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Yorodumi- EMDB-21504: Structures of Capsid and Capsid-Associated Tegument Complex insid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21504 | |||||||||||||||
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Title | Structures of Capsid and Capsid-Associated Tegument Complex inside the Epstein-Barr Virus | |||||||||||||||
Map data | I3 capsid reconstruction for EBV | |||||||||||||||
Sample |
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Keywords | gamma-herpesvirus / EBV / CATC / Structural plasticity / VIRUS | |||||||||||||||
Function / homology | Function and homology information T=16 icosahedral viral capsid / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | |||||||||||||||
Biological species | Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) / Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||||||||
Authors | Liu W / Cui YX | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus. Authors: Wei Liu / Yanxiang Cui / Caiyan Wang / Zihang Li / Danyang Gong / Xinghong Dai / Guo-Qiang Bi / Ren Sun / Z Hong Zhou / Abstract: As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been ...As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies. | |||||||||||||||
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_21504.map.gz | 450.6 MB | EMDB map data format | |
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Header (meta data) | emd-21504-v30.xml emd-21504.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
Images | emd_21504.png | 215.5 KB | ||
Filedesc metadata | emd-21504.cif.gz | 6.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21504 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21504 | HTTPS FTP |
-Validation report
Summary document | emd_21504_validation.pdf.gz | 803.8 KB | Display | EMDB validaton report |
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Full document | emd_21504_full_validation.pdf.gz | 803.4 KB | Display | |
Data in XML | emd_21504_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_21504_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21504 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21504 | HTTPS FTP |
-Related structure data
Related structure data | 6w19MC 6w2dC 6w2eC C: citing same article (ref.) M: atomic model generated by this map |
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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_21504.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | I3 capsid reconstruction for EBV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.71 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 herpesvirus 4 strain B95-8
Entire | Name: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) |
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Components |
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-Supramolecule #1: Human herpesvirus 4 strain B95-8
Supramolecule | Name: Human herpesvirus 4 strain B95-8 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10377 / Sci species name: Human herpesvirus 4 strain B95-8 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: B95-8 |
Molecular weight | Theoretical: 154.086828 KDa |
Sequence | String: MASNEGVENR PFPYLTVDAD LLSNLRQSAA EGLFHSFDLL VGKDAREAGI KFEVLLGVYT NAIQYVRFLE TALAVSCVNT EFKDLSRMT DGKIQFRISV PTIAHGDGRR PSKQRTFIVV KNCHKHHIST EMELSMLDLE ILHSIPETPV EYAEYVGAVK T VASALQFG ...String: MASNEGVENR PFPYLTVDAD LLSNLRQSAA EGLFHSFDLL VGKDAREAGI KFEVLLGVYT NAIQYVRFLE TALAVSCVNT EFKDLSRMT DGKIQFRISV PTIAHGDGRR PSKQRTFIVV KNCHKHHIST EMELSMLDLE ILHSIPETPV EYAEYVGAVK T VASALQFG VDALERGLIN TVLSVKLRHA PPMFILQTLA DPTFTERGFS KTVKSDLIAM FKRHLLEHSF FLDRAENMGS GF SQYVRSR LSEMVAAVSG ESVLKGVSTY TTAKGGEPVG GVFIVTDNVL RQLLTFLGEE ADNQIMGPSS YASFVVRGEN LVT AVSYGR VMRTFEHFMA RIVDSPEKAG STKSDLPAVA AGVEDQPRVP ISAAVIKLGN HAVAVESLQK MYNDTQSPYP LNRR MQYSY YFPVGLFMPN PKYTTSAAIK MLDNPTQQLP VEAWIVNKNN LLLAFNLQNA LKVLCHPRLH TPAHTLNSLN AAPAP RDRR ETYSLQHRRP NHMNVLVIVD EFYDNKYAAP VTDIALKCGL PTEDFLHPSN YDLLRLELHP LYDIYIGRDA GERARH RAV HRLMVGNLPT PLAPAAFQEA RGQQFETATS LAHVVDQAVI ETVQDTAYDT AYPAFFYVVE AMIHGFEEKF VMNVPLV SL CINTYWERSG RLAFVNSFSM IKFICRHLGN NAISKEAYSM YRKIYGELIA LEQALMRLAG SDVVGDESVG QYVCALLD P NLLPPVAYTD IFTHLLTVSD RAPQIIIGNE VYADTLAAPQ FIERVGNMDE MAAQFVALYG YRVNGDHDHD FRLHLGPYV DEGHADVLEK IFYYVFLPTC TNAHMCGLGV DFQHVAQTLA YNGPAFSHHF TRDEDILDNL ENGTLRDLLE ISDLRPTVGM IRDLSASFM TCPTFTRAVR VSVDNDVTQQ LAPNPADKRT EQTVLVNGLV AFAFSERTRA VTQCLFHAIP FHMFYGDPRV A ATMHQDVA TFVMRNPQQR AVEAFNRPEQ LFAEYREWHR SPMGKYAAEC LPSLVSISGM TAMHIKMSPM AYIAQAKLKI HP GVAMTVV RTDEILSENI LFSSRASTSM FIGTPNVSRR EARVDAVTFE VHHEMASIDT GLSYSSTMTP ARVAAITTDM GIH TQDFFS VFPAEAFGNQ QVNDYIKAKV GAQRNGTLLR DPRTYLAGMT NVNGAPGLCH GQQATCEIIV TPVTADVAYF QKSN SPRGR AACVVSCENY NQEVAEGLIY DHSRPDAAYE YRSTVNPWAS QLGSLGDIMY NSSYRQTAVP GLYSPCRAFF NKEEL LRNN RGLYNMVNEY SQRLGGHPAT SNTEVQFVVI AGTDVFLEQP CSFLQEAFPA LSASSRALID EFMSVKQTHA PIHYGH YII EEVAPVRRIL KFGNKVVF UniProtKB: Major capsid protein |
-Macromolecule #2: Small capsomere-interacting protein
Macromolecule | Name: Small capsomere-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: B95-8 |
Molecular weight | Theoretical: 18.1691 KDa |
Sequence | String: MARRLPKPTL QGRLEADFPD SPLLPKFQEL NQNNLPNDVF REAQRSYLVF LTSQFCYEEY VQRTFGVPRR QRAIDKRQRA SVAGAGAHA HLGGSSATPV QQAQAAASAG TGALASSAPS TAVAQSATPS VSSSISSLRA ATSGATAAAS AAAAVDTGSG G GGQPHDTA PRGARKKQ UniProtKB: Small capsomere-interacting protein |
-Macromolecule #3: Triplex capsid protein 1
Macromolecule | Name: Triplex capsid protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: B95-8 |
Molecular weight | Theoretical: 39.231539 KDa |
Sequence | String: MKVQGSVDRR RLQRRIAGLL PPPARRLNIS RGSEFTRDVR GLVEEHAQAS SLSAAAVWRA GLLAPGEVAV AGGGSGGGSF SWSGWRPPV FGDFLIHASS FNNAEATGTP LFQFKQSDPF SGVDAVFTPL SLFILMNHGR GVAARVEAGG GLTRMANLLY D SPATLADL ...String: MKVQGSVDRR RLQRRIAGLL PPPARRLNIS RGSEFTRDVR GLVEEHAQAS SLSAAAVWRA GLLAPGEVAV AGGGSGGGSF SWSGWRPPV FGDFLIHASS FNNAEATGTP LFQFKQSDPF SGVDAVFTPL SLFILMNHGR GVAARVEAGG GLTRMANLLY D SPATLADL VPDFGRLVAD RRFHNFITPV GPLVENIKST YLNKITTVVH GPVVSKAIPR STVKVTVPQE AFVDLDAWLS GG AGGGGGV CFVGGLGLQP CPADARLYVA LTYEEAGPRF TFFQSSRGHC QIMNILRIYY SPSIMHRYAV VQPLHIEELT FGA VACLGT FSATDGWRRS AFNYRGSSLP VVEIDSFYSN VSDWEVIL UniProtKB: Triplex capsid protein 1 |
-Macromolecule #4: Triplex capsid protein 2
Macromolecule | Name: Triplex capsid protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: B95-8 |
Molecular weight | Theoretical: 33.654039 KDa |
Sequence | String: MDLKVVVSLS SRLYTDEIAK MQQRIGCILP LASTHGTQNV QGLGLGQVYS LETVPDYVSM YNYLSDCTLA VLDEVSVDSL ILTKIVPGQ TYAIKNKYQP FFQWHGTGSL SVMPPVFGRE HATVKLESND VDIVFPMVLP TPIAEEVLQK ILLFNVYSRV V MQAPGNAD ...String: MDLKVVVSLS SRLYTDEIAK MQQRIGCILP LASTHGTQNV QGLGLGQVYS LETVPDYVSM YNYLSDCTLA VLDEVSVDSL ILTKIVPGQ TYAIKNKYQP FFQWHGTGSL SVMPPVFGRE HATVKLESND VDIVFPMVLP TPIAEEVLQK ILLFNVYSRV V MQAPGNAD MLDVHMHLGS VSYLGHHYEL ALPEVPGPLG LALLDNLSLY FCIMVTLLPR ASMRLVRGLI RHEHHDLLNL FQ EMVPDEI ARIDLDDLSV ADDLSRMRVM MTYLQSLASL FNLGPRLATA AYSQETLTAT CWLR UniProtKB: Triplex capsid protein 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS buffer, pH 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: The grids were manually plunged into the ethane.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1833 / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |