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- EMDB-53000: Legobody dimer -

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ID or keywords:

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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


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

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Structure visualization

Supplemental images

emd_53000.png

Downloads & links

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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 °

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Supplemental data

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Mask #1

Fileemd_53000_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53000_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53000_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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Supramolecule #1: Legobody dimer

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

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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

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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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

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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)

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