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- EMDB-38157: Structure of hemagglutinin from HN/4-10 H3N8 influenza virus G228... -

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Basic information

Entry
Database: EMDB / ID: EMD-38157
TitleStructure of hemagglutinin from HN/4-10 H3N8 influenza virus G228 mutant complexed with human receptor analog LSTc
Map data
Sample
  • Complex: HN/4-10 H3N8 G228 HA complexed with LSTc
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza virus / H3N8 / hemagglutinin / avian receptor / VIRAL PROTEIN
Biological speciesInfluenza A virus / unidentified influenza virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsHao TJ / Xie YF / Chai Y / Song H / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of hemagglutinin from HN/4-10 H3N8 influenza virus G228 mutant complexed with human receptor analog LSTc
Authors: Hao TJ / Xie YF / Chai Y / Song H / Gao GF
History
DepositionNov 28, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38157.png

Downloads & links

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Map

FileDownload / File: emd_38157.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.3644906 - 2.4530554
Average (Standard dev.)-0.001167371 (±0.079269215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38157_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_38157_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 : HN/4-10 H3N8 G228 HA complexed with LSTc

EntireName: HN/4-10 H3N8 G228 HA complexed with LSTc
Components
  • Complex: HN/4-10 H3N8 G228 HA complexed with LSTc
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HN/4-10 H3N8 G228 HA complexed with LSTc

SupramoleculeName: HN/4-10 H3N8 G228 HA complexed with LSTc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Details: HN/4-10 H3N8 HA G228 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: unidentified influenza virus
Molecular weightTheoretical: 57.124691 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LQQNLPGKDS STATLCLGHH SVPNGTIVKT ITDDQIEVTN ATELVQNSST GKICNNPHKV LDGRDCTLID AMLGDPHCDV FQDEKWDLF VERSSAFSNC YPYDVPDYAS LRSLIASSGT LDFITESFTW AGVSQNGGSS ACKRGPANGF FSRLNWLTKS G SSYPLLNV ...String:
LQQNLPGKDS STATLCLGHH SVPNGTIVKT ITDDQIEVTN ATELVQNSST GKICNNPHKV LDGRDCTLID AMLGDPHCDV FQDEKWDLF VERSSAFSNC YPYDVPDYAS LRSLIASSGT LDFITESFTW AGVSQNGGSS ACKRGPANGF FSRLNWLTKS G SSYPLLNV TMPNNYNFDK LYIWGVHHPS TNQEQTNLYV QASGRVTVST RRSQQTIVPN IGSRPWVRGQ SGRISIYWTI VK PGDVLVI NSNGNLIAPR GFFKIRTGRS SIMRSDAPIE TCISECITPN GSIPNDKPFQ NVNKITYGAC PKYVKQNTLK LAT GMRNVP EKQTRGLFGA IAGFIENGWE GMIDGWYGFR HQNSEGTGQA ADLKSTQAAI DQINGKLNRV IEKTNEKFHQ IEKE FSEVE GRIQDLEKYV EDTKVDLWSY NAELLVALEN QHTIDLTDSE MNKLFEKTRR QLRENAEDMG NGCFKIYHKC DNACI ESIR NGTYDHDIYR DEALNNRFQI RGVEF

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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: 3 / 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: 8
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22596
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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