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- EMDB-27441: CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) h... -

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Basic information

Entry
Database: EMDB / ID: EMD-27441
TitleCryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) hemagglutinin bound to CR6261 Fab
Map data
Sample
  • Complex: CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) hemagglutinin bound to CR6261 Fab
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: CR6261 Fab heavy chain
    • Protein or peptide: CR6261 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsNIAID hemagglutinin stalk binding antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) hemagglutinin bound to CR6261 Fab
Authors: Yang M / Edwards TE / Horanyi PS / Lorimer DD
History
DepositionJun 29, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27441.png

Downloads & links

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Map

FileDownload / File: emd_27441.map.gz / Format: CCP4 / Size: 662.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 558 pix.
= 376.65 Å		0.68 Å/pix.
x 558 pix.
= 376.65 Å		0.68 Å/pix.
x 558 pix.
= 376.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.531
Minimum - Maximum-2.1623297 - 4.1360598
Average (Standard dev.)-0.0012238818 (±0.059381094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions558558558
Spacing558558558
CellA=B=C: 376.65 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27441_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_27441_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 : CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) h...

EntireName: CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) hemagglutinin bound to CR6261 Fab
Components
  • Complex: CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) hemagglutinin bound to CR6261 Fab
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: CR6261 Fab heavy chain
    • Protein or peptide: CR6261 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) h...

SupramoleculeName: CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) hemagglutinin bound to CR6261 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Melbourne/1/1946(H1N1)
Molecular weightTheoretical: 40.34752 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAGS DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAP LQLGKCNIAG WILGNPECDS LLPASSWSYI VETPNSKNGI CYPGDFIDYE ELREQLSSVS SFERFEIFPK E SSWPKHST ...String:
MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAGS DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAP LQLGKCNIAG WILGNPECDS LLPASSWSYI VETPNSKNGI CYPGDFIDYE ELREQLSSVS SFERFEIFPK E SSWPKHST TKGVTAACSH AGKSSFYRNL LWLTKKEDSY PKLSNSYVNK KGKEVLVLWG VHHPSSSKEQ QTLYQNENAY VS VVSSNYN RRFIPEIAER PEVKDQAGRI NYYWTLLEPG DTIIFEANGN LVAPWYAFAL SRGFGSGIIT SNASMHECNT KCQ TPQGAI NSSLPFQNIH PVTIGECPKY VKSAKLRMVT GLRNIPSI

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Melbourne/1/1946(H1N1)
Molecular weightTheoretical: 23.845508 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GLFGAIAGFI EGGWTGMIDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NNLEKRMENL NKKVDDGFL DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKIQLKNN AKEIGNGCFE FYHKCDNECM ESVRNGTYDY P KYSKEFLV ...String:
GLFGAIAGFI EGGWTGMIDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NNLEKRMENL NKKVDDGFL DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKIQLKNN AKEIGNGCFE FYHKCDNECM ESVRNGTYDY P KYSKEFLV PRGSPGSGYI PEAPRDGQAY VRKDGEWVLL STFLGHHHHH H

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Macromolecule #3: CR6261 Fab heavy chain

MacromoleculeName: CR6261 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.066621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEWSWVFLFF LSVTTGVHSE VQLVESGAEV KKPGSSVKVS CKASGGPFRS YAISWVRQAP GQGPEWMGGI IPIFGTTKYA PKFQGRVTI TADDFAGTVY MELSSLRSED TAMYYCAKHM GYQVRETMDV WGKGTTVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
MEWSWVFLFF LSVTTGVHSE VQLVESGAEV KKPGSSVKVS CKASGGPFRS YAISWVRQAP GQGPEWMGGI IPIFGTTKYA PKFQGRVTI TADDFAGTVY MELSSLRSED TAMYYCAKHM GYQVRETMDV WGKGTTVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EP KSCDKHH HHHH

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Macromolecule #4: CR6261 Fab light chain

MacromoleculeName: CR6261 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.514395 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEWSWVFLFF LSVTTGVHSQ SVLTQPPSVS AAPGQKVTIS CSGSSSNIGN DYVSWYQQLP GTAPKLLIYD NNKRPSGIPD RFSGSKSGT SATLGITGLQ TGDEANYYCA TWDRRPTAYV VFGGGTKLTV LGAAAGQPKA APSVTLFPPS SEELQANKAT L VCLISDFY ...String:
MEWSWVFLFF LSVTTGVHSQ SVLTQPPSVS AAPGQKVTIS CSGSSSNIGN DYVSWYQQLP GTAPKLLIYD NNKRPSGIPD RFSGSKSGT SATLGITGLQ TGDEANYYCA TWDRRPTAYV VFGGGTKLTV LGAAAGQPKA APSVTLFPPS SEELQANKAT L VCLISDFY PGAVTVAWKA DSSPVKAGVE TTTPSKQSNN KYAASSYLSL TPEQWKSHRS YSCQVTHEGS TVEKTVAPTE CS

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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: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 61 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
25.0 mMTris(hydroxymethyl)aminomethane hydrochloride
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9179 / Average exposure time: 2.4 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 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: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 367154
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6uyn

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.2.0) / Number images used: 367154
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6uyn


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 120.6
Output model

PDB-8dis:
CryoEM structure of Influenza A virus A/Melbourne/1/1946 (H1N1) hemagglutinin bound to CR6261 Fab

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