[English] 日本語
Yorodumi
- EMDB-4551: Near Atomic Structure of an Atadenovirus Shows a possible gene du... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4551
TitleNear Atomic Structure of an Atadenovirus Shows a possible gene duplication event and Intergenera Variations in Cementing Proteins
Map dataCryo-EM structure of a lizard atadenovirus, LAdV-2, at 3.4 A resolution
Sample
  • Virus: Lizard adenovirus 2
    • Protein or peptide: Hexon protein
    • Protein or peptide: Protein LH3
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: PIIIa
    • Protein or peptide: Penton protein
Keywordsadenovirus atadenovirus virus evolution / VIRUS
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / hexon binding / endocytosis involved in viral entry into host cell / host cell / viral capsid / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Adenovirus large t-antigen, E1B 55kDa protein / Adenovirus EB1 55K protein / large t-antigen / Adenovirus Pll, hexon, subdomain 3 / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain ...Adenovirus large t-antigen, E1B 55kDa protein / Adenovirus EB1 55K protein / large t-antigen / Adenovirus Pll, hexon, subdomain 3 / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / 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 / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Penton protein / Pre-hexon-linking protein VIII / Protein LH3 / PIIIa / Hexon protein
Similarity search - Component
Biological speciesLizard adenovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCondezo GN / Marabini R
Citation
Journal: Sci Adv / Year: 2021
Title: Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins.
Authors: Roberto Marabini / Gabriela N Condezo / Mart Krupovic / Rosa Menéndez-Conejero / Josué Gómez-Blanco / Carmen San Martín /
Abstract: Of five known adenovirus genera, high-resolution structures are available only for mammalian-infecting mastadenoviruses. We present the first high-resolution structure of an adenovirus with ...Of five known adenovirus genera, high-resolution structures are available only for mammalian-infecting mastadenoviruses. We present the first high-resolution structure of an adenovirus with nonmammalian host: lizard atadenovirus LAdV-2. We find a large conformational difference in the internal vertex protein IIIa between mast- and atadenoviruses, induced by the presence of an extended polypeptide. This polypeptide, and α-helical clusters beneath the facet, likely correspond to genus-specific proteins LH2 and p32k. Another genus-specific protein, LH3, with a fold typical of bacteriophage tailspikes, contacts the capsid surface via a triskelion structure identical to that used by mastadenovirus protein IX, revealing a conserved capsid-binding motif and an ancient gene duplication event. Our data also suggest that mastadenovirus E1B-55 K was exapted from the atadenovirus-like LH3 protein. This work provides new information on the evolution of adenoviruses, emphasizing the importance of minor coat proteins for determining specific physicochemical properties of virions and most likely their tropism.
#1: Journal: Biorxiv / Year: 2020
Title: Near Atomic Structure of an Atadenovirus Reveals a Conserved Capsid-Binding Motif and Intergenera Variations in Cementing Proteins
Authors: Marabini R / Condezo GN / Gomez-Blanco J / San Martin C
History
DepositionJan 17, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseAug 5, 2020-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qi5
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qi5
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4551.png

Downloads & links

-
Map

FileDownload / File: emd_4551.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a lizard atadenovirus, LAdV-2, at 3.4 A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 780 pix.
= 1053. Å		1.35 Å/pix.
x 780 pix.
= 1053. Å		1.35 Å/pix.
x 780 pix.
= 1053. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.05
Minimum - Maximum-0.2957798 - 0.5360727
Average (Standard dev.)0.0033348403 (±0.038650833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-390-390-390
Dimensions780780780
Spacing780780780
CellA=B=C: 1053.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z780780780
origin x/y/z0.0000.0000.000
length x/y/z1053.0001053.0001053.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS-390-390-390
NC/NR/NS780780780
D min/max/mean-0.2960.5360.003

-
Supplemental data

-
Sample components

-
Entire : Lizard adenovirus 2

EntireName: Lizard adenovirus 2
Components
  • Virus: Lizard adenovirus 2
    • Protein or peptide: Hexon protein
    • Protein or peptide: Protein LH3
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: PIIIa
    • Protein or peptide: Penton protein

-
Supramolecule #1: Lizard adenovirus 2

SupramoleculeName: Lizard adenovirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 874272 / Sci species name: Lizard adenovirus 2 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Heloderma horridum (Mexican beaded lizard)
Molecular weightTheoretical: 150 MDa
Virus shellShell ID: 1 / Diameter: 940.0 Å / T number (triangulation number): 25

-
Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Lizard adenovirus 2
Molecular weightTheoretical: 101.86193 KDa
SequenceString: MEPQREFFHI AGRSAKEYLS ENLVQFIQAT QNYFNIGEKF RDPYVAPSAG VTTDRSQKLQ LRVVPIQTED NVNYYKARFT LNVGDNRLV DLGSSYFDIK GTLDRGPSFK PYGGTAYNPL APKSAPINSA FTVGNDTHFV AQLPQTYAAG GTGVTEAIQQ Q VSGVDPNP ...String:
MEPQREFFHI AGRSAKEYLS ENLVQFIQAT QNYFNIGEKF RDPYVAPSAG VTTDRSQKLQ LRVVPIQTED NVNYYKARFT LNVGDNRLV DLGSSYFDIK GTLDRGPSFK PYGGTAYNPL APKSAPINSA FTVGNDTHFV AQLPQTYAAG GTGVTEAIQQ Q VSGVDPNP QVGQPNYAGP VVVNTTNNAG LGRIVSADSE GQQFPCYGAY APPQSAGGDV STAAVTKTYI NTTNNNGRVS GT MATDTIT WENPDAHFAD FVDDRRATAA GNRPNYIGFR DNFIGMMYYN SGSNTGSFSS QTQQLNIVLD LNDRNSELSY QYL LADLTS RWHYFALWNQ AVDDYDHHVR ILENDGYEEG PPNLAFPPHV ISNPFAPAAV GTGMTVNEQQ QTAAVTANTV ALIG YGNIP AVEMNLPANL KRTFLYSNVA MYLPDTYKFT PANVDLPENH LSYGYINGRL PLPNIVDTWT DIGARWSLDV MDTVN PFNH HRNTGLKYRS QLLGNGRYCD FHIQVPQKFF AIKNLLLLPG TYNYEWYFRK DPNMVLQSTL GNDLRADGAS ITYTQI NLY VSFFPMNYDT QSELELMLRN ATNDQNFSDY LGAVNNLYQI PAGSSTVVVN IPDRSWGAFR GWSFTRLKVS ETPRIGA TQ DPNFQYSGSI PYLDGTFYLS HTFQRCSIQW DSSVPWPGND RMLTPNWFEI KRPINQDAEG NDTMQSNLTK DFFMVQMA A SYNQGYQGFN WPNCTKHYGF INNFEPMSRQ VPEYGANYPN LMAAYLANPQ TMPIWNNCGF QQKTATNVLL ERCGHPYVA NWPYPLSGRN AVPNQVTERK FLVDRYLWQI PFSSNFLNMG TLTDLGQNVM YANSSHSLNM QFTVDPMTEP TYLMLLFGVF DQVVINQPT RSGISVAYLR LPFASGSAAT

UniProtKB: Hexon protein

-
Macromolecule #2: Protein LH3

MacromoleculeName: Protein LH3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Lizard adenovirus 2
Molecular weightTheoretical: 41.158344 KDa
SequenceString: MTSVEELYVI NPINQWPAPG SFSSQKPPGT LLPGEDPEAV FKQYHVVYLV PGAQYHWKNI LIEKPVWIYG NGATVRTSGT GPILRIVGN RTEKRDVRIQ DISFFGEDCT PNRMEPMSEK LVYQMAIWVT DMKRVTIKGC NFTNFAGAAV FFEETAYNGF F WSMQHLIT ...String:
MTSVEELYVI NPINQWPAPG SFSSQKPPGT LLPGEDPEAV FKQYHVVYLV PGAQYHWKNI LIEKPVWIYG NGATVRTSGT GPILRIVGN RTEKRDVRIQ DISFFGEDCT PNRMEPMSEK LVYQMAIWVT DMKRVTIKGC NFTNFAGAAV FFEETAYNGF F WSMQHLIT ECRFTGCRIG IANGGRSEYS TASFNNFFDC QICFNVVGGN WNRCGNIAAN CRCVYLHTTN MWYEGAGGNF NA AHGSFTG NTMNHCDYGG NLWPTAFQLP DREIQLAGFY FDNARARCPT WTGNTQYYGD MKILNFNQAN DAAIFVIDGC ALY GQPGDT GSIETTAALT DKVFIQGCQG NKVTLFNIKA ANVVPAIGTI KQKP

UniProtKB: Protein LH3

-
Macromolecule #3: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lizard adenovirus 2
Molecular weightTheoretical: 30.744453 KDa
SequenceString: MDAPVTPYIW QYQPQTGKAA GARQNYGAVI NWLSADNNMF HRVQTVNRAR NLIDEIREET VRPDLAASFN DWTYDQLTQP PGTAYLPAP DPLTGPTTIR DKVLSAEGEQ LAGSRPSVLH GGASLPPSAY SLGDGREYMK LTRDALPFPQ NWMVKENGVW T PIVEQRAA ...String:
MDAPVTPYIW QYQPQTGKAA GARQNYGAVI NWLSADNNMF HRVQTVNRAR NLIDEIREET VRPDLAASFN DWTYDQLTQP PGTAYLPAP DPLTGPTTIR DKVLSAEGEQ LAGSRPSVLH GGASLPPSAY SLGDGREYMK LTRDALPFPQ NWMVKENGVW T PIVEQRAA LRGGSANALS SYPTLLFNQP PILRYRRPGQ QLQGSGVIAP SSKVLSLLSE APRIPRTEGM TPYQFANSFP PV VYEDPFS QNLAVFPKEF SPLFEPENQV LASSLATLQY N

UniProtKB: Pre-hexon-linking protein VIII

-
Macromolecule #4: PIIIa

MacromoleculeName: PIIIa / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lizard adenovirus 2
Molecular weightTheoretical: 67.049266 KDa
SequenceString: MDPGLKPSSL WTHKIIDSII ANRSLSAVQN FRKQPLANKL TALEDAIVQP RKDTTPETVA AILQELVAMG ALQPNEVGPM FSDLMIRVH KYNSTNVQNN LSVLLGDIRA AQSEAIRSTN VGELSNQVVL NDFLSREPAV VPQGQHNYEA FKQTLRLMVN E APNVTLFK ...String:
MDPGLKPSSL WTHKIIDSII ANRSLSAVQN FRKQPLANKL TALEDAIVQP RKDTTPETVA AILQELVAMG ALQPNEVGPM FSDLMIRVH KYNSTNVQNN LSVLLGDIRA AQSEAIRSTN VGELSNQVVL NDFLSREPAV VPQGQHNYEA FKQTLRLMVN E APNVTLFK SGPDTLMQVN IRGVNTVNLN SAFKNLKNFW GVQLDTEIVP GSISSKLSSN TRVLLLFLAP FTNDSTFTPD TF ISQIMRL YRETVAASIE QPQETELEVA ETIRELGGDV EDIGRTMAFL LKNKEEIVSN PRTLSPRQLN VLRYVQESLQ DRI DRNGEE PEDALRNLVF SFAPSYFEAN GPFIRRLISY LEVALINSPN YFREIYSNKY WTPPASFWTQ NYGDFHLERE AEAE RRAAS EAGYGDFEEG DFALPDNLGE GSDLAWDDFN TAMSPSVPPT PSVRSAPASL SYGRTSPSSV SSLTASDRNI GATLA RAVI PPAAAAIGSA AGEALYPSLG QYLAPAASLA ATRLLNLTRA RRQRLKRDSL ARHRRITEVR GVYPKAAPTR SSSSSS VSS TPTVFEPLPG AFSVINPLMR PEGDRDVSGT GIVNPFSHLK PRNGLQ

UniProtKB: PIIIa

-
Macromolecule #5: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lizard adenovirus 2
Molecular weightTheoretical: 50.619848 KDa
SequenceString: MEVYVPPPRV MAPTEGRNSI SYNPIAPLQD TTHIYIIDNK TSDIENLNIH KDHSNFYTNI VQNVDVAPSD AATQTIKLDE RSRWGGELH TILKTNAPNV TEFFNSNSFK ALLMSDKTDP ANPVYTWFEL SIPEGDYTVG SLIDMLNNAV VENYLEVGRQ K GVQISDIG ...String:
MEVYVPPPRV MAPTEGRNSI SYNPIAPLQD TTHIYIIDNK TSDIENLNIH KDHSNFYTNI VQNVDVAPSD AATQTIKLDE RSRWGGELH TILKTNAPNV TEFFNSNSFK ALLMSDKTDP ANPVYTWFEL SIPEGDYTVG SLIDMLNNAV VENYLEVGRQ K GVQISDIG VKFDTRNFSL GRDPLTSLVT PGNYTFKAFH PDIVLLPGCG VDFTHSRINN MLGMRKRFPY EPGYVITYED LV GGNIPAL LDLAKYPGET SPVLQDPDGN SYHVEEVSPK KWQTKYRSWC LAYNSSQGTL KSEQILTVPD ITGGLGQLYW SLP DAFKPP VTFTNNTTDI STQPVTGMHL FPLSQRIVYN TSAVYAQLVE QMTNNTKVFN RFPKNAILMQ PPYDTTQWIS ENVP YVADH GIQPLKNSLT GVQRVTLTDD RRRSCPYIYK TLATVTPKVL SSATLQ

UniProtKB: Penton protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: PBS
GridModel: Quantifoil R2/4 / Material: COPPER/RHODIUM
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.0 sec. / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, Scipion) / Number images used: 16071
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION, Scipion)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION, Scipion)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more