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- EMDB-24408: The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adeno... -

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Basic information

Entry
Database: EMDB / ID: EMD-24408
TitleThe Capsid Structure of the ChAdOx1 viral vector/chimpanzee adenovirus Y25
Map dataRelion-generated, post-processed map
Sample
  • Virus: Chimpanzee adenovirus Y25
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Pre-hexon-linking protein VIII
KeywordsAdenovirus / 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
Function and homology information


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 / hexon binding / viral release from host cell / endocytosis involved in viral entry into host cell / host cell / viral capsid ...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 / hexon binding / viral release from host cell / endocytosis involved in viral entry into host cell / 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
Adenovirus Pll, hexon, subdomain 3 / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal ...Adenovirus Pll, hexon, subdomain 3 / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII
Similarity search - Domain/homology
Hexon-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-protein VI / Hexon protein / Pre-hexon-linking protein VIII
Similarity search - Component
Biological speciesChimpanzee adenovirus Y25
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsBaker AT / Boyd RJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1531991 United States
Citation
Journal: Sci Adv / Year: 2021
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: Journal: Biorxiv / Year: 2021
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
DepositionJul 8, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.005
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  • Surface view with fitted model
  • Atomic models: PDB-7rd1
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rd1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24408.png

Downloads & links

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Map

FileDownload / File: emd_24408.map.gz / Format: CCP4 / Size: 7.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion-generated, post-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.53 Å/pix.
x 1260 pix.
= 1929.601 Å		1.53 Å/pix.
x 1260 pix.
= 1929.601 Å		1.53 Å/pix.
x 1260 pix.
= 1929.601 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.53143 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.05644682 - 0.0945594
Average (Standard dev.)0.0001226028 (±0.0024764268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions126012601260
Spacing126012601260
CellA=B=C: 1929.6006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.53142936507941.53142936507941.5314293650794
M x/y/z126012601260
origin x/y/z0.0000.0000.000
length x/y/z1929.6011929.6011929.601
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS126012601260
D min/max/mean-0.0560.0950.000

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Supplemental data

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Mask #1

Fileemd_24408_msk_1.map
Projections & Slices
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Additional map: DeepEMhancer-sharpened using highRes model

Fileemd_24408_additional_1.map
AnnotationDeepEMhancer-sharpened using highRes model
Projections & Slices
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Histogram

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Additional map: DeepEMhancer-sharpened using wideTarget model

Fileemd_24408_additional_2.map
AnnotationDeepEMhancer-sharpened using wideTarget model
Projections & Slices
AxesZYX

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Additional map: DeepEMhancer-sharpened using wideTarget model and low pass-filtered

Fileemd_24408_additional_3.map
AnnotationDeepEMhancer-sharpened using wideTarget model and low pass-filtered
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Additional map: Hollowed to remove noise generated by nonstructured genome

Fileemd_24408_additional_4.map
AnnotationHollowed to remove noise generated by nonstructured genome
Projections & Slices
AxesZYX

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Histogram

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Half map: Random half map

Fileemd_24408_half_map_1.map
AnnotationRandom half map
Projections & Slices
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Histogram

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Half map: Random half map

Fileemd_24408_half_map_2.map
AnnotationRandom half map
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Sample components

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Entire : Chimpanzee adenovirus Y25

EntireName: Chimpanzee adenovirus Y25
Components
  • Virus: Chimpanzee adenovirus Y25
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Pre-hexon-linking protein VIII

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Supramolecule #1: Chimpanzee adenovirus Y25

SupramoleculeName: 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
Host (natural)Organism: Pan troglodytes (chimpanzee)
Virus shellShell ID: 1 / Name: Icosahedral Capsid / Diameter: 500.0 Å / T number (triangulation number): 25

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Macromolecule #1: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 26.299689 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 106.121141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 59.533656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #4: Hexon-interlacing protein

MacromoleculeName: Hexon-interlacing protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 14.468118 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSGSGSFEGG VFSPYLTGRL PSWAGVRQNV MGSTVDGRPV QPANSSTLTY ATLSSSSVDA AAAAAAASAA SAVRGMAMGA GYYGTLVAN SSSTNNPASL NEEKLLLLMA QLEALTQRLG ELTQQVAQLQ EQTRAAVATV KSK

UniProtKB: Hexon-interlacing protein

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Macromolecule #5: Pre-hexon-linking protein IIIa

MacromoleculeName: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 65.9545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #6: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 24.779684 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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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: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSalt
1.0 mMMgCl2Magnesium Chloride
20.0 mMC4H11NO3Tris
GridModel: UltrAuFoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen 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..
DetailsConcentrated by centrifugation

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8375
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 5748
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7rd1:
The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adenovirus Y25

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