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Yorodumi- EMDB-7034: Improved cryoEM structure of human adenovirus type 5 with atomic ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7034 | ||||||||||||||||||||||||
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Title | Improved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII | ||||||||||||||||||||||||
Map data | human adenovirus type 5 | ||||||||||||||||||||||||
Sample | Human adenovirus 5 != Human adenovirus C serotype 5 Human adenovirus 5
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Function / homology | Function and homology information hexon binding / protein transport along microtubule / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / viral release from host cell ...hexon binding / protein transport along microtubule / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / viral release from host cell / viral life cycle / viral penetration into host nucleus / host cell / viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / cell adhesion / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding / nucleus Similarity search - Function | ||||||||||||||||||||||||
Biological species | HAdV-5 (virus) / Human adenovirus C serotype 5 | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||||||||
Authors | Dai XH / Wu L / Sun R / Zhou ZH | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: J Virol / Year: 2017 Title: Atomic Structures of Minor Proteins VI and VII in Human Adenovirus. Authors: Xinghong Dai / Lily Wu / Ren Sun / Z Hong Zhou / Abstract: Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic ...Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts toward more effective applications. Since 2010, atomic models of human Ad5 have been derived independently from photographic film cryo-electron microscopy (cryo-EM) and X-ray crystallography studies, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII, and IX. To clarify these discrepancies, we employed the technology of direct electron counting to obtain a cryo-EM structure of human Ad5 at 3.2-Å resolution. Our improved structure unambiguously confirms our previous cryo-EM models of proteins IIIa, VIII, and IX and explains the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavity of hexon-the cleaved N terminus of precursor protein VI (pVIn), the cleaved N terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2-and, by extension, that of genome-condensing pVII-to hexons is consistent with the previously proposed dsDNA genome-capsid coassembly for adenoviruses, which resembles that of single-stranded RNA (ssRNA) viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid exemplified by tailed bacteriophages and herpesviruses. Adenovirus is a double-edged sword to humans: it is a widespread pathogen but can be used as a bioengineering tool for anticancer and gene therapies. The atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models for the important cement proteins IIIa, VIII, and IX from conventional/film cryo-EM and X-ray crystallography studies have caused confusion. Using cutting-edge cryo-EM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our previous models of cement proteins IIIa, VIII, and IX, thus clarifying the inconsistent structures. The improved structure also reveals atomic details of membrane-lytic protein VI and genome-condensing protein VII and supports the previously proposed genome-capsid coassembly mechanism for adenoviruses. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7034.map.gz | 1.9 GB | EMDB map data format | |
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Header (meta data) | emd-7034-v30.xml emd-7034.xml | 24 KB 24 KB | Display Display | EMDB header |
Images | emd_7034.png | 337.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7034 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7034 | HTTPS FTP |
-Validation report
Summary document | emd_7034_validation.pdf.gz | 498.2 KB | Display | EMDB validaton report |
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Full document | emd_7034_full_validation.pdf.gz | 497.7 KB | Display | |
Data in XML | emd_7034_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_7034_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7034 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7034 | HTTPS FTP |
-Related structure data
Related structure data | 3izoM 6b1tMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7034.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | human adenovirus type 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human adenovirus 5
Entire | Name: Human adenovirus 5 |
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Components |
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-Supramolecule #1: Human adenovirus C serotype 5
Supramolecule | Name: Human adenovirus C serotype 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cultured in HEK293T cells and purified from media / NCBI-ID: 28285 / Sci species name: Human adenovirus C serotype 5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 150 MDa |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 900.0 Å / T number (triangulation number): 25 |
-Macromolecule #1: Hexon protein
Macromolecule | Name: Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: HAdV-5 (virus) |
Molecular weight | Theoretical: 108.107617 KDa |
Sequence | String: MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNPCEWDEAA TALEINLEEE DDDNEDEVDE Q AEQQKTHV ...String: MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNPCEWDEAA TALEINLEEE DDDNEDEVDE Q AEQQKTHV FGQAPYSGIN ITKEGIQIGV EGQTPKYADK TFQPEPQIGE SQWYETEINH AAGRVLKKTT PMKPCYGSYA KP TNENGGQ GILVKQQNGK LESQVEMQFF STTEATAGNG DNLTPKVVLY SEDVDIETPD THISYMPTIK EGNSRELMGQ QSM PNRPNY IAFRDNFIGL MYYNSTGNMG VLAGQASQLN AVVDLQDRNT ELSYQLLLDS IGDRTRYFSM WNQAVDSYDP DVRI IENHG TEDELPNYCF PLGGVINTET LTKVKPKTGQ ENGWEKDATE FSDKNEIRVG NNFAMEINLN ANLWRNFLYS NIALY LPDK LKYSPSNVKI SDNPNTYDYM NKRVVAPGLV DCYINLGARW SLDYMDNVNP FNHHRNAGLR YRSMLLGNGR YVPFHI QVP QKFFAIKNLL LLPGSYTYEW NFRKDVNMVL QSSLGNDLRV DGASIKFDSI CLYATFFPMA HNTASTLEAM LRNDTND QS FNDYLSAANM LYPIPANATN VPISIPSRNW AAFRGWAFTR LKTKETPSLG SGYDPYYTYS GSIPYLDGTF YLNHTFKK V AITFDSSVSW PGNDRLLTPN EFEIKRSVDG EGYNVAQCNM TKDWFLVQML ANYNIGYQGF YIPESYKDRM YSFFRNFQP MSRQVVDDTK YKDYQQVGIL HQHNNSGFVG YLAPTMREGQ AYPANFPYPL IGKTAVDSIT QKKFLCDRTL WRIPFSSNFM SMGALTDLG QNLLYANSAH ALDMTFEVDP MDEPTLLYVL FEVFDVVRVH RPHRGVIETV YLRTPFSAGN ATT |
-Macromolecule #2: Penton protein
Macromolecule | Name: Penton protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: HAdV-5 (virus) |
Molecular weight | Theoretical: 63.356602 KDa |
Sequence | String: MRRAAMYEEG PPPSYESVVS AAPVAAALGS PFDAPLDPPF VPPRYLRPTG GRNSIRYSEL APLFDTTRVY LVDNKSTDVA SLNYQNDHS NFLTTVIQNN DYSPGEASTQ TINLDDRSHW GGDLKTILHT NMPNVNEFMF TNKFKARVMV SRLPTKDNQV E LKYEWVEF ...String: MRRAAMYEEG PPPSYESVVS AAPVAAALGS PFDAPLDPPF VPPRYLRPTG GRNSIRYSEL APLFDTTRVY LVDNKSTDVA SLNYQNDHS NFLTTVIQNN DYSPGEASTQ TINLDDRSHW GGDLKTILHT NMPNVNEFMF TNKFKARVMV SRLPTKDNQV E LKYEWVEF TLPEGNYSET MTIDLMNNAI VEHYLKVGRQ NGVLESDIGV KFDTRNFRLG FDPVTGLVMP GVYTNEAFHP DI ILLPGCG VDFTHSRLSN LLGIRKRQPF QEGFRITYDD LEGGNIPALL DVDAYQASLK DDTEQGGGGA GGSNSSGSGA EEN SNAAAA AMQPVEDMND HAIRGDTFAT RAEEKRAEAE AAAEAAAPAA QPEVEKPQKK PVIKPLTEDS KKRSYNLISN DSTF TQYRS WYLAYNYGDP QTGIRSWTLL CTPDVTCGSE QVYWSLPDMM QDPVTFRSTR QISNFPVVGA ELLPVHSKSF YNDQA VYSQ LIRQFTSLTH VFNRFPENQI LARPPAPTIT TVSENVPALT DHGTLPLRNS IGGVQRVTIT DARRRTCPYV YKALGI VSP RVLSSRTF |
-Macromolecule #3: Pre-hexon-linking protein IIIa
Macromolecule | Name: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: HAdV-5 (virus) |
Molecular weight | Theoretical: 65.322805 KDa |
Sequence | String: MMQDATDPAV RAALQSQPSG LNSTDDWRQV MDRIMSLTAR NPDAFRQQPQ ANRLSAILEA VVPARANPTH EKVLAIVNAL AENRAIRPD EAGLVYDALL QRVARYNSGN VQTNLDRLVG DVREAVAQRE RAQQQGNLGS MVALNAFLST QPANVPRGQE D YTNFVSAL ...String: MMQDATDPAV RAALQSQPSG LNSTDDWRQV MDRIMSLTAR NPDAFRQQPQ ANRLSAILEA VVPARANPTH EKVLAIVNAL AENRAIRPD EAGLVYDALL QRVARYNSGN VQTNLDRLVG DVREAVAQRE RAQQQGNLGS MVALNAFLST QPANVPRGQE D YTNFVSAL RLMVTETPQS EVYQSGPDYF FQTSRQGLQT VNLSQAFKNL QGLWGVRAPT GDRATVSSLL TPNSRLLLLL IA PFTDSGS VSRDTYLGHL LTLYREAIGQ AHVDEHTFQE ITSVSRALGQ EDTGSLEATL NYLLTNRRQK IPSLHSLNSE EER ILRYVQ QSVSLNLMRD GVTPSVALDM TARNMEPGMY ASNRPFINRL MDYLHRAAAV NPEYFTNAIL NPHWLPPPGF YTGG FEVPE GNDGFLWDDI DDSVFSPQPQ TLLELQQREQ AEAALRKESF RRPSSLSDLG AAAPRSDASS PFPSLIGSLT STRTT RPRL LGEEEYLNNS LLQPQREKNL PPAFPNNGIE SLVDKMSRWK TYAQEHRDVP GPRPPTRRQR HDRQRGLVWE DDDSAD DSS VLDLGGSGNP FAHLRPRLGR MF |
-Macromolecule #4: Pre-hexon-linking protein VIII
Macromolecule | Name: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: HAdV-5 (virus) |
Molecular weight | Theoretical: 24.71059 KDa |
Sequence | String: MSKEIPTPYM WSYQPQMGLA AGAAQDYSTR INYMSAGPHM ISRVNGIRAH RNRILLEQAA ITTTPRNNLN PRSWPAALVY QESPAPTTV VLPRDAQAEV QMTNSGAQLA GGFRHRVRSP GQGITHLTIR GRGIQLNDES VSSSLGLRPD GTFQIGGAGR P SFTPRQAI ...String: MSKEIPTPYM WSYQPQMGLA AGAAQDYSTR INYMSAGPHM ISRVNGIRAH RNRILLEQAA ITTTPRNNLN PRSWPAALVY QESPAPTTV VLPRDAQAEV QMTNSGAQLA GGFRHRVRSP GQGITHLTIR GRGIQLNDES VSSSLGLRPD GTFQIGGAGR P SFTPRQAI LTLQTSSSEP RSGGIGTLQF IEEFVPSVYF NPFSGPPGHY PDQFIPNFDA VKDSADGYD |
-Macromolecule #5: Hexon-interlacing protein
Macromolecule | Name: Hexon-interlacing protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: HAdV-5 (virus) |
Molecular weight | Theoretical: 14.468134 KDa |
Sequence | String: MSTNSFDGSI VSSYLTTRMP PWAGVRQNVM GSSIDGRPVL PANSTTLTYE TVSGTPLETA ASAAASAAAA TARGIVTDFA FLSPLASSA ASRSSARDDK LTALLAQLDS LTRELNVVSQ QLLDLRQQVS ALKASSPPNA V |
-Macromolecule #6: Pre-protein VI
Macromolecule | Name: Pre-protein VI / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: HAdV-5 (virus) |
Molecular weight | Theoretical: 3.584953 KDa |
Sequence | String: MEDINFASLA PRHGSRPFMG NWQDIGTSNM SGG |
-Macromolecule #7: Pre-histone-like nucleoprotein
Macromolecule | Name: Pre-histone-like nucleoprotein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: HAdV-5 (virus) |
Molecular weight | Theoretical: 1.198438 KDa |
Sequence | String: GLRFPSKMFG G |
-Macromolecule #8: Pre-protein VI
Macromolecule | Name: Pre-protein VI / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: HAdV-5 (virus) |
Molecular weight | Theoretical: 23.460559 KDa |
Sequence | String: AFSWGSLWSG IKNFGSTVKN YGSKAWNSST GQMLRDKLKE QNFQQKVVDG LASGISGVVD LANQAVQNKI NSKLDPRPPV EEPPPAVET VSPEGRGEKR PRPDREETLV TQIDEPPSYE EALKQGLPTT RPIAPMATGV LGQHTPVTLD LPPPADTQQK P VLPGPTAV ...String: AFSWGSLWSG IKNFGSTVKN YGSKAWNSST GQMLRDKLKE QNFQQKVVDG LASGISGVVD LANQAVQNKI NSKLDPRPPV EEPPPAVET VSPEGRGEKR PRPDREETLV TQIDEPPSYE EALKQGLPTT RPIAPMATGV LGQHTPVTLD LPPPADTQQK P VLPGPTAV VVTRPSRASL RRAASGPRSL RPVASGNWQS TLNSIVGLGV QSLKRRRCF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK II | ||||||||||||
Details | Purified virion |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K |
Specialist optics | Energy filter - Name: Gatan Image Filter / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 2.5 µm / Digitization - Frames/image: 2-32 / Number grids imaged: 1 / Number real images: 5608 / Average exposure time: 9.0 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
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Output model | PDB-3izo: PDB-6b1t: |