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- EMDB-8703: A 3.9 Angstrom resolution density map of the human cytomegaloviru... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8703 | |||||||||||||||||||||
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Title | A 3.9 Angstrom resolution density map of the human cytomegalovirus (HCMV) capsid and its securing layer of pp150 tegument protein | |||||||||||||||||||||
![]() | Human herpesvirus 5 strain AD169 | |||||||||||||||||||||
![]() | Human herpesvirus 5 strain AD169 != Human cytomegalovirus (strain AD169) Human herpesvirus 5 strain AD169
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Function / homology | ![]() 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 / ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||||||||
![]() | Yu X / Jih J / Jiang J / Zhou H | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic structure of the human cytomegalovirus capsid with its securing tegument layer of pp150. Authors: Xuekui Yu / Jonathan Jih / Jiansen Jiang / Z Hong Zhou / ![]() Abstract: Herpesviruses possess a genome-pressurized capsid. The 235-kilobase genome of human cytomegalovirus (HCMV) is by far the largest of any herpesvirus, yet it has been unclear how its capsid, which is ...Herpesviruses possess a genome-pressurized capsid. The 235-kilobase genome of human cytomegalovirus (HCMV) is by far the largest of any herpesvirus, yet it has been unclear how its capsid, which is similar in size to those of other herpesviruses, is stabilized. Here we report a HCMV atomic structure consisting of the herpesvirus-conserved capsid proteins MCP, Tri1, Tri2, and SCP and the HCMV-specific tegument protein pp150-totaling ~4000 molecules and 62 different conformers. MCPs manifest as a complex of insertions around a bacteriophage HK97 gp5-like domain, which gives rise to three classes of capsid floor-defining interactions; triplexes, composed of two "embracing" Tri2 conformers and a "third-wheeling" Tri1, fasten the capsid floor. HCMV-specific strategies include using hexon channels to accommodate the genome and pp150 helix bundles to secure the capsid via cysteine tetrad-to-SCP interactions. Our structure should inform rational design of countermeasures against HCMV, other herpesviruses, and even HIV/AIDS. | |||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.1 KB 16.1 KB | Display Display | ![]() |
Images | ![]() | 265.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vkuMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human herpesvirus 5 strain AD169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.61 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Human herpesvirus 5 strain AD169
Entire | Name: ![]() ![]() |
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Components |
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-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) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Virus shell | Shell ID: 1 / Diameter: 1320.0 Å / T number (triangulation number): 16 |
-Macromolecule #1: Tegument protein pp150
Macromolecule | Name: Tegument protein pp150 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO |
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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 #2: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO |
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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 #3: Small capsomere-interacting protein
Macromolecule | Name: Small capsomere-interacting protein / type: protein_or_peptide / ID: 3 / Number of copies: 16 / Enantiomer: LEVO |
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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: 5 / Enantiomer: LEVO |
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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: 10 / Enantiomer: LEVO |
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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 |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39600 |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |