+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34704 | |||||||||
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Title | One CVSC-binding penton vertex in HCMV B-capsid | |||||||||
Map data | ||||||||||
Sample |
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Keywords | B-capsid / one CVSC-binding penton vertex / asymmetric reconstruction / VIRUS / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information T=16 icosahedral viral capsid / viral genome packaging / viral capsid assembly / viral release from host cell / chromosome organization / viral process / virion component / viral capsid / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | |||||||||
Biological species | Human betaherpesvirus 5 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Li Z / Yu X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-electron microscopy structures of capsids and in situ portals of DNA-devoid capsids of human cytomegalovirus. Authors: Zhihai Li / Jingjing Pang / Rongchao Gao / Qingxia Wang / Maoyan Zhang / Xuekui Yu / Abstract: The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold ...The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold interaction and the conformational changes that occur to the portal during the different stages of capsid formation have yet to be elucidated structurally. Here we present high-resolution structures of the A- and B-capsids and in-situ portals of human cytomegalovirus. We show that scaffolds bind to the hydrophobic cavities formed by the dimerization and Johnson-fold domains of the major capsid proteins. We further show that 12 loop-helix-loop fragments-presumably from the scaffold domain-insert into the hydrophobic pocket of the portal crown domain. The portal also undergoes significant changes both positionally and conformationally as it accompanies DNA packaging. These findings unravel the mechanism by which the portal interacts with the scaffold to nucleate capsid assembly and further our understanding of scaffold expulsion and DNA incorporation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34704.map.gz | 58.3 MB | EMDB map data format | |
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Header (meta data) | emd-34704-v30.xml emd-34704.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34704_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_34704.png | 113 KB | ||
Filedesc metadata | emd-34704.cif.gz | 7.2 KB | ||
Others | emd_34704_half_map_1.map.gz emd_34704_half_map_2.map.gz | 49.2 MB 49.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34704 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34704 | HTTPS FTP |
-Validation report
Summary document | emd_34704_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_34704_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_34704_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_34704_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34704 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34704 | HTTPS FTP |
-Related structure data
Related structure data | 8heyMC 8heuC 8hevC 8hexC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34704.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.625 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34704_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34704_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human betaherpesvirus 5
Entire | Name: Human betaherpesvirus 5 |
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Components |
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-Supramolecule #1: Human betaherpesvirus 5
Supramolecule | Name: Human betaherpesvirus 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10359 / Sci species name: Human betaherpesvirus 5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Small capsomere-interacting protein
Macromolecule | Name: Small capsomere-interacting protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 8.495924 KDa |
Sequence | String: MSNTAPGPTV ANKRDEKHRH VVNVVLELPT EISEATHPVL ATMLSKYTRM SSLFNDKCAF KLDLLRMVAV SRTRR UniProtKB: Small capsomere-interacting protein |
-Macromolecule #2: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
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 UniProtKB: Major capsid protein |
-Macromolecule #3: Triplex capsid protein 2
Macromolecule | Name: Triplex capsid protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
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 UniProtKB: Capsid triplex subunit 2 |
-Macromolecule #4: Triplex capsid protein 1
Macromolecule | Name: Triplex capsid protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
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 UniProtKB: Capsid triplex subunit 1 |
-Macromolecule #5: Capsid vertex component 1
Macromolecule | Name: Capsid vertex component 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 68.567211 KDa |
Sequence | String: METHLYSDLA FEARFADDEQ LPLHLVLDQE VLSNEEAETL RYVYYRNVDS AGRSTGRAPG GDEDDAPASD DAEDAVGGDR AFDRERRTW QRACFRVLPR PLELLDYLRQ SGLTVTLEKE QRVRMFYAVF TTLGLRCPDN RLSGAQTLHL RLVWPDGSYR D WEFLARDL ...String: METHLYSDLA FEARFADDEQ LPLHLVLDQE VLSNEEAETL RYVYYRNVDS AGRSTGRAPG GDEDDAPASD DAEDAVGGDR AFDRERRTW QRACFRVLPR PLELLDYLRQ SGLTVTLEKE QRVRMFYAVF TTLGLRCPDN RLSGAQTLHL RLVWPDGSYR D WEFLARDL LREEMEANKR DRQHQLATTT NHRRRGGLRN NLDNGSDRRL PEAAVASLET AVSTPFFEIP NGAGTSSANG DG RFSNLEQ RVARLLRGDE EFIYHAGPLE PPSKIRGHEL VQLRLDVNPD LMYATDPHDR DEVARTDEWK GAGVSRLREV WDV QHRVRL RVLWYVNSFW RSRELSYDDH EVELYRALDA YRARIAVEYV LIRAVRDEIY AVLRRDGGAL PQRFACHVSR NMSW RVVWE LCRHALALWM DWADVRSCII KALTPRLSRG AAAAAQRARR QRERSAPKPQ ELLFGPRNES GPPAEQTWYA DVVRC VRAQ VDLGVEVRAA RCPRTGLWIV RDRRGRLRRW LSQPEVCVLY VTPDLDFYWV LPGGFAVSSR VTLHGLAQRA LRDRFQ NFE AVLARGMHVE AGRQEPETPR VSGRRLPFDD L UniProtKB: Capsid vertex component 1 |
-Macromolecule #6: Capsid vertex component 2
Macromolecule | Name: Capsid vertex component 2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Molecular weight | Theoretical: 71.26957 KDa |
Sequence | String: MSLLHTFWRL PVAVFFEPHE ENVLRCPERV LRRLLEDAAV TMRGGGWRED VLMDRVRKRY LRQELRDLGH RVQTYCEDLE GRVSEAEAL LNQQCELDEG PSPRTLLQPP CRPRSSSPGT GVAGASAVPH GLYSRHDAIT GPAAAPSDVV APSDAVAASA A AGASSTWL ...String: MSLLHTFWRL PVAVFFEPHE ENVLRCPERV LRRLLEDAAV TMRGGGWRED VLMDRVRKRY LRQELRDLGH RVQTYCEDLE GRVSEAEAL LNQQCELDEG PSPRTLLQPP CRPRSSSPGT GVAGASAVPH GLYSRHDAIT GPAAAPSDVV APSDAVAASA A AGASSTWL AQCAERPLPG NVPSYFGITQ NDPFIRFHTD FRGEVVNTMF ENASTWTFSF GIWYYRLKRG LYTQPRWKRV YH LAQMDNF SISQELLLGV VNALENVTVY PTYDCVLSDL EAAACLLAAY GHALWEGRDP PDSVATVLGE LPQLLPRLAD DVS REIAAW EGPVAAGNNY YAYRDSPDLR YYMPLSGGRH YHPGTFDRHV LVRLFHKRGV IQHLPGYGTI TEELVQERLS GQVR DDVLS LWSRRLLVGK LGRDVPVFVH EQQYLRSGLT CLAGLLLLWK VTNADSVFAP RTGKFTLADL LGSDAVAGGG LPGGR AGGE EEGYGGRHGR VRNFEFLVRY YIGPWYARDP AVTLSQLFPG LALLAVTESV RSGWDPSRRE DSAGGGDGGG AVLMQL SKS NPVADYMFAQ SSKQYGDLRR LEVHDALLFH YEHGLGRLLS VTLPRHRVST LGSSLFNVND IYELLYFLVL GFLPSVA VL UniProtKB: UL77 protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |