[English] 日本語
Yorodumi
- EMDB-63031: LayV-G Head in complex of LayG-1069 and LayG-1133 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63031
TitleLayV-G Head in complex of LayG-1069 and LayG-1133
Map data
Sample
  • Complex: LayV-G Head in complex of LayG-1046 and LayG-1133
    • Protein or peptide: LayG-1069 heavy chain
    • Protein or peptide: LayG-1069 light chain
    • Protein or peptide: LayG-1133 heavy chain
    • Protein or peptide: LayG-1133 light chain
    • Protein or peptide: Attachment glycoprotein
Keywordscomplex / virus protein / Antibody / Glycoprotein / Henipa Virus / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell membrane / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Attachment glycoprotein
Similarity search - Component
Biological speciesLangya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsYan RH / Wu SY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LayV-G Head in complex of LayG-1069 and LayG-1133
Authors: Yan RH / Wu SY
History
DepositionJan 7, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_63031.png

Downloads & links

-
Map

FileDownload / File: emd_63031.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 256.5 Å		0.86 Å/pix.
x 300 pix.
= 256.5 Å		0.86 Å/pix.
x 300 pix.
= 256.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.33827585 - 0.8952271
Average (Standard dev.)-0.0000723709 (±0.025278559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 256.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_63031_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63031_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LayV-G Head in complex of LayG-1046 and LayG-1133

EntireName: LayV-G Head in complex of LayG-1046 and LayG-1133
Components
  • Complex: LayV-G Head in complex of LayG-1046 and LayG-1133
    • Protein or peptide: LayG-1069 heavy chain
    • Protein or peptide: LayG-1069 light chain
    • Protein or peptide: LayG-1133 heavy chain
    • Protein or peptide: LayG-1133 light chain
    • Protein or peptide: Attachment glycoprotein

-
Supramolecule #1: LayV-G Head in complex of LayG-1046 and LayG-1133

SupramoleculeName: LayV-G Head in complex of LayG-1046 and LayG-1133 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Langya virus

-
Macromolecule #1: LayG-1069 heavy chain

MacromoleculeName: LayG-1069 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.106867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLQESGPD LVKPSQSLSL TCTVTGYSIT SGYSWHWIRQ FPGNKLEWMG SIHFSGISNY NPSLKGRISI TRDTSKNQFF LQLNSVTTE DTATYYCVRK DFGSSHHFDY WGQGTTLTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
DVQLQESGPD LVKPSQSLSL TCTVTGYSIT SGYSWHWIRQ FPGNKLEWMG SIHFSGISNY NPSLKGRISI TRDTSKNQFF LQLNSVTTE DTATYYCVRK DFGSSHHFDY WGQGTTLTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSC

-
Macromolecule #2: LayG-1069 light chain

MacromoleculeName: LayG-1069 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.586225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SIVMTQTPKF LLVSAGDRVA MTCKASQSVN DDVAWYQQKP GQSPKLLINF ASNRYTGVPD RFTGSGYGTD FTFTISTVQA EDLAFYFCQ QDYSSPFTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
SIVMTQTPKF LLVSAGDRVA MTCKASQSVN DDVAWYQQKP GQSPKLLINF ASNRYTGVPD RFTGSGYGTD FTFTISTVQA EDLAFYFCQ QDYSSPFTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #3: LayG-1133 heavy chain

MacromoleculeName: LayG-1133 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.107777 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYAWNWIRQ FPGNKLEWMG YISYSGSTSY NPSLKSRISI TRDTSKNQFF LQLNSVTTE DTATYYCARY YDAPYYFDYW GQGTTLTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
DVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYAWNWIRQ FPGNKLEWMG YISYSGSTSY NPSLKSRISI TRDTSKNQFF LQLNSVTTE DTATYYCARY YDAPYYFDYW GQGTTLTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSC

-
Macromolecule #4: LayG-1133 light chain

MacromoleculeName: LayG-1133 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.22076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPAS LSASVGETVT ITCGASENIY GALNWYQRKQ GKSPQLLIYG ATNLADGMSS RFSGSGSGRQ YSLKISSLHP DDVATYYCQ NVLSTPFTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPAS LSASVGETVT ITCGASENIY GALNWYQRKQ GKSPQLLIYG ATNLADGMSS RFSGSGSGRQ YSLKISSLHP DDVATYYCQ NVLSTPFTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #5: Attachment glycoprotein

MacromoleculeName: Attachment glycoprotein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Langya virus
Molecular weightTheoretical: 49.605688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DKPDDDTTDD DKVDTTIKPV EYYKPDGCNK TNDHFTMQPG VNFYTVPNLG PSSSSADECY TNPSFSIGSS IYMFSQEIRK TDCTTGEIL SIQIVLGRIV DKGQQGPQAS PLLVWSVPNP KIINSCAVAA GDETGWVLCS VTLTAASGEP IPHMFDGFWL Y KFEPDTEV ...String:
DKPDDDTTDD DKVDTTIKPV EYYKPDGCNK TNDHFTMQPG VNFYTVPNLG PSSSSADECY TNPSFSIGSS IYMFSQEIRK TDCTTGEIL SIQIVLGRIV DKGQQGPQAS PLLVWSVPNP KIINSCAVAA GDETGWVLCS VTLTAASGEP IPHMFDGFWL Y KFEPDTEV VAYRITGFAY LLDKVYDSVF IGKGGGIQRG NDLYFQMFGL SRNRQSIKAL CEHGSCLGTG GGGYQVLCDR AV MSFGSEE SLISNAYLKV NDVASGKPTI ISQTFPPSDS YKGSNGRIYT IGERYGIYLA PSSWNRYLRF GLTPDISVRS TTW LKEKDP IMKVLTTCTN TDKDMCPEIC NTRGYQDIFP LSEDSSFYTY IGITPSNEGT KSFVAVKDDA GHVASITILP NYYS ITSAT ISCFMYKEEI WCIAVTEGRK QKENPQRIYA HSYRVQKMCF NI

UniProtKB: Attachment glycoprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8jzb

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 260375
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