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- EMDB-76684: Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-76684
TitlePneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab
Map data
Sample
  • Complex: Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab
    • Protein or peptide: Choline binding protein E CbpE
    • Protein or peptide: 5992-2 Fab Heavy Chain
    • Protein or peptide: 5992-2 Fab Light Chain
KeywordsPNEUMOCOCCAL CHOLINE BINDING / CryoEM / HUMAN MONOCLONAL ANTIBODY / IMMUNE SYSTEM
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity
Similarity search - Function
ComA-like, MBL domain / : / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Choline binding protein E CbpE
Similarity search - Component
Biological speciesHomo sapiens (human) / Streptococcus pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsMcCormick A / Ghazi Esfahani B / Vidal J / Lee FE / Tompkins M / McCaffrey K / Mousa J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI173084 United States
CitationJournal: To Be Published
Title: BROADLY REACTIVE HUMAN MONOCLONAL ANTIBODY TARGETING CONSERVED PNEUMOCOCCAL CHOLINE BINDING DOMAIN INCREASES PROTECTION AGAINST LETHAL PNEUMOCOCCAL INFECTION
Authors: McCormick A / Ghazi Esfahani B / Vida J / Lee FE / Tompkins M / McCaffrey K / Mousa J
History
DepositionApr 15, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76684.png

Downloads & links

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Map

FileDownload / File: emd_76684.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 360 pix.
= 284.4 Å		0.79 Å/pix.
x 360 pix.
= 284.4 Å		0.79 Å/pix.
x 360 pix.
= 284.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.7822372 - 2.7444031
Average (Standard dev.)-0.00090901303 (±0.03929501)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 284.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_76684_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76684_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76684_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 : Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab

EntireName: Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab
Components
  • Complex: Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab
    • Protein or peptide: Choline binding protein E CbpE
    • Protein or peptide: 5992-2 Fab Heavy Chain
    • Protein or peptide: 5992-2 Fab Light Chain

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Supramolecule #1: Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab

SupramoleculeName: Pneumococcal choline binding CbpE surface protein bounds to 5992-2 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Choline binding protein E CbpE

MacromoleculeName: Choline binding protein E CbpE / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 45.515266 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: SSGNKIHFIN VQEGGSDAII LESNGHFAMV DTGEDYDFPD GSDSRYPWRE GIETSYKHVL TDRVFRRLKE LGVQKLDFIL VTHTHSDHI GNVDELLSTY PVDRVYLKKY SDNRITNSER LWDNLYGYDK VLQTASEKGV SVIQNITQGD AHFQFGDMDI Q LYNYENET ...String:
SSGNKIHFIN VQEGGSDAII LESNGHFAMV DTGEDYDFPD GSDSRYPWRE GIETSYKHVL TDRVFRRLKE LGVQKLDFIL VTHTHSDHI GNVDELLSTY PVDRVYLKKY SDNRITNSER LWDNLYGYDK VLQTASEKGV SVIQNITQGD AHFQFGDMDI Q LYNYENET DSSGELKKIW DDNSNSLISV VKVNGKKIYL GGDLDNVHGA EDKYGPLIGK VDLMKFNHHH DTNKSNTKDF IK NLSPSLI VQTSDSLPWK NGVDSEYVNW LKERGIERIN AASKDYDATV FDIRQDGLVN ISTSYKPIPS FQAGWHKSSY GNW WYQAPD STGEYAVGWN EIKGEWYYFN QTGILLQNQW KKWNNRWFYL TDSGVAAKNW KKIAGIWYYF NKENQMEI

UniProtKB: Choline binding protein E CbpE

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Macromolecule #2: 5992-2 Fab Heavy Chain

MacromoleculeName: 5992-2 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.679229 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPR LVKVSETLSL TCSLSGHSIS SGHHWAWIRQ SPGRGLEWIA TVDHNGRTYY NPSLRGRVIL SKDTTKNSFS VQLTSVTAA DTAVYYCARR EAPSPGTGWY PPFGQWGQGA LVTVST

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Macromolecule #3: 5992-2 Fab Light Chain

MacromoleculeName: 5992-2 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.381578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSL SGAPGQTVTI SCTGSSSNIG AGYDVHWYRQ LPGTAPTLLI SVFDNRPLGV PGRISGSKSG TSASLAITGL QAEDEADYY CQSHDNMLSG SVFGGGTKLT VL

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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: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alphafold 3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 59000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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