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Yorodumi- EMDB-24881: Structure of a cell-entry defective human adenovirus provides ins... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24881 | |||||||||
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Title | Structure of a cell-entry defective human adenovirus provides insights into precursor proteins and capsid maturation | |||||||||
Map data | Cropped map file from the original 928x928x928 pixel size map | |||||||||
Sample |
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Keywords | Adenovirus / ts1 mutant / minor protein precursors / virus maturation / VIRUS | |||||||||
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 / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral life cycle / viral capsid ...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 / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral life cycle / viral capsid / host cell / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Human adenovirus C serotype 5 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.72 Å | |||||||||
Authors | Reddy VS / Yu X | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Mol Biol / Year: 2022 Title: Structure of a Cell Entry Defective Human Adenovirus Provides Insights into Precursor Proteins and Capsid Maturation. Authors: Xiaodi Yu / Tina-Marie Mullen / Vahid Abrishami / Juha T Huiskonen / Glen R Nemerow / Vijay S Reddy / Abstract: Maturation of adenoviruses is distinguished by proteolytic processing of several interior minor capsid proteins and core proteins by the adenoviral protease and subsequent reorganization of ...Maturation of adenoviruses is distinguished by proteolytic processing of several interior minor capsid proteins and core proteins by the adenoviral protease and subsequent reorganization of adenovirus core. We report the results derived from the icosahedrally averaged cryo-EM structure of a cell entry defective form of adenovirus, designated ts1, at a resolution of 3.7 Å as well as of the localized reconstructions of unique hexons and penton base. The virion structure revealed the structures and organization of precursors of minor capsid proteins, pIIIa, pVI and pVIII, which are closely associated with the hexons on the capsid interior. In addition to a well-ordered helical domain (a.a. 310-397) of pIIIa, highlights of the structure include the precursors of VIII display significantly different structures near the cleavage sites. Moreover, we traced residues 4-96 of the membrane lytic protein (pVI) that includes an amphipathic helix occluded deep in the hexon cavity suggesting the possibility of co-assembly of hexons with the precursors of VI. In addition, we observe a second copy of pVI ordered up to residue L40 in the peripentonal hexons and a few fragments of density corresponding to 2nd and 3rd copies of pVI in other hexons. However, we see no evidence of precursors of VII binding in the hexon cavity. These findings suggest the possibility that differently bound pVI molecules undergo processing at the N-terminal cleavage sites at varying efficiencies, subsequently creating competition between the cleaved and uncleaved forms of VI, followed by reorganization, processing, and release of VI molecules from the hexon cavities. | |||||||||
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_24881.map.gz | 2 GB | EMDB map data format | |
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Header (meta data) | emd-24881-v30.xml emd-24881.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24881_fsc.xml | 33.7 KB | Display | FSC data file |
Images | emd_24881.png | 213 KB | ||
Filedesc metadata | emd-24881.cif.gz | 7.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24881 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24881 | HTTPS FTP |
-Validation report
Summary document | emd_24881_validation.pdf.gz | 859.8 KB | Display | EMDB validaton report |
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Full document | emd_24881_full_validation.pdf.gz | 859.4 KB | Display | |
Data in XML | emd_24881_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | emd_24881_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24881 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24881 | HTTPS FTP |
-Related structure data
Related structure data | 7s78MC 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_24881.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cropped map file from the original 928x928x928 pixel size map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 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 C serotype 5
Entire | Name: Human adenovirus C serotype 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 / NCBI-ID: 28285 / Sci species name: Human adenovirus C serotype 5 / Sci species strain: Ad2-ts1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) / Strain: Ad2-ts1 |
Molecular weight | Theoretical: 150 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 1000.0 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: Human adenovirus C serotype 5 / Strain: Ad2-ts1 |
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 UniProtKB: Hexon protein |
-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: Human adenovirus C serotype 5 / Strain: Ad2-ts1 |
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 UniProtKB: Penton protein |
-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: Human adenovirus C serotype 5 / Strain: Ad2-ts1 |
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 UniProtKB: Pre-hexon-linking protein IIIa |
-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: Human adenovirus C serotype 5 / Strain: Ad2-ts1 |
Molecular weight | Theoretical: 14.468134 KDa |
Sequence | String: MSTNSFDGSI VSSYLTTRMP PWAGVRQNVM GSSIDGRPVL PANSTTLTYE TVSGTPLETA ASAAASAAAA TARGIVTDFA FLSPLASSA ASRSSARDDK LTALLAQLDS LTRELNVVSQ QLLDLRQQVS ALKASSPPNA V UniProtKB: Hexon-interlacing protein |
-Macromolecule #5: Pre-hexon-linking protein VIII
Macromolecule | Name: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus C serotype 5 / Strain: Ad2-ts1 |
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 UniProtKB: Pre-hexon-linking protein VIII |
-Macromolecule #6: Pre-protein VI
Macromolecule | Name: Pre-protein VI / type: protein_or_peptide / ID: 6 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus C serotype 5 / Strain: Ad2-ts1 |
Molecular weight | Theoretical: 27.02751 KDa |
Sequence | String: MEDINFASLA PRHGSRPFMG NWQDIGTSNM SGGAFSWGSL WSGIKNFGST VKNYGSKAWN SSTGQMLRDK LKEQNFQQKV VDGLASGIS GVVDLANQAV QNKINSKLDP RPPVEEPPPA VETVSPEGRG EKRPRPDREE TLVTQIDEPP SYEEALKQGL P TTRPIAPM ...String: MEDINFASLA PRHGSRPFMG NWQDIGTSNM SGGAFSWGSL WSGIKNFGST VKNYGSKAWN SSTGQMLRDK LKEQNFQQKV VDGLASGIS GVVDLANQAV QNKINSKLDP RPPVEEPPPA VETVSPEGRG EKRPRPDREE TLVTQIDEPP SYEEALKQGL P TTRPIAPM ATGVLGQHTP VTLDLPPPAD TQQKPVLPGP TAVVVTRPSR ASLRRAASGP RSLRPVASGN WQSTLNSIVG LG VQSLKRR RCF UniProtKB: Pre-protein VI |
-Macromolecule #7: Unknown-1
Macromolecule | Name: Unknown-1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus C serotype 5 / Strain: Ad2-ts1 |
Molecular weight | Theoretical: 1.379692 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #8: Unknown-2
Macromolecule | Name: Unknown-2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human adenovirus C serotype 5 / Strain: Ad2-ts1 |
Molecular weight | Theoretical: 869.063 Da |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8.1 / Component - Concentration: 40.0 mM / Component - Name: Tris / Details: 40 mM Tris, pH 8.1 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 6 sec. / Details: 20mA |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 1510 / Average electron dose: 12.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500 |
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
Initial model | PDB ID: 3iyn Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-7s78: |