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- EMDB-28833: Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-28833
TitleCryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab
Map dataMain map
Sample
  • Complex: Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab
    • Protein or peptide: CR6261 Fab light chain
    • Protein or peptide: CR6261 Fab heavy chain
    • Protein or peptide: hemagglutinin
  • 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 speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 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: Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab
Authors: Yang M / Edwards TE / Horanyi PS / Lorimer DD
History
DepositionNov 9, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28833.png

Downloads & links

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Map

FileDownload / File: emd_28833.map.gz / Format: CCP4 / Size: 662.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Voxel sizeX=Y=Z: 0.675 Å
Density
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-2.5526536 - 3.7533712
Average (Standard dev.)-0.00050466415 (±0.079270884)
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: handedness corrected half map B

Fileemd_28833_half_map_1.map
Annotationhandedness corrected half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: handedness corrected half map A

Fileemd_28833_half_map_2.map
Annotationhandedness corrected half 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 : Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab

EntireName: Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab
Components
  • Complex: Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab
    • Protein or peptide: CR6261 Fab light chain
    • Protein or peptide: CR6261 Fab heavy chain
    • Protein or peptide: hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab

SupramoleculeName: Cryo-EM structure of X6 COBRA (H1N1) 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: CR6261 Fab light chain

MacromoleculeName: CR6261 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.257783 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SAAPGQKVTI SCSGSSSNIG NDYVSWYQQL PGTAPKLLIY DNNKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEANYYC ATWDRRPTAY VVFGGGTKLT VLGAAAGQPK AAPSVTLFPP SSEELQANKA TLVCLISDFY PGAVTVAWKA D SSPVKAGV ...String:
QSVLTQPPSV SAAPGQKVTI SCSGSSSNIG NDYVSWYQQL PGTAPKLLIY DNNKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEANYYC ATWDRRPTAY VVFGGGTKLT VLGAAAGQPK AAPSVTLFPP SSEELQANKA TLVCLISDFY PGAVTVAWKA D SSPVKAGV ETTTPSKQSN NKYAASSYLS LTPEQWKSHR SYSCQVTHEG STVEKTVAPT ECS

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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: 24.810018 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGAE VKKPGSSVKV SCKASGGPFR SYAISWVRQA PGQGPEWMGG IIPIFGTTKY APKFQGRVTI TADDFAGTVY MELSSLRSE DTAMYYCAKH MGYQVRETMD VWGKGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
EVQLVESGAE VKKPGSSVKV SCKASGGPFR SYAISWVRQA PGQGPEWMGG IIPIFGTTKY APKFQGRVTI TADDFAGTVY MELSSLRSE DTAMYYCAKH MGYQVRETMD VWGKGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSCDKHH HHHH

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Macromolecule #3: hemagglutinin

MacromoleculeName: hemagglutinin / type: protein_or_peptide / ID: 3 / Details: X6 COBRA (H1N1) hemagglutinin construct / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 63.171098 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEARLLVLLC AFAATNADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS KESWSYIVET PNPENGTCYP GYFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTVTGVS ASCSHNGKSS F YRNLLWLT ...String:
MEARLLVLLC AFAATNADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS KESWSYIVET PNPENGTCYP GYFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTVTGVS ASCSHNGKSS F YRNLLWLT GKNGLYPNLS KSYANNKEKE VLVLWGVHHP PNIGDQRALY HTENAYVSVV SSHYSRKFTP EIAKRPKVRD QE GRINYYW TLLEPGDTII FEANGNLIAP RYAFALSRGF GSGIITSNAP MDECDAKCQT PQGAINSSLP FQNVHPVTIG ECP KYVRSA KLRMVTGLRN IPSIQSRGLF GAIAGFIEGG WTGMVDGWYG YHHQNEQGSG YAADQKSTQN AINGITNKVN SVIE KMNTQ FTAVGKEFNK LERRMENLNK KVDDGFLDIW TYNAELLVLL ENERTLDFHD SNVKNLYEKV KSQLKNNAKE IGNGC FEFY HKCNNECMES VKNGTYDYPK YSEESKLNRE KIDGVKLESM GVYQILAIYS TVASSLVLLV SLGAISFWMC SNGSLQ CRI CI

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 50 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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 chlorideSodium 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8973 / Average exposure time: 2.4 sec. / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 385474
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6uyn

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.2.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.2.0) / Number images used: 385474
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: 115.1
Output model

PDB-8f38:
Cryo-EM structure of X6 COBRA (H1N1) hemagglutinin bound to CR6261 Fab

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