[English] 日本語
Yorodumi
- EMDB-30939: Lamprey serum virus-like lectin-LSVL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30939
TitleLamprey serum virus-like lectin-LSVL
Map data
Sample
  • Tissue: lamprey serum virus-like lectin-LSVL
    • Protein or peptide: Serum lectin
  • Ligand: CALCIUM IONCalcium
Function / homologyFibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / carbohydrate binding / Serum lectin
Function and homology information
Biological speciesLethenteron camtschaticum (Arctic lamprey) / Japanese lamprey (Arctic lamprey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsPeng Y
CitationJournal: To Be Published
Title: Structure of lamprey serum virus-like lectin with high binding capacity, involved in initiation and regulation of innate immunity
Authors: Qingwei L / Peng Y
History
DepositionFeb 1, 2021-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_30939.png

Downloads & links

-
Map

FileDownload / File: emd_30939.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.30654 Å
Density
Contour LevelBy AUTHOR: 0.0521
Minimum - Maximum-0.09379877 - 0.20229246
Average (Standard dev.)0.001149745 (±0.008649251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 334.47424 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : lamprey serum virus-like lectin-LSVL

EntireName: lamprey serum virus-like lectin-LSVL
Components
  • Tissue: lamprey serum virus-like lectin-LSVL
    • Protein or peptide: Serum lectin
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: lamprey serum virus-like lectin-LSVL

SupramoleculeName: lamprey serum virus-like lectin-LSVL / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Lethenteron camtschaticum (Arctic lamprey)

-
Macromolecule #1: Serum lectin

MacromoleculeName: Serum lectin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Japanese lamprey (Arctic lamprey)
Molecular weightTheoretical: 36.481047 KDa
SequenceString: MEASRLLLLL LLPLLLLFCN SVAAACSCTD SCSDAKESES KCGCKHEEET KQLPRSCKEI KLKTKTKEDG VYCLQTKSGQ FYQAFCDMN TNGGGWTLVA SVHENNIAAK CAIGDRWSSQ LGSNPAVGFV DGDRSWANLN TFGRVESATD DDYKNPGYFD V DAEDISVW ...String:
MEASRLLLLL LLPLLLLFCN SVAAACSCTD SCSDAKESES KCGCKHEEET KQLPRSCKEI KLKTKTKEDG VYCLQTKSGQ FYQAFCDMN TNGGGWTLVA SVHENNIAAK CAIGDRWSSQ LGSNPAVGFV DGDRSWANLN TFGRVESATD DDYKNPGYFD V DAEDISVW HVPNGTPLAQ WKISSIFRYH TATEFLTPLG GNLYFLYKIF YPLVYGSGTC PASNGPAIPI VYDFGNTISV AS QVCPACL GGTLQGYVHL RVFNNERAPF ALCSGLRVLD NCNTEHYCIG GAGYVPEQTP RQCGDFSAFD WSGIGTHVEW SAS KSLLEA AVFIFYR

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225296

+
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