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- EMDB-30707: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30707
TitleHemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
Map data
Sample
  • Complex: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fv-clasp heavy chain
    • Protein or peptide: Fv-clasp light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsneutralizing antibody / Influenza A virus / Hemagglutinin / Fv-clasp / Okuda / VIRAL PROTEIN
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 speciesInfluenza A virus (A/Okuda/1957(H2N2)) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShirouzu M
CitationJournal: To Be Published
Title: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
Authors: Makino-Okamura C / Hata H / Watanabe T / Kim S / Hebrard M / Sato R / Yan M / Onodera T / Takahashi Y / Li Q / Taylor T / Okuno Y / Kurosaki T / Tomabechi Y / Uchikubo-Kamo T / Kamada K / Shirouzu M / Fukuyama H
History
DepositionNov 24, 2020-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dkj
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30707.png

Downloads & links

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Map

FileDownload / File: emd_30707.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 150 pix.
= 220.5 Å		1.47 Å/pix.
x 150 pix.
= 220.5 Å		1.47 Å/pix.
x 150 pix.
= 220.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.47 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.23131429 - 0.38815513
Average (Standard dev.)0.00022026051 (±0.0155124795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 220.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.471.471.47
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z220.500220.500220.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.2310.3880.000

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Supplemental data

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Half map: #1

Fileemd_30707_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_30707_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 : Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a ...

EntireName: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
Components
  • Complex: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fv-clasp heavy chain
    • Protein or peptide: Fv-clasp light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a ...

SupramoleculeName: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus (A/Okuda/1957(H2N2))
Molecular weightTheoretical: 290 KDa

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Okuda/1957(H2N2)) / Strain: A/Okuda/1957(H2N2)
Molecular weightTheoretical: 67.423797 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFADQ ICIGYHANNS TEKVDTICER NVTVTHAKDI LEKTHNGKLC KLNGIPPLE LGDCSIAGWL LGNPKCDRLL SVPEWSYIME KENPRDGLCF PGSFSDYEEL KHLLSSVKHF EKVKILPKDR W TQHTTTGG ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFADQ ICIGYHANNS TEKVDTICER NVTVTHAKDI LEKTHNGKLC KLNGIPPLE LGDCSIAGWL LGNPKCDRLL SVPEWSYIME KENPRDGLCF PGSFSDYEEL KHLLSSVKHF EKVKILPKDR W TQHTTTGG SRACAVSGNP SFFRNMVWLT EKGSNYPVAK GSYNNTSGEQ MLIIWGVHHP NDETEQRTLY QNVGTYVSVS TS TLNKRST PETATRPKVN GQGGRMEFFW TLLDMWDTIN FESTGNLIAP EYGFKISKRG SSGIIKTEGT LENCETKCQT PLG AINTTL PFHNVHPLTI GECPKYVKSE KLVLATGLRN VPQIESRGLF GAIAGFIEGG WQGMVDGWYG YHHSNDQGSG YAAD KESTQ KAFDCITNKV NSVIEKINTQ FEAVGKEFGN LEKRLENLNK KMEDGFIDVW TYNAELLVLM ENERTLDFHD SNVKN LYSK VRMQLRDNVK ELGNGCFEFY HKCDDECMNS VKNGTYDYPK YEEESKLNRN EIKGVLVPRG SPGSGYIPEA PRDGQA YVR KDGEWVLLST FLGSGLNDIF EAQKIEWHEG HHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #2: Fv-clasp heavy chain

MacromoleculeName: Fv-clasp heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.083908 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG EVKLVESGGG LVQPGGSLRL SCGTSGFTLT DDYMTWVRQP PGKALEWLGF IRDRANGYT TEYSASVKGR FTISRDNSQS IVYLQMNTLR VEDSATYYCA RPKGYFPYAM DYWGQGTSVI VCSGSDYEFL K SWTVEDLQ ...String:
MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG EVKLVESGGG LVQPGGSLRL SCGTSGFTLT DDYMTWVRQP PGKALEWLGF IRDRANGYT TEYSASVKGR FTISRDNSQS IVYLQMNTLR VEDSATYYCA RPKGYFPYAM DYWGQGTSVI VCSGSDYEFL K SWTVEDLQ KRLLALDPMM EQEIEEIRQK YQSKRQPILD AIEAK

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Macromolecule #3: Fv-clasp light chain

MacromoleculeName: Fv-clasp light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.287729 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG DIQMTQSPAS LSVSVGETVT ITCRASENIY SNLAWYQQKQ GKSPQLLVYA ATNLADGVP SRFSGSGSGT QYSLKINSLQ SEDFGSYYCQ HFWGTPWTFG GGTKLEIKAG SDYEFLKSWT VEDLQKRLLA L DPMMEQEI EEIRQKYQCK RQPILDAIEA K

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / 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

Concentration0.03 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2043 / Average exposure time: 12.0 sec. / Average electron dose: 50.0 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: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1768385
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 52314
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4hlz

source_name: PDB, initial_model_type: experimental model

5xcx

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 141.37 / Target criteria: Corelation coefficient
Output model

PDB-7dkj:
Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody

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