[English] 日本語
Yorodumi- EMDB-23386: Structure of human transfer RNA visualized in the cytomegalovirus... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23386 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human transfer RNA visualized in the cytomegalovirus, a DNA virus | ||||||||||||||||||
Map data | C1 3-fold sub-particles reconstruction of HCMV virion particles | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Function / homology | Function and homology information host cell viral assembly compartment / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / host cell cytoplasmic vesicle / viral process / viral capsid / host cell perinuclear region of cytoplasm / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | ||||||||||||||||||
Biological species | Human herpesvirus 5 strain AD169, HHV-5 / Human cytomegalovirus (strain AD169) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
Authors | Liu YT / Strugatsky D / Liu W / Zhou ZH | ||||||||||||||||||
Funding support | United States, 5 items
| ||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150. Authors: Yun-Tao Liu / David Strugatsky / Wei Liu / Z Hong Zhou / Abstract: Under the Baltimore nucleic acid-based virus classification scheme, the herpesvirus human cytomegalovirus (HCMV) is a Class I virus, meaning that it contains a double-stranded DNA genome-and no RNA. ...Under the Baltimore nucleic acid-based virus classification scheme, the herpesvirus human cytomegalovirus (HCMV) is a Class I virus, meaning that it contains a double-stranded DNA genome-and no RNA. Here, we report sub-particle cryoEM reconstructions of HCMV virions at 2.9 Å resolution revealing structures resembling non-coding transfer RNAs (tRNAs) associated with the virion's capsid-bound tegument protein, pp150. Through deep sequencing, we show that these RNA sequences match human tRNAs, and we built atomic models using the most abundant tRNA species. Based on our models, tRNA recruitment is mediated by the electrostatic interactions between tRNA phosphate groups and the helix-loop-helix motif of HCMV pp150. The specificity of these interactions may explain the absence of such tRNA densities in murine cytomegalovirus and other human herpesviruses. | ||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23386.map.gz | 58 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23386-v30.xml emd-23386.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_23386.png | 228.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23386 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23386 | HTTPS FTP |
-Validation report
Summary document | emd_23386_validation.pdf.gz | 663.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23386_full_validation.pdf.gz | 662.9 KB | Display | |
Data in XML | emd_23386_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_23386_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23386 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23386 | HTTPS FTP |
-Related structure data
Related structure data | 7livMC 7lj3C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_23386.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | C1 3-fold sub-particles reconstruction of HCMV virion particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.61 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Human cytomegalovirus (strain AD169)
Entire | Name: Human cytomegalovirus (strain AD169) |
---|---|
Components |
|
-Supramolecule #1: Human cytomegalovirus (strain AD169)
Supramolecule | Name: Human cytomegalovirus (strain AD169) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10360 / Sci species name: Human cytomegalovirus (strain AD169) / Sci species strain: AD169 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|
-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human herpesvirus 5 strain AD169, HHV-5 / Strain: AD169 |
Molecular weight | Theoretical: 154.048906 KDa |
Sequence | String: MENWSALELL PKVGIPTDFL THVKTSAGEE MFEALRIYYG DDPERYNIHF EAIFGTFCNR LEWVYFLTSG LAAAAHAIKF HDLNKLTTG KMLFHVQVPR VASGAGLPTS RQTTIMVTKY SEKSPITIPF ELSAACLTYL RETFEGTILD KILNVEAMHT V LRALKNTA ...String: MENWSALELL PKVGIPTDFL THVKTSAGEE MFEALRIYYG DDPERYNIHF EAIFGTFCNR LEWVYFLTSG LAAAAHAIKF HDLNKLTTG KMLFHVQVPR VASGAGLPTS RQTTIMVTKY SEKSPITIPF ELSAACLTYL RETFEGTILD KILNVEAMHT V LRALKNTA DAMERGLIHS FLQTLLRKAP PYFVVQTLVE NATLARQALN RIQRSNILQS FKAKMLATLF LLNRTRDRDY VL KFLTRLA EAATDSILDN PTTYTTSSGA KISGVMVSTA NVMQIIMSLL SSHITKETVS APATYGNFVL SPENAVTAIS YHS ILADFN SYKAHLTSGQ PHLPNDSLSQ AGAHSLTPLS MDVIRLGEKT VIMENLRRVY KNTDTKDPLE RNVDLTFFFP VGLY LPEDR GYTTVESKVK LNDTVRNALP TTAYLLNRDR AVQKIDFVDA LKTLCHPVLH EPAPCLQTFT ERGPPSEPAM QRLLE CRFQ QEPMGGAARR IPHFYRVRRE VPRTVNEMKQ DFVVTDFYKV GNITLYTELH PFFDFTHCQE NSETVALCTP RIVIGN LPD GLAPGPFHEL RTWEIMEHMR LRPPPDYEET LRLFKTTVTS PNYPELCYLV DVLVHGNVDA FLLIRTFVAR CIVNMFH TR QLLVFAHSYA LVTLIAEHLA DGALPPQLLF HYRNLVAVLR LVTRISALPG LNNGQLAEEP LSAYVNALHD HRLWPPFV T HLPRNMEGVQ VVADRQPLNP ANIEARHHGV SDVPRLGAMD ADEPLFVDDY RATDDEWTLQ KVFYLCLMPA MTNNRACGL GLNLKTLLVD LFYRPAFLLM PAATAVSTSG TTSKESTSGV TPEDSIAAQR QAVGEMLTEL VEDVATDAHT PLLQACRELF LAVQFVGEH VKVLEVRAPL DHAQRQGLPD FISRQHVLYN GCCVVTAPKT LIEYSLPVPF HRFYSNPTIC AALSDDIKRY V TEFPHYHR HDGGFPLPTA FAHEYHNWLR SPFSRYSATC PNVLHSVMTL AAMLYKISPV SLVLQTKAHI HPGFALTAVR TD TFEVDML LYSGKSCTSV IINNPIVTKE ERDISTTYHV TQNINTVDMG LGYTSNTCVA YVNRVRTDMG VRVQDLFRVF PMN VYRHDE VDRWIRHAAG VERPQLLDTE TISMLTFGSM SERNAAATVH GQKAACELIL TPVTMDVNYF KIPNNPRGRA SCML AVDPY DTEAATKAIY DHREADAQTF AATHNPWASQ AGCLSDVLYN TRHRERLGYN SKFYSPCAQY FNTEEIIAAN KTLFK TIDE YLLRAKDCIR GDTDTQYVCV EGTEQLIENP CRLTQEALPI LSTTTLALME TKLKGGAGAF ATSETHFGNY VVGEII PLQ QSMLFNS |
-Macromolecule #2: Tegument protein pp150
Macromolecule | Name: Tegument protein pp150 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human herpesvirus 5 strain AD169, HHV-5 / Strain: AD169 |
Molecular weight | Theoretical: 33.232418 KDa |
Sequence | String: MSLQFIGLQR RDVVALVNFL RHLTQKPDVD LEAHPKILKK CGEKRLHRRT VLFNELMLWL GYYRELRFHN PDLSSVLEEF EVRCVAVAR RGYTYPFGDR GKARDHLAVL DRTEFDTDVR HDAEIVERAL VSAVILAKMS VRETLVTAIG QTEPIAFVHL K DTEVQRIE ...String: MSLQFIGLQR RDVVALVNFL RHLTQKPDVD LEAHPKILKK CGEKRLHRRT VLFNELMLWL GYYRELRFHN PDLSSVLEEF EVRCVAVAR RGYTYPFGDR GKARDHLAVL DRTEFDTDVR HDAEIVERAL VSAVILAKMS VRETLVTAIG QTEPIAFVHL K DTEVQRIE ENLEGVRRNM FCVKPLDLNL DRHANTALVN AVNKLVYTGR LIMNVRRSWE ELERKCLARI QERCKLLVKE LR MCLSFDS NYCRNILKHA VENGDSADTL LELLIEDFDI YVDSFPQS |
-Macromolecule #3: Small capsomere-interacting protein
Macromolecule | Name: Small capsomere-interacting protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human herpesvirus 5 strain AD169, HHV-5 / Strain: AD169 |
Molecular weight | Theoretical: 8.495924 KDa |
Sequence | String: MSNTAPGPTV ANKRDEKHRH VVNVVLELPT EISEATHPVL ATMLSKYTRM SSLFNDKCAF KLDLLRMVAV SRTRR |
-Macromolecule #4: Triplex capsid protein 1
Macromolecule | Name: Triplex capsid protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human herpesvirus 5 strain AD169, HHV-5 / Strain: AD169 |
Molecular weight | Theoretical: 33.07127 KDa |
Sequence | String: MDARAVAKRP RDPADEDNEL VTALKAKREV NTISVRYLYH ADHQALTARF FVPEGLVEFE AQPGALLIRM ETGCDSPRHL YISLYLLGI RASNVSASTR CLLESVYTAS AARAALQWLD LGPHLLHRRL ETLGCVKTVS LGITSLLTCV MRGYLYNTLK T EVFALMIP ...String: MDARAVAKRP RDPADEDNEL VTALKAKREV NTISVRYLYH ADHQALTARF FVPEGLVEFE AQPGALLIRM ETGCDSPRHL YISLYLLGI RASNVSASTR CLLESVYTAS AARAALQWLD LGPHLLHRRL ETLGCVKTVS LGITSLLTCV MRGYLYNTLK T EVFALMIP KDMYLTWEET RGRLQYVYLI IVYDYDGPET RPGIYVLTSS IAHWQTLVDV ARGKFARERC SFVNRRITRP RQ IPLCTGV IQKLGWCLAD DIHTSFLVHK ELKLSVVRLD NFSVELGDFR EFV |
-Macromolecule #5: Triplex capsid protein 2
Macromolecule | Name: Triplex capsid protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human herpesvirus 5 strain AD169, HHV-5 / Strain: AD169 |
Molecular weight | Theoretical: 34.63575 KDa |
Sequence | String: MAAMEANIFC TFDHKLSIAD VGKLTKLVAA VVPIPQRLHL IKHYQLGLHQ FVDHTRGYVR LRGLLRNMTL TLMRRVEGNQ ILLHVPTHG LLYTVLNTGP VTWEKGDALC VLPPLFHGPL ARENLLTLGQ WELVLPWIVP MPLALEINQR LLIMGLFSLD R SYEEVKAA ...String: MAAMEANIFC TFDHKLSIAD VGKLTKLVAA VVPIPQRLHL IKHYQLGLHQ FVDHTRGYVR LRGLLRNMTL TLMRRVEGNQ ILLHVPTHG LLYTVLNTGP VTWEKGDALC VLPPLFHGPL ARENLLTLGQ WELVLPWIVP MPLALEINQR LLIMGLFSLD R SYEEVKAA VQQLQTITFR DATFTIPDPV IDQHLLIDMK TACLSMSMVA NLASELTMTY VRKLALEDSS MLLVKCQELL MR LDRERSV GEPRTPARPQ HVSPDDEIAR LSALFVMLRQ LDDLIREQVV FTVCDVSPDN KSATCIFKG |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 18.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97166 |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |