodumi
- EMDB-82430: PC-Int1 + 13H11-Fab + 2C12-Fab + 7I13-Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-82430
TitlePC-Int1 + 13H11-Fab + 2C12-Fab + 7I13-Fab
Map data
Sample
  • Complex: HCMV pentamer in complex with 3Fabs
    • Protein or peptide: x 11 types
  • Ligand: x 1 types
KeywordsVirus / Antibody / VIRAL PROTEIN
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu TC / Liu P
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure-guided stabilization of the HCMV pentamer enhances thermostability and neutralizing antibody responses
Authors: Liu P / Yu JP / Liu TC / Liu Y / Wang XX
History
DepositionJul 22, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_82430.png

Downloads & links

-
Map

FileDownload / File: emd_82430.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.371
Minimum - Maximum-0.4785744 - 1.0589375
Average (Standard dev.)0.00083711743 (±0.037833996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_82430_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_82430_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : HCMV pentamer in complex with 3Fabs

EntireName: HCMV pentamer in complex with 3Fabs
Components
  • Complex: HCMV pentamer in complex with 3Fabs
    • Protein or peptide: gH
    • Protein or peptide: gL
    • Protein or peptide: UL128
    • Protein or peptide: UL130
    • Protein or peptide: UL131A
    • Protein or peptide: 7I13 Heavy chain
    • Protein or peptide: 7I13 Light chain
    • Protein or peptide: 2C12 Heavy chain
    • Protein or peptide: 2C12 Light chain
    • Protein or peptide: 13H11 heavy chain
    • Protein or peptide: 13H11 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

+
Supramolecule #1: HCMV pentamer in complex with 3Fabs

SupramoleculeName: HCMV pentamer in complex with 3Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Human betaherpesvirus 5

+
Macromolecule #1: gH

MacromoleculeName: gH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 84.4045 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPGLPSYLI ILAVCLFSHL LSSQYGADAA SEALDPHAFH LLLNTYGRPI RFLRENTTQC TYNSSLRNST VVRENAISFN FFQSYNQYY VFHMPRCLFA GPLAEQFLNQ VDLTETLERY QQRLNTYALV SKDLASYRSF SQQLKAQDSL GEQPTTVPPP I DLSIPHVW ...String:
MRPGLPSYLI ILAVCLFSHL LSSQYGADAA SEALDPHAFH LLLNTYGRPI RFLRENTTQC TYNSSLRNST VVRENAISFN FFQSYNQYY VFHMPRCLFA GPLAEQFLNQ VDLTETLERY QQRLNTYALV SKDLASYRSF SQQLKAQDSL GEQPTTVPPP I DLSIPHVW MPPQTTPHGW TESHTTSGLH RPHFNQTCIL FDGHDLLFST VTPCLHQGFY LIDELRYVKI TLTEDFFVVT VS IDDDTPM LLIFGHLPRV LFKAPYQRDN FILRQTEKHE LLVLVKKDQL NRHSYLKDPD FLDAALDFNY LDLSALLRNS FHR YAVDVL KSGRCQMLDR RTVEMAFAYA LALFAAARQE EAGAQVSVPR ALDRQAALLQ IQEFMITCLS QTPPRTTLLL YPTA VDLAK RALWTPNQIT DITSLVRLVY ILSKQNQQHL IPQWALRQIA DFALKLHKTH LASFLSAFAR QELYLMGSLV HSMLV HTTE RREIFIVETG LCSLAELSHF TQLLAHPHHE YLSDLYTPCS SSGRRDHSLE RLTRLFPDAT VPTTVPAALS ILSTMQ PST LETFPDLFCL PLGESFSALT VSEHVSYVVT NQYLIKGISY PVSTTVVGQS LIITQTDSQT KCELTRNMHT THSITAA LN ISLENCAFCQ SALLEYDDTQ GVINIMYMHD SDDVLFALDP YNEVVVSSPR THYLMLLKNG TVLEVTDVVV DATDSRLL M MSVYALSAII GIYLLYRMLK TC

+
Macromolecule #2: gL

MacromoleculeName: gL / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 30.845508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MCRRPDCGFS FSPGPVILLW CCLLLPIVSS AAVSVAPTAA EKVPAECPEL TRRCLLGEVF QGDKYESWLR PLVNVTGRDG PLSQLIRYR PVTPEAANSV LLDEAFLDTL ALLYNNPDQL RALLTLLSSD TAPRWMTVMR GYSECGDGSP AVYTCVDDLC R GYDLTRLS ...String:
MCRRPDCGFS FSPGPVILLW CCLLLPIVSS AAVSVAPTAA EKVPAECPEL TRRCLLGEVF QGDKYESWLR PLVNVTGRDG PLSQLIRYR PVTPEAANSV LLDEAFLDTL ALLYNNPDQL RALLTLLSSD TAPRWMTVMR GYSECGDGSP AVYTCVDDLC R GYDLTRLS YGRSIFTEHV LGFELVPPSL FNVVVAIRNE ATRTNRAVRL PVSTAAAPEG ITLFYGLYNA VKEFCLRHQL DP PLLRHLD KYYAGLPPEL KQTRVNLPAH SRYGPQAVDA R

+
Macromolecule #3: UL128

MacromoleculeName: UL128 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 19.777035 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSPKDLTPFL TTLWLLLGHS RVPRVRAEEC CEFINVNHPP ERCYDFKMCN RFTVALRCPD GEVCYSPEKT AEIRGIVTTM THSLTRQVV HNKLTSCNYN PLYLEADGRI RCGKVNDKAQ YLLGAAGSVP YRWINLEYDK ITRIVGLDQY LESVKKHKRL D VCRAKMGY MLQ

+
Macromolecule #4: UL130

MacromoleculeName: UL130 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 24.773584 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLRLLLRHHF HCLLLCAVWA TPCLASPWST LTANKNPSPP WSKLTYSKPH DAATFYCPFL YPSPEFSPLQ FSGFQRVSTG PECRNETLY LLYNREGQIL VERSSTWVKK VIWYLSGRNQ TILQRMPRTA SKPSDGNVQI SVEDAKIFGA HMVPKQTKLL R FVVNDGTR ...String:
MLRLLLRHHF HCLLLCAVWA TPCLASPWST LTANKNPSPP WSKLTYSKPH DAATFYCPFL YPSPEFSPLQ FSGFQRVSTG PECRNETLY LLYNREGQIL VERSSTWVKK VIWYLSGRNQ TILQRMPRTA SKPSDGNVQI SVEDAKIFGA HMVPKQTKLL R FVVNDGTR YQMCVMKLES WAHVFRDYSV SFQVRLTFTE ANNQTYTFCT HPNLIV

+
Macromolecule #5: UL131A

MacromoleculeName: UL131A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 15.011043 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MRLCRVWLSV CLCAVVLGQC QRETAEKNDY YRVPHYWDAC SRALPDQTRY KYVEQLVDLT LNYHYDASHG LDNFDVLKRI NVTEVSLLI SDFRRQNRRG GTNKRTTFNA AGSLAPHARS LEFSVRLFAN

+
Macromolecule #6: 7I13 Heavy chain

MacromoleculeName: 7I13 Heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.740323 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS NYGMHWVRQG PGKGLEWVAV ISYDASSKYY TDSVQGRFTI SRDNSKNTLF LQMNSLRGE DTAVYYCAKA LRYLDWFLSD PFDYWGQGTL VTVS

+
Macromolecule #7: 7I13 Light chain

MacromoleculeName: 7I13 Light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.548807 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SDFLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYAASPPFG QGTRLEIK

+
Macromolecule #8: 2C12 Heavy chain

MacromoleculeName: 2C12 Heavy chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.723137 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QITLRESGPT LVKPTQTLTL TCTFSGFSLN TNGVGVGWIR QPPGKALEWL ALIYWNGNEG YSPSLKSRLT ITKDTSKNQV VLTMTNMDP VDTATYYCVH WPQGLTTVTR LAFDIWGQGT MVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVS

+
Macromolecule #9: 2C12 Light chain

MacromoleculeName: 2C12 Light chain / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.91617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPRSV SGSPGQSVTI SCTGTTSDVG RYNFVSWYQQ HPGKAPKLLM YDVSQRPSGV PSRFSGSKSG NTASLTISGL QAEDEAVFY CCSYAGGNFF SYVFGTGTKV TVLG

+
Macromolecule #10: 13H11 heavy chain

MacromoleculeName: 13H11 heavy chain / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.380985 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT NYYIHWVRQA PGQGLEWMGI IHPSSGGTSY AQKFQGRVTM TRDTSTSTVS MDLSSLRSE DTAVYYCGRA FRILGLSDVF VNDWGQGTVV TVSS

+
Macromolecule #11: 13H11 light chain

MacromoleculeName: 13H11 light chain / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.241583 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQGIN NYLAWYQQKP GKVPKLLIYA ASTLQSGVPS RFSGSGSGTA FTLTILSLQP EDVATYYCQ KYNSAPFTFG PGTKVD

+
Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.35
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 564374
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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