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- EMDB-27440: CryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutini... -

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Basic information

Entry
Database: EMDB / ID: EMD-27440
TitleCryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab
Map data
Sample
  • Complex: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab
    • Protein or peptide: hemagglutinin
    • 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/Ohio/09/2015 hemagglutinin bound to CR6261 Fab
Authors: Yang M / Edwards TE / Horanyi PS / Lorimer DD
History
DepositionJun 29, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27440.png

Downloads & links

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Map

FileDownload / File: emd_27440.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: 0.64
Minimum - Maximum-2.177364 - 4.117815
Average (Standard dev.)-0.00029238017 (±0.07496955)
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: #2

Fileemd_27440_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_27440_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 : Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab

EntireName: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab
Components
  • Complex: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab
    • Protein or peptide: hemagglutinin
    • 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: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab

SupramoleculeName: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 450 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 / Strain: A/Ohio/09/2015
Molecular weightTheoretical: 64.428137 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAGS DKICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLENKHNGK LCKLRGVAP LHLGKCNIAG WLLGNPECES LATASSWSYI VETSSSNNGT CYPGDFINYE ELREQLSSVS SFEKFEIFPK T SSWPNHET ...String:
MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAGS DKICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLENKHNGK LCKLRGVAP LHLGKCNIAG WLLGNPECES LATASSWSYI VETSSSNNGT CYPGDFINYE ELREQLSSVS SFEKFEIFPK T SSWPNHET NKGVTAACPH AGTNSFYKNL IWLVKKENSY PKINISYTNN RGKEVLVLWA IHHPPTSTDQ QSLYQNANSY VF VGSSRYS RKFEPEIATR PKVRGQAGRM NYYWTLVEPG DKITFEATGN LVVPRYAFAL KRNSGSGIII SETPVHDCDT TCQ TPNGAI NTSLPFQNIH PVTIGECPKY VKSTKLRMAT GLRNIPSIQS RGLFGAIAGF IEGGWTGMID GWYGYHHQNE QGSG YAADL KSTQNAIDGI TNKVNSVIEK MNTQFTAVGK EFSHLERRIE NLNKKVDDGF IDIWTYNAEL LVLLENERTL DYHDS NVKT LYEKVRSQLK NNAKEIGNGC FEFYHKCDDT CMESVKNGTY DYPKYSEEFL VPRGSPGSGY IPEAPRDGQA YVRKDG EWV LLSTFLGHHH HHH

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Macromolecule #2: CR6261 Fab heavy chain

MacromoleculeName: CR6261 Fab heavy chain / type: protein_or_peptide / ID: 2 / 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 #3: CR6261 Fab light chain

MacromoleculeName: CR6261 Fab light chain / type: protein_or_peptide / ID: 3 / 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 #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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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 18 / 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 real images: 12095 / Average exposure time: 2.3 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

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-8dim:
CryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab

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