[English] 日本語
Yorodumi
- EMDB-39457: Nanobody in complex with LILRB3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39457
TitleNanobody in complex with LILRB3
Map data
Sample
  • Complex: Nanobody in complex with LILRB3
    • Protein or peptide: nanobody
    • Protein or peptide: LILRB3
KeywordsLILRB3 Nanobody Dimer / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


cell communication / membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsJin C / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2020YFA0509300 China
CitationJournal: To Be Published
Title: Nanobody in complex with LILRB3
Authors: Jin C / Shi Y
History
DepositionMar 13, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_39457.png

Downloads & links

-
Map

FileDownload / File: emd_39457.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.04
Minimum - Maximum-6.6195264 - 9.216329
Average (Standard dev.)-0.0021580518 (±0.15972811)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.0624 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_39457_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39457_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nanobody in complex with LILRB3

EntireName: Nanobody in complex with LILRB3
Components
  • Complex: Nanobody in complex with LILRB3
    • Protein or peptide: nanobody
    • Protein or peptide: LILRB3

-
Supramolecule #1: Nanobody in complex with LILRB3

SupramoleculeName: Nanobody in complex with LILRB3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: nanobody

MacromoleculeName: nanobody / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.64026 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGSIFV YVPMGWYRQA PGKEREFVAA ISLGSNTNYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCAVTG LRIYPFVYWG QGTQVTVSSH HHHHH

-
Macromolecule #2: LILRB3

MacromoleculeName: LILRB3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.352352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTPALTALLC LGLSLGPRTR VQAGPFPKPT LWAEPGSVIS WGSPVTIWCQ GSLEAQEYRL DKEGSPEPLD RNNPLEPKNK ARFSIPSMT EHHAGRYRCH YYSSAGWSEP SDPLELVMTG FYNKPTLSAL PSPVVASGGN MTLRCGSQKG YHHFVLMKEG E HQLPRTLD ...String:
MTPALTALLC LGLSLGPRTR VQAGPFPKPT LWAEPGSVIS WGSPVTIWCQ GSLEAQEYRL DKEGSPEPLD RNNPLEPKNK ARFSIPSMT EHHAGRYRCH YYSSAGWSEP SDPLELVMTG FYNKPTLSAL PSPVVASGGN MTLRCGSQKG YHHFVLMKEG E HQLPRTLD SQQLHSGGFQ ALFPVGPVNP SHRWRFTCYY YYMNTPQVWS HPSDPLEILP SGVSRKPSLL TLQGPVLAPG QS LTLQCGS DVGYDRFVLY KEGERDFLQR PGQQPQAGLS QANFTLGPVS RSHGGQYRCY GAHNLSSEWS APSDPLNILM AGQ IYDTVS LSAQPGPTVA SGENVTLLCQ SWWQFDTFLL TKEGAAHPPL RLRSMYGAHK YQAEFPMSPV TSAHAGTYRC YGSY SSNPH LLSFPSEPLE LMVSGHSGGS SLPPTGPPST PGLGRYLELE GSDEVDAGSH HHHHHHHHHG SVEDYKDDDD K

UniProtKB: LILRB3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1992467
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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