[English] 日本語
Yorodumi
- EMDB-53000: Legobody dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53000
TitleLegobody dimer
Map data
Sample
  • Complex: Legobody dimer
    • Protein or peptide: Nanobody ALFA-H6
    • Protein or peptide: Fab antibody 8D3_2_H-H6
    • Protein or peptide: Fa antibody 8D3_2_L
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
  • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
Keywordslegobody / dimer / anti-alfa / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host signal transduction pathway via antagonism of host cell surface receptor / IgG binding / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Lysin motif ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Maltose/maltodextrin-binding periplasmic protein / Immunoglobulin G-binding protein G / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesMus musculus (house mouse) / Vicugna pacos (alpaca) / Streptococcus sp. 'group G' (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPacesa M / Van Hall-Beauvais A / Marchand A / Georgeon S / Correia BE
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Structure of a cryoEM scaffold
Authors: Pacesa M / Van Hall-Beauvais A / Marchand A / Georgeon S / Correia BE
History
DepositionMar 3, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53000.png

Downloads & links

-
Map

FileDownload / File: emd_53000.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 280 pix.
= 259.28 Å		0.93 Å/pix.
x 280 pix.
= 259.28 Å		0.93 Å/pix.
x 280 pix.
= 259.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.25093457 - 0.49222967
Average (Standard dev.)0.00021730733 (±0.01426387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 259.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53000_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53000_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53000_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Legobody dimer

EntireName: Legobody dimer
Components
  • Complex: Legobody dimer
    • Protein or peptide: Nanobody ALFA-H6
    • Protein or peptide: Fab antibody 8D3_2_H-H6
    • Protein or peptide: Fa antibody 8D3_2_L
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
  • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

-
Supramolecule #1: Legobody dimer

SupramoleculeName: Legobody dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Nanobody ALFA-H6

MacromoleculeName: Nanobody ALFA-H6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.81354 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLQESGGG LVQPGGSLRL SCTASGVTIS ALNAMAMGWY RQAPGERRVM VAAVSERGNA MYRESVQGRF TVTRDFTNKM VSLQMDNLK PEDTAVYYCH VLEDRVDSFH DYWGQGTQVT VSSLEGTKHH HHHH

-
Macromolecule #2: Fab antibody 8D3_2_H-H6

MacromoleculeName: Fab antibody 8D3_2_H-H6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.539551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLVESGGG LVQPGKSLRL SCAASGFTFS NFGMHWVRQA PEMGLEWVAY ISSGSTTKYY GDTVKGRFTI SRDNPKNTLY LQMNSLRSE DTAMYYCARR PLYDGDYGYP MDYWGQGTSV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
DVQLVESGGG LVQPGKSLRL SCAASGFTFS NFGMHWVRQA PEMGLEWVAY ISSGSTTKYY GDTVKGRFTI SRDNPKNTLY LQMNSLRSE DTAMYYCARR PLYDGDYGYP MDYWGQGTSV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCGS GTKHHHHHH

-
Macromolecule #3: Fa antibody 8D3_2_L

MacromoleculeName: Fa antibody 8D3_2_L / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.095852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NIMLTQSPSS LAVSAGERVT MSCKSTQSIL YNSNQKTYLA WYQQKPGQSP KLLIYWASTR ASGVPDRFTG SGSGTDFTLT INSVQPEDL AVYYCHQYLS AWTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
NIMLTQSPSS LAVSAGERVT MSCKSTQSIL YNSNQKTYLA WYQQKPGQSP KLLIYWASTR ASGVPDRFTG SGSGTDFTLT INSVQPEDL AVYYCHQYLS AWTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

-
Macromolecule #4: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus sp. 'group G' (bacteria)
Molecular weightTheoretical: 59.047051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGSK IEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEIT PDKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN L QEPYFTWP ...String:
MHHHHHHGSK IEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEIT PDKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN L QEPYFTWP LIAADGGYAF KYENGKYDIK DVGVDNAGAK AGLTFLVDLI KNKHMNADTD YSIAEAAFNK GETAMTINGP WA WSNIDTS KVNYGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EEL AKDPRI AATMENAQKG EIMPNIPQMS AFWYAVRTAV INAASGRQTV DQALAFAQIL IMPNLTEEQR NGFIQSLKDD PSVS KEILA EAKKLNEHQA PKGGSGGAGS GDQQSAFYEI LNMPNLNEAQ RNGFIQSLKD DPSQSTNVLG EAKKLNESQA GGGSG GGSG GSAVTTYKLV INGKTLKGET TTKAVDAETA EKAFKQYAND NGVDGVWTYD DATKTFTVT

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Immunoglobulin G-binding protein A, Immunoglobulin G-binding protein A, Immunoglobulin G-binding protein G

-
Macromolecule #5: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus sp. 'group G' (bacteria)
Molecular weightTheoretical: 59.176168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGSK IEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEIT PDKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN L QEPYFTWP ...String:
MHHHHHHGSK IEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEIT PDKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN L QEPYFTWP LIAADGGYAF KYENGKYDIK DVGVDNAGAK AGLTFLVDLI KNKHMNADTD YSIAEAAFNK GETAMTINGP WA WSNIDTS KVNYGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EEL AKDPRI AATMENAQKG EIMPNIPQMS AFWYAVRTAV INAASGRQTV DQALAFAQIL IMPNLTEEQR NGFIQSLKDD PSVS KEILA EAKKLNEHQA PKGGSGGAGS GDQQSAFYEI LNMPNLNEAQ RNGFIQSLKD DPSQSTNVLG EAKKLNESQA GGGSG GGSG GSAVTTYKLV INGKTLKGET TTKAVDAETA EKAFKQYAND NGVDGVWTYD DATKTFTVTE

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Immunoglobulin G-binding protein A, Immunoglobulin G-binding protein A, Immunoglobulin G-binding protein G

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 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: 0.8 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114803
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