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- EMDB-11108: The atomic structure of HAdV-F41 at pH 7.4 -

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Basic information

Entry
Database: EMDB / ID: EMD-11108
TitleThe atomic structure of HAdV-F41 at pH 7.4
Map dataFull map masked
Sample
  • Virus: Human adenovirus 41
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Core-capsid bridging protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Fiber proteinFibrous protein
    • Protein or peptide: Unknown
    • Protein or peptide: Unknown
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / virion component => GO:0044423 / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / endocytosis involved in viral entry into host cell ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / virion component => GO:0044423 / host cell nucleolus / 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 / DNA binding
Similarity search - Function
Adenovirus core-capsid bridging protein V / Adenovirus minor core protein PV / : / 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) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII ...Adenovirus core-capsid bridging protein V / Adenovirus minor core protein PV / : / 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) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / 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
Similarity search - Domain/homology
Hexon-interlacing protein / Core-capsid bridging protein / Hexon protein / Pre-hexon-linking protein VIII / Pre-protein VI / Hexon-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein
Similarity search - Component
Biological speciesHAdV-41 (virus) / Human adenovirus 41
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsCarlson L-A / Rafie K
Funding support Sweden, 4 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)CDA00047/2017-C Sweden
Swedish Research CouncilDnr 2017-00859 Sweden
Swedish Research CouncilDnr 2019-01472 Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Sci Adv / Year: 2021
Title: The structure of enteric human adenovirus 41-A leading cause of diarrhea in children.
Authors: K Rafie / A Lenman / J Fuchs / A Rajan / N Arnberg / L-A Carlson /
Abstract: Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and ...Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and pathogenicity from respiratory and ocular adenoviruses, but the structural basis for this divergence has been unknown. Here, we present the first structure of an enteric HAdV-HAdV-F41-determined by cryo-electron microscopy to a resolution of 3.8 Å. The structure reveals extensive alterations to the virion exterior as compared to nonenteric HAdVs, including a unique arrangement of capsid protein IX. The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of core protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Our findings provide the structural basis for adaptation of enteric HAdVs to a fundamentally different tissue tropism.
History
DepositionMay 31, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-6z7n
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6z7n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11108.png

Downloads & links

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Map

FileDownload / File: emd_11108.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map masked
Voxel sizeX=Y=Z: 1.041 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.04871885 - 0.067119084
Average (Standard dev.)0.0004667922 (±0.00480041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin145145145
Dimensions900900900
Spacing900900900
CellA=B=C: 936.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0411.0411.041
M x/y/z900900900
origin x/y/z0.0000.0000.000
length x/y/z936.900936.900936.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS145145145
NC/NR/NS900900900
D min/max/mean-0.0490.0670.000

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Supplemental data

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Mask #1

Fileemd_11108_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ASU map for model building

Fileemd_11108_additional_1.map
AnnotationASU map for model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 1

Fileemd_11108_half_map_1.map
AnnotationHalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 2

Fileemd_11108_half_map_2.map
AnnotationHalf 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human adenovirus 41

EntireName: Human adenovirus 41
Components
  • Virus: Human adenovirus 41
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Core-capsid bridging protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Fiber proteinFibrous protein
    • Protein or peptide: Unknown
    • Protein or peptide: Unknown

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Supramolecule #1: Human adenovirus 41

SupramoleculeName: Human adenovirus 41 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10524 / Sci species name: Human adenovirus 41 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Diameter: 900.0 Å

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Macromolecule #1: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: HAdV-41 (virus)
Molecular weightTheoretical: 29.170145 KDa
SequenceString: MEDINFASLA PRHGSRPFMG TWNEIGTSQL NGGAFSWSSL WSGIKNFGSS IKSFGNKAWN SNTGQMLRDK LKDQNFQQKV VDGLASGIN GVVDIANQAL QNQINQRLEN SRQPPVALKQ RPTPEPEEVE VEEKLPPLET APPLPSKGEK RPRPELEETL V VESREPPS ...String:
MEDINFASLA PRHGSRPFMG TWNEIGTSQL NGGAFSWSSL WSGIKNFGSS IKSFGNKAWN SNTGQMLRDK LKDQNFQQKV VDGLASGIN GVVDIANQAL QNQINQRLEN SRQPPVALKQ RPTPEPEEVE VEEKLPPLET APPLPSKGEK RPRPELEETL V VESREPPS YEQALKEGAS YPMTRPIGSM ARPVYGKEKT PVTLELPPPA PTVPPMPTPT LGTNVPRLAA PTVAVATPAR RV RGANWQS TLNSIVGLGV KSLKRRRCY

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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: HAdV-41 (virus)
Molecular weightTheoretical: 104.064234 KDa
SequenceString: MATPSMMPQW SYMHIAGQDA SEYLSPGLVQ FARATDTYFS LGNKFRNPTV APTHDVTTDR SQRLTLRFVP VDREDTAYSY KVRFTLAVG DNRVLDMAST YFDIRGVLDR GPSFKPYSGT AYNSLAPKTA PNPCEWKDNN KIKVRGQAPF IGTNINKDNG I QIGTDTTN ...String:
MATPSMMPQW SYMHIAGQDA SEYLSPGLVQ FARATDTYFS LGNKFRNPTV APTHDVTTDR SQRLTLRFVP VDREDTAYSY KVRFTLAVG DNRVLDMAST YFDIRGVLDR GPSFKPYSGT AYNSLAPKTA PNPCEWKDNN KIKVRGQAPF IGTNINKDNG I QIGTDTTN QPIYADKTYQ PEPQVGQTQW NSEVGAAQKV AGRVLKDTTP MLPCYGSYAK PTNEKGGQAS LITNGTDQTL TS DVNLQFF ALPSTPNEPK AVLYAENVSI EAPDTHLVYK PDVAQGTISS ADLLTQQAAP NRPNYIGFRD NFIGLMYYNS TGN MGVLAG QASQLNAVVD LQDRNTELSY QLMLDALGDR SRYFSMWNQA VDSYDPDVRI IENHGVEDEL PNYCFPLGGS AATD TYSGI KANGQTWTAD DNYADRGAEI ESGNIFAMEI NLAANLWRSF LYSNVALYLP DSYKITPDNI TLPENKNTYA YMNGR VAVP SALDTYVNIG ARWSPDPMDN VNPFNHHRNA GLRYRSMLLG NGRYVPFHIQ VPQKFFAIKN LLLLPGSYTY EWNFRK DVN MILQSSLGND LRVDGASVRF DSINLYANFF PMAHNTASTL EAMLRNDTND QSFNDYLCAA NMLYPIPSNA TSVPISI PS RNWAAFRGWS FTRLKTKETP SLGSGFDPYF TYSGSVPYLD GTFYLNHTFK KVSIMFDSSV SWPGNDRLLT PNEFEIKR T VDGEGYNVAQ CNMTKDWFLI QMLSHYNIGY QGFYVPESYK DRMYSFFRNF QPMSRQVVNT TTYKEYQNVT LPFQHNNSG FVGYMGPTMR EGQAYPANYP YPLIGQTAVP SLTQKKFLCD RTMWRIPFSS NFMSMGALTD LGQNMLYANS AHALDMTFEV DPMDEPTLL YVLFEVFDVV RIHQPHRGVI EAVYLRTPFS AGNATT

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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: HAdV-41 (virus)
Molecular weightTheoretical: 57.14216 KDa
SequenceString: MRRAVGVPPV MAYAEGPPPS YESVMGSADS PATLEALYVP PRYLGPTEGR NSIRYSELAP LYDTTRVYLV DNKSADIASL NYQNDHSNF QTTVVQNNDF TPAEAGTQTI NFDERSRWGA DLKTILRTNM PNINEFMSTN KFKARLMVEK KNKETGLPRY E WFEFTLPE ...String:
MRRAVGVPPV MAYAEGPPPS YESVMGSADS PATLEALYVP PRYLGPTEGR NSIRYSELAP LYDTTRVYLV DNKSADIASL NYQNDHSNF QTTVVQNNDF TPAEAGTQTI NFDERSRWGA DLKTILRTNM PNINEFMSTN KFKARLMVEK KNKETGLPRY E WFEFTLPE GNYSETMTID LMNNAIVDNY LEVGRQNGVL ESDIGVKFDT RNFRLGWDPV TKLVMPGVYT NEAFHPDIVL LP GCGVDFT QSRLSNLLGI RKRLPFQEGF QIMYEDLEGG NIPALLDVAK YEASIQKAKE EGKEIGDDTF ATRPQDLVIE PVA KDSKNR SYNLLPNDQN NTAYRSWFLA YNYGDPKKGV QSWTLLTTAD VTCGSQQVYW SLPDMMQDPV TFRPSTQVSN YPVV GVELL PVHAKSFYNE QAVYSQLIRQ STALTHVFNR FPENQILVRP PAPTITTVSE NVPALTDHGT LPLRSSISGV QRVTI TDAR RRTCPYVHKA LGIVAPKVLS SRTF

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Macromolecule #4: Core-capsid bridging protein

MacromoleculeName: Core-capsid bridging protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-41 (virus)
Molecular weightTheoretical: 39.843855 KDa
SequenceString: MSKRKFKEEL LEALVPEIYG PAADVKPDIK PRALKRVKKR EKKEETGLLD DDVEFVRTFA PRRQVQWRGR KVKRVLRPGT TVVFTPGER SATRALKREY DEVYADEDIL EQAAQQIGEF AYGKRGRYGE VGLLLDQSNP TPSLKPATQQ QILPVTETKR G VKRENKDE ...String:
MSKRKFKEEL LEALVPEIYG PAADVKPDIK PRALKRVKKR EKKEETGLLD DDVEFVRTFA PRRQVQWRGR KVKRVLRPGT TVVFTPGER SATRALKREY DEVYADEDIL EQAAQQIGEF AYGKRGRYGE VGLLLDQSNP TPSLKPATQQ QILPVTETKR G VKRENKDE LQPTMQLMVP KRQKLEEVLE NMKVDPSVEP EVKVRPIKEI GPGLGVQTVD IQIPVRTTPA VAMAEAMETQ TD QPAAVTT REIGLQTDPR YESVTSTRRS RGRKYTAANS ILPEYALHPS ITPTPGYRGT IFRPSRPRTT RRRRTTRRRS RRI TPISVH RVTRRGRTIT LPNARYHPSI LI

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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: HAdV-41 (virus)
Molecular weightTheoretical: 64.825246 KDa
SequenceString: MQRSTAVVDG SQQVDPAMLA ALQSQPSGVT PSDDWAAAMD RILALTTRNP EAFRQQPQAN RFSAILEAVV PSRTNPTHEK VLAIVNALT ESKAIRKDEA GLIYNALLER VARYNSTNVQ ANLDRLTTDV REAVAQRERF MHDTNLGSQV ALNAFLSTLP A NVPRGQED ...String:
MQRSTAVVDG SQQVDPAMLA ALQSQPSGVT PSDDWAAAMD RILALTTRNP EAFRQQPQAN RFSAILEAVV PSRTNPTHEK VLAIVNALT ESKAIRKDEA GLIYNALLER VARYNSTNVQ ANLDRLTTDV REAVAQRERF MHDTNLGSQV ALNAFLSTLP A NVPRGQED YVSFISALRL LVAEVPQSEV YQSGPDYFFQ TSRQGLQTVN LTQAFKNLQG MWGVRAPVGD RATISSLLTP NT RLLLLLI APFTNSSTIS RDSYLGHLIT LYREAIGQTQ VDEQTFQEIT SVSRALGQQD TGSLEATLNF LLTNRQQKIP SQF TLSTEE ERILRYVQQS VSLYLMREGM TPSSALDMTA RNMEPSLYSS NRPFINRLMD YLHRAAAMNS EYFTNAILNP HWMP PSGFY TGEFDMPEGD DGFLWDDVSD SIFVPARYRK KEGGDELPLP LVEAASRGQS PFPSLPSLVS SSNSGRVLRP RLPGE TDYL NDPLLQPVRN KNFPNNGVES LVDKMNRWKT YAQEQREWEE SQSRPLAGPF SRWRRREDDQ DDSADDNSVL DLGGTG ASS NPFAHLRPQG RLGRLY

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Macromolecule #6: Hexon-interlacing protein

MacromoleculeName: Hexon-interlacing protein / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: HAdV-41 (virus)
Molecular weightTheoretical: 13.617179 KDa
SequenceString:
MSGSMEGNAV SFKGGVFSPY LTTRLPAWAG VRQNVMGSNV DGRPVAPANS ATLTYATVGS SVDTAAAAAA SAAASTARGM AADFGLYNQ LAASRSLREE DALSVVLTRL EELSQQLQDL FAKVALLNPP ANAS

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Macromolecule #7: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HAdV-41 (virus)
Molecular weightTheoretical: 25.330234 KDa
SequenceString: MSKEIPTPYM WSYQPQMGLA AGASQDYSSR MNWLSAGPHM IGRVNGIRAT RNQILLEQAA LTSTPRSQLN PPNWPAAQVY QENPAPTTV LLPRDAEAEV QMTNSGAQLA GGSRHVRFRG RSSPYSPGPI KRLIIRGRGI QLNDEVVSSL TGLRPDGVFQ L GGAGRSSF ...String:
MSKEIPTPYM WSYQPQMGLA AGASQDYSSR MNWLSAGPHM IGRVNGIRAT RNQILLEQAA LTSTPRSQLN PPNWPAAQVY QENPAPTTV LLPRDAEAEV QMTNSGAQLA GGSRHVRFRG RSSPYSPGPI KRLIIRGRGI QLNDEVVSSL TGLRPDGVFQ L GGAGRSSF TPRQAYLTLQ SSSSQPRSGG IGTLQFVEEF VPSVYFNPFS GAPGLYPDDF IPNYDAVSES VDGYD

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Macromolecule #8: Fiber protein

MacromoleculeName: Fiber protein / type: protein_or_peptide / ID: 8
Details: belongs to one of the two fibre proteins: P14267 or P16883
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 41
Molecular weightTheoretical: 899 Da
SequenceString:
FNPVYPY

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Macromolecule #9: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 41
Molecular weightTheoretical: 869.063 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #10: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 41
Molecular weightTheoretical: 528.644 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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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

Concentration4.2 mg/mL
BufferpH: 7.4
Details: PBS buffer made from comemrcial PBS tablets Medicargo, PBS tablets, 09-9400-100
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.037 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 6929 / Average electron dose: 1.03 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 25667
CTF correctionSoftware - Name: Gctf (ver. 1.18) / Software - details: icle CTF correction
Startup modelType of model: EMDB MAP
EMDB ID:

7034

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta)
Final 3D classificationSoftware - Name: RELION (ver. 3.0-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta) / Number images used: 19472

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Atomic model buiding 1

Initial modelPDB ID:

5tx1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6z7n:
The atomic structure of HAdV-F41 at pH 7.4

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