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- EMDB-29738: Influenza A H3N2 X-31 Hemagglutinin in complex with FL-1061 -

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Basic information

Entry
Database: EMDB / ID: EMD-29738
TitleInfluenza A H3N2 X-31 Hemagglutinin in complex with FL-1061
Map dataHA X-31 head in complex with FL-1061, FL-1086, and S5V2-29 Fabs
Sample
  • Complex: Influenza A H3N
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: FL-1086 heavy chain
    • Protein or peptide: FL-1061 heavy chain
  • Protein or peptide: S5V2-29 heavy chain
  • Protein or peptide: FL-1086 light chain
  • Protein or peptide: FL-1061 light chain
  • Protein or peptide: S5V2-29 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) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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: Fabs elicited by hyperglycosylated immunogen
Authors: Windsor IW / Schmidt AG
History
DepositionFeb 12, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29738.png

Downloads & links

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Map

FileDownload / File: emd_29738.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHA X-31 head in complex with FL-1061, FL-1086, and S5V2-29 Fabs
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.12677282 - 0.19378576
Average (Standard dev.)0.00016927502 (±0.0064102993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 198.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_29738_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_29738_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 : Influenza A H3N

EntireName: Influenza A H3N
Components
  • Complex: Influenza A H3N
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: FL-1086 heavy chain
    • Protein or peptide: FL-1061 heavy chain
  • Protein or peptide: S5V2-29 heavy chain
  • Protein or peptide: FL-1086 light chain
  • Protein or peptide: FL-1061 light chain
  • Protein or peptide: S5V2-29 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Influenza A H3N

SupramoleculeName: Influenza A H3N / 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 41.643637 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAST NATELVQSSS TGKICNNPHR ILDGIDCTLI DALLGDPHCD VFQNETWDL FVERSKAFSN CYPYDVPDYA SLRSLVASSG TLEFITEGFT WTGVTQNGGS NACKRGPGSG FFSRLNWLTK S GSTYPVLN ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAST NATELVQSSS TGKICNNPHR ILDGIDCTLI DALLGDPHCD VFQNETWDL FVERSKAFSN CYPYDVPDYA SLRSLVASSG TLEFITEGFT WTGVTQNGGS NACKRGPGSG FFSRLNWLTK S GSTYPVLN VTMPNNDNFD KLYIWGIHHP STDQEQTSLY VQASGRVTVS TRRSQQTIIP NIGSRPWVRG LSSRISIYWT IV KPGDVLV INSNGNLIAP RGYFKMRTGK SSIMRSDAPI DTCISECITP NGSIPNDKPF QNVNKITYGA CPKYVKQNTL KLA TGAGGA GSGGGGAGSG GPGSGYIPEA PRDGQAYVRK DGEWVLLSTF LGGGLEVLFQ GPGGHHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #2: FL-1086 heavy chain

MacromoleculeName: FL-1086 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.499045 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS ASEVQLQESG AELVMPGASV KLSCKASGYT FTRYWMHWVK QRPGQGLEWI GEIDPSDSYT YYNQKFKGK STLTVDKSSS TAYMQLNSLT SEDSAVYYCA RNYGSSYGYF DVWGTGTTVT VGASTKGPSV FPLAPSSKST S GGTAALGC ...String:
MKRGLCCVLL LCGAVFVSPS ASEVQLQESG AELVMPGASV KLSCKASGYT FTRYWMHWVK QRPGQGLEWI GEIDPSDSYT YYNQKFKGK STLTVDKSSS TAYMQLNSLT SEDSAVYYCA RNYGSSYGYF DVWGTGTTVT VGASTKGPSV FPLAPSSKST S GGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VE PKSCDKG SSLEVLFQGP LGHHHHHH

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Macromolecule #3: FL-1061 heavy chain

MacromoleculeName: FL-1061 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.099656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS ASQVQLQQSG AELMQPGASV KLSCKATGYT FAGYWIEWVK QRPGHGLEWI GEILPGIGST NYNGKFKGK ATFTADSSSN TAYMELSSLT TEDSAIYYCA RSGAQATFAM DYWGQGTSVT VSGASTKGPS VFPLAPSSKS T SGGTAALG ...String:
MKRGLCCVLL LCGAVFVSPS ASQVQLQQSG AELMQPGASV KLSCKATGYT FAGYWIEWVK QRPGHGLEWI GEILPGIGST NYNGKFKGK ATFTADSSSN TAYMELSSLT TEDSAIYYCA RSGAQATFAM DYWGQGTSVT VSGASTKGPS VFPLAPSSKS T SGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RV EPKSCDK GSSLEVLFQG PLGHHHHHH

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Macromolecule #4: S5V2-29 heavy chain

MacromoleculeName: S5V2-29 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.984266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCTVSGGSVS SNIYYWSWIR QTPGKGLEWL GYFYHSGSSN YNPSLKSRVT ISGDMSKNQF SLKLKSVTA ADTAIYYCAR GGVENLMLVA VIQEMWYFDL WGRGTLVTVS GASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
QVQLQESGPG LVKPSETLSL TCTVSGGSVS SNIYYWSWIR QTPGKGLEWL GYFYHSGSSN YNPSLKSRVT ISGDMSKNQF SLKLKSVTA ADTAIYYCAR GGVENLMLVA VIQEMWYFDL WGRGTLVTVS GASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKSCDKHHH HH H

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Macromolecule #5: FL-1086 light chain

MacromoleculeName: FL-1086 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.255592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS ASDIVMTQAA FSNPVTLGTS ASISCRSSKS LLHSNGITYL YWYLQRPGQS PQLLIYQMSN LASGVPDRF SSSGSGTDFT LRISRVEAED VGVYYCAQNL ELPWTFGGGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV V CLLNNFYP ...String:
MKRGLCCVLL LCGAVFVSPS ASDIVMTQAA FSNPVTLGTS ASISCRSSKS LLHSNGITYL YWYLQRPGQS PQLLIYQMSN LASGVPDRF SSSGSGTDFT LRISRVEAED VGVYYCAQNL ELPWTFGGGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV V CLLNNFYP REAKVQWKVD NALQSGNSQE SVTEQDSKDS TYSLSSTLTL SKADYEKHKV YACEVTHQGL SSPVTKSFNR GE C

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Macromolecule #6: FL-1061 light chain

MacromoleculeName: FL-1061 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.773969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRGLCCVLL LCGAVFVSPS ASDVQMTQSP SYLAASPGET ITINCRASKS ISKFLAWYQE KPGKTNKLLI YSGSTLQSGI PSRFSGSGS GTDFTLTISS LEPEDFAMYY CQQHNEYPYT FGAGTKLELK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV ...String:
MKRGLCCVLL LCGAVFVSPS ASDVQMTQSP SYLAASPGET ITINCRASKS ISKFLAWYQE KPGKTNKLLI YSGSTLQSGI PSRFSGSGS GTDFTLTISS LEPEDFAMYY CQQHNEYPYT FGAGTKLELK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #7: S5V2-29 light chain

MacromoleculeName: S5V2-29 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.803189 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQTPSS LSASVGDRVT ITCRASQSIG ASLNWYQQKP GEAPKFLIYA ASNLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QQGTFGQGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA LQSGNSQESV T EQDSKDST ...String:
DIQMTQTPSS LSASVGDRVT ITCRASQSIG ASLNWYQQKP GEAPKFLIYA ASNLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QQGTFGQGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA LQSGNSQESV T EQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / 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
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: 1.06 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 396166
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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