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- EMDB-44734: 16E10 Fab bound to norovirus GI.1 P domain -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44734
Title16E10 Fab bound to norovirus GI.1 P domain
Map data
Sample
  • Complex: P domain dimer bound by two copies of 16E10 Fab
    • Complex: P domain dimer from GI.1 norovirus
      • Protein or peptide: Capsid protein VP1
    • Complex: 16E10 Fab
      • Protein or peptide: 16E10 Light Chain
      • Protein or peptide: 16E10 Heavy Chain
Keywordsnorovirus / VP1 / P-domain / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesNorovirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsOlia AS / Morano NC / Shapiro L / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: A Protective Human Norovirus Antibody with Broad GI Recognition
Authors: Rimkute I / Olia AS / Morano NC / Shapiro L / Kwong PD / Roederer M
History
DepositionMay 3, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44734.png

Downloads & links

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Map

FileDownload / File: emd_44734.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.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.158
Minimum - Maximum-0.24736898 - 0.5017555
Average (Standard dev.)0.000873665 (±0.017618582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44734_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_44734_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 : P domain dimer bound by two copies of 16E10 Fab

EntireName: P domain dimer bound by two copies of 16E10 Fab
Components
  • Complex: P domain dimer bound by two copies of 16E10 Fab
    • Complex: P domain dimer from GI.1 norovirus
      • Protein or peptide: Capsid protein VP1
    • Complex: 16E10 Fab
      • Protein or peptide: 16E10 Light Chain
      • Protein or peptide: 16E10 Heavy Chain

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Supramolecule #1: P domain dimer bound by two copies of 16E10 Fab

SupramoleculeName: P domain dimer bound by two copies of 16E10 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Norovirus

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Supramolecule #2: P domain dimer from GI.1 norovirus

SupramoleculeName: P domain dimer from GI.1 norovirus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Norovirus

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Supramolecule #3: 16E10 Fab

SupramoleculeName: 16E10 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Norovirus
Molecular weightTheoretical: 31.337105 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPKTRPFTLP NLPLSSLSNS RAPLPISSIG ISPDNVQSVQ FQNGRCTLDG RLVGTTPVSL SHVAKIRGTS NGTVINLTEL DGTPFHPFE GPAPIGFPDL GGCDWHINMT QFGHSSQTQY DVDTTPDTFV PHLGSIQANG IGSGNYVGVL SWISPPSHPS G SQVDLWKI ...String:
GPKTRPFTLP NLPLSSLSNS RAPLPISSIG ISPDNVQSVQ FQNGRCTLDG RLVGTTPVSL SHVAKIRGTS NGTVINLTEL DGTPFHPFE GPAPIGFPDL GGCDWHINMT QFGHSSQTQY DVDTTPDTFV PHLGSIQANG IGSGNYVGVL SWISPPSHPS G SQVDLWKI PNYGSSITEA THLAPSVYPP GFGEVLVFFM SKMPGPGAYN LPCLLPQEYI SHLASEQAPT VGEAALLHYV DP DTGRNLG EFKAYPDGFL TCVPNGASSG PQQLPINGVF VFVSWVSRFY QLKPVGT

UniProtKB: Capsid protein VP1

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Macromolecule #2: 16E10 Light Chain

MacromoleculeName: 16E10 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.908594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMSQSPVS LPVTPGEPAS ISCRSSQSLL HSNGYNYVDW YLQKPGQSPQ LLLYLGSNRA AGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PYTFGQGTKL DIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMSQSPVS LPVTPGEPAS ISCRSSQSLL HSNGYNYVDW YLQKPGQSPQ LLLYLGSNRA AGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PYTFGQGTKL DIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #3: 16E10 Heavy Chain

MacromoleculeName: 16E10 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.514283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLLESGGAL VHPGGSLRLS CAASGFTFSS SSFSWVRQAP GKGLEWVSGI NPSGHDTYYA DSVKGRFTIS RDNSKDTLFL EMNSLRAED TAQYYCAKKI DFPFRGGRRY SDSRPYNTGS LDSWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String:
VQLLESGGAL VHPGGSLRLS CAASGFTFSS SSFSWVRQAP GKGLEWVSGI NPSGHDTYYA DSVKGRFTIS RDNSKDTLFL EMNSLRAED TAQYYCAKKI DFPFRGGRRY SDSRPYNTGS LDSWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKV

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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: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 393251
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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