+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29738 | ||||||||||||
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Title | Influenza A H3N2 X-31 Hemagglutinin in complex with FL-1061 | ||||||||||||
Map data | HA X-31 head in complex with FL-1061, FL-1086, and S5V2-29 Fabs | ||||||||||||
Sample |
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Keywords | influenza / 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 | ||||||||||||
Biological species | Influenza A virus / Mus musculus (house mouse) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Windsor IW / Thornlow D / Schmidt AG | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: Fabs elicited by hyperglycosylated immunogen Authors: Windsor IW / Schmidt AG | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29738.map.gz | 49.3 MB | EMDB map data format | |
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Header (meta data) | emd-29738-v30.xml emd-29738.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29738_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_29738.png | 89.4 KB | ||
Filedesc metadata | emd-29738.cif.gz | 6.4 KB | ||
Others | emd_29738_half_map_1.map.gz emd_29738_half_map_2.map.gz | 40.8 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29738 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29738 | HTTPS FTP |
-Validation report
Summary document | emd_29738_validation.pdf.gz | 905.9 KB | Display | EMDB validaton report |
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Full document | emd_29738_full_validation.pdf.gz | 905.5 KB | Display | |
Data in XML | emd_29738_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_29738_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29738 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29738 | HTTPS FTP |
-Related structure data
Related structure data | 8g5bMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29738.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | HA X-31 head in complex with FL-1061, FL-1086, and S5V2-29 Fabs | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 1
File | emd_29738_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_29738_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Influenza A H3N
Entire | Name: Influenza A H3N |
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Components |
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-Supramolecule #1: Influenza A H3N
Supramolecule | Name: Influenza A H3N / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Influenza A virus |
-Macromolecule #1: Hemagglutinin
Macromolecule | Name: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Molecular weight | Theoretical: 41.643637 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #2: FL-1086 heavy chain
Macromolecule | Name: FL-1086 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 28.499045 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: FL-1061 heavy chain
Macromolecule | Name: FL-1061 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 28.099656 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: S5V2-29 heavy chain
Macromolecule | Name: S5V2-29 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.984266 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #5: FL-1086 light chain
Macromolecule | Name: FL-1086 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 26.255592 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #6: FL-1061 light chain
Macromolecule | Name: FL-1061 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 25.773969 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #7: S5V2-29 light chain
Macromolecule | Name: S5V2-29 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.803189 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.06 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |