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- EMDB-24408: The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adeno... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24408 | |||||||||
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Title | The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adenovirus Y25 | |||||||||
![]() | Relion-generated, post-processed map | |||||||||
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![]() | Adenovirus / simian adenovirus / chimpanzee adenovirus / vaccine vector / DNA virus / AdV / ChAdV-Y25 / adenovirus Y25 / Y25 / viral vector / ChAdOx1 / chimp Ad / dsDNA virus / icosahedral / chimpanzee adenovirus Y25 / Y-25 / Y 25 / ChAdV / VIRUS | |||||||||
Function / homology | ![]() hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / endocytosis involved in viral entry into host cell / viral capsid / host cell cytoplasm ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / endocytosis involved in viral entry into host cell / viral capsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 Å | |||||||||
![]() | Baker AT / Boyd RJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome. Authors: Alexander T Baker / Ryan J Boyd / Daipayan Sarkar / Alicia Teijeira-Crespo / Chun Kit Chan / Emily Bates / Kasim Waraich / John Vant / Eric Wilson / Chloe D Truong / Magdalena Lipka-Lloyd / ...Authors: Alexander T Baker / Ryan J Boyd / Daipayan Sarkar / Alicia Teijeira-Crespo / Chun Kit Chan / Emily Bates / Kasim Waraich / John Vant / Eric Wilson / Chloe D Truong / Magdalena Lipka-Lloyd / Petra Fromme / Josh Vermaas / Dewight Williams / LeeAnn Machiesky / Meike Heurich / Bolni M Nagalo / Lynda Coughlan / Scott Umlauf / Po-Lin Chiu / Pierre J Rizkallah / Taylor S Cohen / Alan L Parker / Abhishek Singharoy / Mitesh J Borad / ![]() ![]() Abstract: Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory ...Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic. As part of the largest vaccination campaign in history, ultrarare side effects not seen in phase 3 trials, including thrombosis with thrombocytopenia syndrome (TTS), a rare condition resembling heparin-induced thrombocytopenia (HIT), have been observed. This study demonstrates that all three adenoviruses deployed as vaccination vectors versus SARS-CoV-2 bind to platelet factor 4 (PF4), a protein implicated in the pathogenesis of HIT. We have determined the structure of the ChAdOx1 viral vector and used it in state-of-the-art computational simulations to demonstrate an electrostatic interaction mechanism with PF4, which was confirmed experimentally by surface plasmon resonance. These data confirm that PF4 is capable of forming stable complexes with clinically relevant adenoviruses, an important step in unraveling the mechanisms underlying TTS. #1: ![]() Title: The Structure of ChAdOx1/AZD-1222 Reveals Interactions with CAR and PF4 with Implications for Vaccine-induced Immune Thrombotic Thrombocytopenia Authors: Baker AT / Boyd RJ / Sarkar D / Vant J / Crespo AT / Waraich K / Truong CD / Bates E / Wilson E / Chan CK / Lipka-Lloyd M / Fromme P / Nagalo MB / Heurich M / Williams D / Chiu PL / ...Authors: Baker AT / Boyd RJ / Sarkar D / Vant J / Crespo AT / Waraich K / Truong CD / Bates E / Wilson E / Chan CK / Lipka-Lloyd M / Fromme P / Nagalo MB / Heurich M / Williams D / Chiu PL / Rizkallah PJ / Parker AL / Singharoy A / Borad MJ | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 715.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 36.1 KB 36.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 44 KB | Display | ![]() |
Images | ![]() | 53.3 KB | ||
Masks | ![]() | 7.5 GB | ![]() | |
Filedesc metadata | ![]() | 8.9 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() | 6.9 GB 6.2 GB 6.9 GB 312.1 MB 6.1 GB 6.1 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rd1MC ![]() 7op2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 1.0 TB Data #1: Raw movies comprising 7RD1 ChAdOx dataset [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Relion-generated, post-processed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.53143 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer-sharpened using highRes model
File | emd_24408_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer-sharpened using highRes model | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer-sharpened using wideTarget model
File | emd_24408_additional_2.map | ||||||||||||
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Annotation | DeepEMhancer-sharpened using wideTarget model | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer-sharpened using wideTarget model and low pass-filtered
File | emd_24408_additional_3.map | ||||||||||||
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Annotation | DeepEMhancer-sharpened using wideTarget model and low pass-filtered | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Hollowed to remove noise generated by nonstructured genome
File | emd_24408_additional_4.map | ||||||||||||
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Annotation | Hollowed to remove noise generated by nonstructured genome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Random half map
File | emd_24408_half_map_1.map | ||||||||||||
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Annotation | Random half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Random half map
File | emd_24408_half_map_2.map | ||||||||||||
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Annotation | Random half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Chimpanzee adenovirus Y25
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Chimpanzee adenovirus Y25
Supramolecule | Name: Chimpanzee adenovirus Y25 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Rescued from a bacterial artificial chromosome containing the ChAdOx1 genome and propagated in HEK293 T-Rex cells. NCBI-ID: 1123958 / Sci species name: Chimpanzee adenovirus Y25 / Sci species strain: ChAdOx1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Name: Icosahedral Capsid / Diameter: 500.0 Å / T number (triangulation number): 25 |
-Macromolecule #1: Pre-protein VI
Macromolecule | Name: Pre-protein VI / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.299689 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MEDINFSSLA PRHGTRPFMG TWSDIGTSQL NGGAFNWSSL WSGLKNFGST LKTYGSKAWN STTGQALRDK LKEQNFQQKV VDGLASGIN GVVDLANQAV QRQINSRLDP VPPAGSVEMP QVEEELPPLD KRGEKRPRPD AEETLLTHTD EPPPYEEAVK L GLPTTRPI ...String: MEDINFSSLA PRHGTRPFMG TWSDIGTSQL NGGAFNWSSL WSGLKNFGST LKTYGSKAWN STTGQALRDK LKEQNFQQKV VDGLASGIN GVVDLANQAV QRQINSRLDP VPPAGSVEMP QVEEELPPLD KRGEKRPRPD AEETLLTHTD EPPPYEEAVK L GLPTTRPI APLATGVLKP ESNKPATLDL PPPASRPSTV AKPLPPVAVA RARPGGSARP HANWQSTLNS IVGLGVQSVK RR RCY UniProtKB: Pre-protein VI |
-Macromolecule #2: Hexon protein
Macromolecule | Name: Hexon protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 106.121141 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MATPSMLPQW AYMHIAGQDA SEYLSPGLVQ FARATDTYFS LGNKFRNPTV APTHDVTTDR SQRLTLRFVP VDREDNTYSY KVRYTLAVG DNRVLDMAST YFDIRGVLDR GPSFKPYSGT AYNSLAPKGA PNSSQWEQKK AGNGDTMETH TFGVAPMGGE N ITIDGLQI ...String: MATPSMLPQW AYMHIAGQDA SEYLSPGLVQ FARATDTYFS LGNKFRNPTV APTHDVTTDR SQRLTLRFVP VDREDNTYSY KVRYTLAVG DNRVLDMAST YFDIRGVLDR GPSFKPYSGT AYNSLAPKGA PNSSQWEQKK AGNGDTMETH TFGVAPMGGE N ITIDGLQI GTDATADQDK PIYADKTFQP EPQVGEENWQ ETESFYGGRA LKKDTSMKPC YGSYARPTNV KGGQAKLKVG AD GVPTKEF DIDLAFFDTP GGTVNGQDEY KADIVMYTEN TYLETPDTHV VYKPGKDDAS SEINLVQQSM PNRPNYIGFR DNF IGLMYY NSTGNMGVLA GQASQLNAVV DLQDRNTELS YQLLLDSLGD RTRYFSMWNQ AVDSYDPDVR IIENHGVEDE LPNY CFPLD GSGTNAAYQG VKVKNGNDGD VESEWENDDT VAARNQLCKG NIFAMEINLQ ANLWRSFLYS NVALYLPDSY KYTPA NITL PTNTNTYDYM NGRVVPPSLV DAYINIGARW SLDPMDNVNP FNHHRNAGLR YRSMLLGNGR YVPFHIQVPQ KFFAIK SLL LLPGSYTYEW NFRKDVNMIL QSSLGNDLRT DGASISFTSI NLYATFFPMA HNTASTLEAM LRNDTNDQSF NDYLSAA NM LYPIPANATN VPISIPSRNW AAFRGWSFTR LKTKETPSLG SGFDPYFVYS GSIPYLDGTF YLNHTFKKVS ITFDSSVS W PGNDRLLTPN EFEIKRTVDG EGYNVAQCNM TKDWFLVQML AHYNIGYQGF YVPEGYKDRM YSFFRNFQPM SRQVVDEVN YKDYQAVTLA YQHNNSGFVG YLAPTMRQGQ PYPANYPYPL IGKSAVTSVT QKKFLCDRVM WRIPFSSNFM SMGALTDLGQ NMLYANSAH ALDMNFEVDP MDESTLLYVV FEVFDVVRVH QPHRGVIEAV YLRTPFSAGN ATT UniProtKB: Hexon protein |
-Macromolecule #3: Penton protein
Macromolecule | Name: Penton protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 59.533656 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MMRRAYPEGP PPSYESVMQQ AMAAAAAMQP PLEAPYVPPR YLAPTEGRNS IRYSELAPLY DTTRLYLVDN KSADIASLNY QNDHSNFLT TVVQNNDFTP TEASTQTINF DERSRWGGQL KTIMHTNMPN VNEFMYSNKF KARVMVSRKT PNGVTVTDGS Q DILEYEWV ...String: MMRRAYPEGP PPSYESVMQQ AMAAAAAMQP PLEAPYVPPR YLAPTEGRNS IRYSELAPLY DTTRLYLVDN KSADIASLNY QNDHSNFLT TVVQNNDFTP TEASTQTINF DERSRWGGQL KTIMHTNMPN VNEFMYSNKF KARVMVSRKT PNGVTVTDGS Q DILEYEWV EFELPEGNFS VTMTIDLMNN AIIDNYLAVG RQNGVLESDI GVKFDTRNFR LGWDPVTELV MPGVYTNEAF HP DIVLLPG CGVDFTESRL SNLLGIRKRQ PFQEGFQIMY EDLEGGNIPA LLDVDAYEKS KEESAAAATA AVATASTEVR GDN FASPAA VAAAEAAETE SKIVIQPVEK DSKDRSYNVL PDKINTAYRS WYLAYNYGDP EKGVRSWTLL TTSDVTCGVE QVYW SLPDM MQDPVTFRST RQVSNYPVVG AELLPVYSKS FFNEQAVYSQ QLRAFTSLTH VFNRFPENQI LVRPPAPTIT TVSEN VPAL TDHGTLPLRS SIRGVQRVTV TDARRRTCPY VYKALGIVAP RVLSSRTF UniProtKB: Penton protein |
-Macromolecule #4: Hexon-interlacing protein
Macromolecule | Name: Hexon-interlacing protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.468118 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSGSGSFEGG VFSPYLTGRL PSWAGVRQNV MGSTVDGRPV QPANSSTLTY ATLSSSSVDA AAAAAAASAA SAVRGMAMGA GYYGTLVAN SSSTNNPASL NEEKLLLLMA QLEALTQRLG ELTQQVAQLQ EQTRAAVATV KSK UniProtKB: Hexon-interlacing protein |
-Macromolecule #5: Pre-hexon-linking protein IIIa
Macromolecule | Name: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 65.9545 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MQQQPPPDPA MRAALQSQPS GINSSDDWTQ AMQRIMALTT RNPEAFRQQP QANRLSAILE AVVPSRSNPT HEKVLAIVNA LVENKAIRG DEAGLVYNAL LERVARYNST NVQTNLDRMV TDVREAVAQR ERFHRESNLG SMVALNAFLS TQPANVPRGQ E DYTNFISA ...String: MQQQPPPDPA MRAALQSQPS GINSSDDWTQ AMQRIMALTT RNPEAFRQQP QANRLSAILE AVVPSRSNPT HEKVLAIVNA LVENKAIRG DEAGLVYNAL LERVARYNST NVQTNLDRMV TDVREAVAQR ERFHRESNLG SMVALNAFLS TQPANVPRGQ E DYTNFISA LRLMVTEVPQ SEVYQSGPDY FFQTSRQGLQ TVNLSQAFKN LQGLWGVQAP VGDRATVSSL LTPNSRLLLL LV APFTDSG SINRNSYLGY LINLYREAIG QAHVDEQTYQ EITHVSRALG QDDPGNLEAT LNFLLTNRSQ KIPPQYTLSA EEE RILRYV QQSVGLFLMQ EGATPSAALD MTARNMEPSM YASNRPFINK LMDYLHRAAA MNSDYFTNAI LNPHWLPPPG FYTG EYDMP DPNDGFLWDD VDSSVFSPRP GANERPLWKK EGSDRRPSSA LSGREGAAAA VPEAASPFPS LPFSLNSIRS SELGR ITRP RLLGEEEYLN DSLLRPEREK NFPNNGIESL VDKMSRWKTY AQEHRDDPSQ GATSRGSAAR KRRWHDRQRG LMWDDE DSA DDSSVLDLGG SGNPFAHLRP RIGRMM UniProtKB: Pre-hexon-linking protein IIIa |
-Macromolecule #6: Pre-hexon-linking protein VIII
Macromolecule | Name: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.779684 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSKEIPTPYM WSYQPQMGLA AGAAQDYSTR MNWLSAGPAM ISRVNDIRAH RNQILLEQSA LTATPRNHLN PRNWPAALVY QEIPQPTTV LLPRDAQAEV QLTNSGVQLA GGATLCRHRP AQGIKRLVIR GRGTQLNDEV VSSSLGLRPD GVFQLAGSGR S SFTPRQAV ...String: MSKEIPTPYM WSYQPQMGLA AGAAQDYSTR MNWLSAGPAM ISRVNDIRAH RNQILLEQSA LTATPRNHLN PRNWPAALVY QEIPQPTTV LLPRDAQAEV QLTNSGVQLA GGATLCRHRP AQGIKRLVIR GRGTQLNDEV VSSSLGLRPD GVFQLAGSGR S SFTPRQAV LTLESSSSQP RSGGIGTLQF VEEFTPSVYF NPFSGSPGHY PDEFIPNFDA ISESVDGYD UniProtKB: Pre-hexon-linking protein VIII |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: Grid was R2/2 UltrAUFoil. Sample was applied and blotted twice before plunging.. | ||||||||||||
Details | Concentrated by centrifugation |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 2875 / Average exposure time: 0.2 sec. / Average electron dose: 1.1802 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7rd1: |