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- EMDB-29737: X-31 hemagglutinin in complex with FL-1061 Fab -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-29737
TitleX-31 hemagglutinin in complex with FL-1061 Fab
Map datahalf map 1
Sample
  • Complex: X-31 hemagglutinin in complex with FL-1061 Fabs
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: FL-1086 Fab heavy chain
    • Protein or peptide: FL-1086 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / fusogen / antibody / 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 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWindsor IW / Thornlow D / Schmidt AG
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI146779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00050 United States
CitationJournal: To Be Published
Title: Antibodies elicited by a hyperglycoslated immunogen
Authors: Windsor IW / Schmidt AG
History
DepositionFeb 12, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29737.png

Downloads & links

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Map

FileDownload / File: emd_29737.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf map 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.04737046 - 0.08890066
Average (Standard dev.)0.00008560795 (±0.0031118894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: X-31 Hemagglutinin full length soluble ectodomain trimer in...

Fileemd_29737_half_map_1.map
AnnotationX-31 Hemagglutinin full length soluble ectodomain trimer in complex with three FL-1061 Fabs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_29737_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : X-31 hemagglutinin in complex with FL-1061 Fabs

EntireName: X-31 hemagglutinin in complex with FL-1061 Fabs
Components
  • Complex: X-31 hemagglutinin in complex with FL-1061 Fabs
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: FL-1086 Fab heavy chain
    • Protein or peptide: FL-1086 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: X-31 hemagglutinin in complex with FL-1061 Fabs

SupramoleculeName: X-31 hemagglutinin in complex with FL-1061 Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus

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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
Molecular weightTheoretical: 70.408609 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKRGLCCVLL LCGAVFVSPS ASQDLPGNDN STATLCLGHH AVPNGTLVKT ITDDQIEVTN ATELVQSSST GKICNNPHRI LDGIDCTLI DALLGDPHCD VFQNETWDLF VERSKAFSNC YPYDVPDYAS LRSLVASSGT LEFITEGFTW TGVTQNGGSN A CKRGPGSG ...String:
MKRGLCCVLL LCGAVFVSPS ASQDLPGNDN STATLCLGHH AVPNGTLVKT ITDDQIEVTN ATELVQSSST GKICNNPHRI LDGIDCTLI DALLGDPHCD VFQNETWDLF VERSKAFSNC YPYDVPDYAS LRSLVASSGT LEFITEGFTW TGVTQNGGSN A CKRGPGSG FFSRLNWLTK SGSTYPVLNV TMPNNDNFDK LYIWGIHHPS TDQEQTSLYV QASGRVTVST RRSQQTIIPN IG SRPWVRG LSSRISIYWT IVKPGDVLVI NSNGNLIAPR GYFKMRTGKS SIMRSDAPID TCISECITPN GSIPNDKPFQ NVN KITYGA CPKYVKQNTL KLATGMRNVP EKQTRGLFGA IAGFIENGWE GMIDGWYGFR HQNSEGTGQA ADLKSTQAAI DQIN GKLNR VIEKTNEKFH QIEKEFSEVE GRIQDLEKYV EDTKIDLWSY NAELLVALEN QHTIDLTDSE MNKLFEKTRR QLREN AEDM GNGCFKIYHK CDNACIESIR NGTYDHDVYR DEALNNRFQI KGVELKSGAG SSLEVLFQGP GSGSSLGGSG YIPEAP RDG QAYVRKDGEW VLLSTFLGSG SSHHHHHHHH GGSGSSMDEK TTGWRGGHVV EGLAGELEQL RARLEHHPQG QREP

UniProtKB: Hemagglutinin

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Macromolecule #2: FL-1086 Fab heavy chain

MacromoleculeName: FL-1086 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.019004 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ASQVQLQQSG AELMQPGASV KLSCKATGYT FAGYWIEWVK QRPGHGLEWI GEILPGIGST NYNGKFKGKA TFTADSSSNT AYMELSSLT TEDSAIYYCA RSGAQATFAM DYWGQGTSVT VSGASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
ASQVQLQQSG AELMQPGASV KLSCKATGYT FAGYWIEWVK QRPGHGLEWI GEILPGIGST NYNGKFKGKA TFTADSSSNT AYMELSSLT TEDSAIYYCA RSGAQATFAM DYWGQGTSVT VSGASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCDKG SSLEVLFQGP LG HHHHHH

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Macromolecule #3: FL-1086 light chain

MacromoleculeName: FL-1086 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.693311 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ASDVQMTQSP SYLAASPGET ITINCRASKS ISKFLAWYQE KPGKTNKLLI YSGSTLQSGI PSRFSGSGSG TDFTLTISSL EPEDFAMYY CQQHNEYPYT FGAGTKLELK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
ASDVQMTQSP SYLAASPGET ITINCRASKS ISKFLAWYQE KPGKTNKLLI YSGSTLQSGI PSRFSGSGSG TDFTLTISSL EPEDFAMYY CQQHNEYPYT FGAGTKLELK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / 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: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.2 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 85028
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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