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- EMDB-47071: #1664 Fab in complex with NG2 COBRA hemagglutinin -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47071
Title#1664 Fab in complex with NG2 COBRA hemagglutinin
Map dataFab in complex with NG2 COBRA hemagglutinin
Sample
  • Complex: Complex of #1664 Fab fragment with NG2 COBRA hemagglutinin
    • Protein or peptide: Fab-1664 heavy chain
    • Protein or peptide: Fab-1664 light chain
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / COBRA / antibody / Fab / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsNagashima K / Mousa J
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: #1664 Fab in complex with NG2 COBRA hemagglutinin
Authors: Nagashima K / Mousa J
History
DepositionSep 18, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47071.png

Downloads & links

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Map

FileDownload / File: emd_47071.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFab in complex with NG2 COBRA hemagglutinin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 768 pix.
= 403.968 Å		0.53 Å/pix.
x 768 pix.
= 403.968 Å		0.53 Å/pix.
x 768 pix.
= 403.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.526 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.8375481 - 1.167109
Average (Standard dev.)0.000023490133 (±0.017634986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 403.96802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_47071_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_47071_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of #1664 Fab fragment with NG2 COBRA hemagglutinin

EntireName: Complex of #1664 Fab fragment with NG2 COBRA hemagglutinin
Components
  • Complex: Complex of #1664 Fab fragment with NG2 COBRA hemagglutinin
    • Protein or peptide: Fab-1664 heavy chain
    • Protein or peptide: Fab-1664 light chain
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of #1664 Fab fragment with NG2 COBRA hemagglutinin

SupramoleculeName: Complex of #1664 Fab fragment with NG2 COBRA hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fab-1664 heavy chain

MacromoleculeName: Fab-1664 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.839373 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQVMQSGAE ARMTGATVKI SCKASGYTFS DYFLHWVKQA PGKGLEWMGL VDVDNGEVRY AEKFQGRVTI TADTSTETAY LEMTTVTSG DTAVYYCAST TPRGGNPSVY NYFFVDVWGK GTTVTVSS

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Macromolecule #2: Fab-1664 light chain

MacromoleculeName: Fab-1664 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.663727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QPVLTQSSSA SASLGSSVKL TCTLSSGHDN YIIAWHQQQP GKAPRYLMQV GAGGTYNKGS GVPHRFSGSS SGADRYLTIS NLQSDDEAD YYCETWDSKT VFGGGTTLTV L

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 64.499406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI LCLVFAQKIP GNDNSTATLC LGHHAVPNGT IVKTITNDRI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFKNE SFNWTGVTQN GTSSACIRGS S SSFFSRLN ...String:
MKTIIALSYI LCLVFAQKIP GNDNSTATLC LGHHAVPNGT IVKTITNDRI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFKNE SFNWTGVTQN GTSSACIRGS S SSFFSRLN WLTHLNYTYP ALNVTMPNNE QFDKLYIWGV HHPGTDKDQI FLYAQSSGRI TVSTKRSQQA VIPNIGSRPR IR DIPSRIS IYWTIVKPGD ILLINSTGNL IAPRGYFKIR SGKSSIMRSD APIGKCKSEC ITPNGSIPND KPFQNVNRIT YGA CPRYVK QSTLKLATGM RNVPEKQTRG IFGAIAGFIE NGWEGMVDGW YGFRHQNSEG RGQAADLKST QAAIDQINGK LNRL IGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKID LWSYNAELLV ALENQHTIDL TDSEMNKLFE KTKKQLRENA EDMGN GCFK IYHKCDNACI GSIRNGTYDH NVYRDEALNN RFQIKGVEGY IPEAPRDGQA YVRKDGEWVL LSTFLGSGLN DIFEAQ KIE WHEGHHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 57.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm

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Image processing

Particle selectionNumber selected: 2948802
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wzt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 110663
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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