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Yorodumi- EMDB-30093: The coordinates of the monomeric terminase complex in the presenc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30093 | |||||||||
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Title | The coordinates of the monomeric terminase complex in the presence of the ADP-BeF3 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | HSV-1 / terminase complex / ADP-BeF3 / monomer / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information viral DNA genome packaging / nuclease activity / viral capsid assembly / chromosome organization / viral release from host cell / protein processing / Hydrolases; Acting on ester bonds / host cell nucleus / DNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) / Human herpesvirus 1 (strain 17) / Human alphaherpesvirus 1 strain 17 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Yang YX / Yang P | |||||||||
Funding support | China, 1 items
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Citation | Journal: Protein Cell / Year: 2020 Title: Architecture of the herpesvirus genome-packaging complex and implications for DNA translocation. Authors: Yunxiang Yang / Pan Yang / Nan Wang / Zhonghao Chen / Dan Su / Z Hong Zhou / Zihe Rao / Xiangxi Wang / Abstract: Genome packaging is a fundamental process in a viral life cycle and a prime target of antiviral drugs. Herpesviruses use an ATP-driven packaging motor/terminase complex to translocate and cleave ...Genome packaging is a fundamental process in a viral life cycle and a prime target of antiviral drugs. Herpesviruses use an ATP-driven packaging motor/terminase complex to translocate and cleave concatemeric dsDNA into procapsids but its molecular architecture and mechanism are unknown. We report atomic structures of a herpesvirus hexameric terminase complex in both the apo and ADP•BeF3-bound states. Each subunit of the hexameric ring comprises three components-the ATPase/terminase pUL15 and two regulator/fixer proteins, pUL28 and pUL33-unlike bacteriophage terminases. Distal to the nuclease domains, six ATPase domains form a central channel with conserved basic-patches conducive to DNA binding and trans-acting arginine fingers are essential to ATP hydrolysis and sequential DNA translocation. Rearrangement of the nuclease domains mediated by regulatory domains converts DNA translocation mode to cleavage mode. Our structures favor a sequential revolution model for DNA translocation and suggest mechanisms for concerted domain rearrangements leading to DNA cleavage. | |||||||||
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_30093.map.gz | 55.8 MB | EMDB map data format | |
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Header (meta data) | emd-30093-v30.xml emd-30093.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_30093.png | 146.2 KB | ||
Filedesc metadata | emd-30093.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30093 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30093 | HTTPS FTP |
-Related structure data
Related structure data | 6m5uMC 6m5rC 6m5sC 6m5tC 6m5vC 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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-Map
File | Download / File: emd_30093.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.062 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 : HSV-1 terminase complex in presence of ADP-BeF3
Entire | Name: HSV-1 terminase complex in presence of ADP-BeF3 |
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Components |
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-Supramolecule #1: HSV-1 terminase complex in presence of ADP-BeF3
Supramolecule | Name: HSV-1 terminase complex in presence of ADP-BeF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Human herpesvirus 1 (Herpes simplex virus type 1) |
-Macromolecule #1: Tripartite terminase subunit 3
Macromolecule | Name: Tripartite terminase subunit 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Human herpesvirus 1 (strain 17) / Strain: 17 |
Molecular weight | Theoretical: 76.501266 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: TMGGDALRVP FLDFATATPK RHQTVVPGVG TLHDCCEHSP LFSAVARRLL FNSLVPAQLK GRDFGGDHTA KLEFLAPELV RAVARLRFK ECAPADVVPQ RNAYYSVLNT FQALHRSEAF RQLVHFVRDF AQLLKTSFRA SSLTETTGPP KKRAKVDVAT H GRTYGTLE ...String: TMGGDALRVP FLDFATATPK RHQTVVPGVG TLHDCCEHSP LFSAVARRLL FNSLVPAQLK GRDFGGDHTA KLEFLAPELV RAVARLRFK ECAPADVVPQ RNAYYSVLNT FQALHRSEAF RQLVHFVRDF AQLLKTSFRA SSLTETTGPP KKRAKVDVAT H GRTYGTLE LFQKMILMHA TYFLAAVLLG DHAEQVNTFL RLVFEIPLFS DAAVRHFRQR ATVFLVPRRH GKTWFLVPLI AL SLASFRG IKIGYTAHIR KATEPVFEEI DACLRGWFGS ARVDHVKGET ISFSFPDGSR STIVFASSHN TNGIRGQDFN LLF VDEANF IRPDAVQTIM GFLNQANCKI IFVSSTNTGK ASTSFLYNLR GAADELLNVV TYICDDHMPR VVTHTNATAC SCYI LNKPV FITMDGAVRR TADLFLADSF MQEIIGGQAR ETGDDRPVLT KSAGERFLLY RPSTTTNSGL MAPDLYVYVD PAFTA NTRA SGTGVAVVGR YRDDYIIFAL EHFFLRALTG SAPADIARCV VHSLTQVLAL HPGAFRGVRV AVEGNSSQDS AVAIAT HVH TEMHRLLASE GADAGSGPEL LFYHCEPPGS AVLYPFFLLN KQKTPAFEHF IKKFNSGGVM ASQEIVSATV RLQTDPV EY LLEQLNNLTE TVSPNTDVRT YSGKRNGASD DLMVAVIMAI YLAAQAGPPH TF UniProtKB: Tripartite terminase subunit 3 |
-Macromolecule #2: Tripartite terminase subunit 1
Macromolecule | Name: Tripartite terminase subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain 17 / Strain: 17 |
Molecular weight | Theoretical: 84.51275 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: AAPVSEPTVA RQKLLALLGQ VQTYVFQIEL LRRCDPHIGR GKLPQLKLNA LQVRALRRRL RPGLEAQAGA FLTPLSVTLE LLLEYAWRE GERLLGSLET FATAGDVAAF FTETMGLARP CPYHQRVRLD TYGGTVHMEL CFLHDVENFL KQLNYCHLIT P SRGATAAL ...String: AAPVSEPTVA RQKLLALLGQ VQTYVFQIEL LRRCDPHIGR GKLPQLKLNA LQVRALRRRL RPGLEAQAGA FLTPLSVTLE LLLEYAWRE GERLLGSLET FATAGDVAAF FTETMGLARP CPYHQRVRLD TYGGTVHMEL CFLHDVENFL KQLNYCHLIT P SRGATAAL ERVREFMVGA VGSGLIVPPE LSDPSHPCAV CFEELCVTAN QGATIASRLA DRICNHVTQQ AQVRLDANEL RR YLPHAAG LSDADRARAL SVLDHALART AGGDGQPHPS PENDSVRKEA DALLEAHDVF QATTPGLYAI SELQFWLASG DRA GQTTMD AFASNLTALA RRELQQETAA VAVELALFGR RAEHFDRAFG SHLAALDMVD ALIIGGQATS PDDQIEALIR ACYD HHLTT PLLRRLVSPE QCDEEALRRV LARMGAGGAA DAPKGGAGPD DDGDRVAVEE GARGLGAPGG GGEDEDRRRG PGGQG PETW GDIATQAAAD VRERRRLYAD RLTKRSLASL GRCVREQRGE LEKMLRVSVH GEVLPATFAA VANGFAARAR FCALTA GAG TVIDNRSAPG VFDAHRFMRA SLLRHQVDPA LLPSITHRFF ELVNGPLFDH STHSFAQPPN TALYYSVENV GLLPHLK EE LARFIMGAGG SGADWAVSEF QRFYCFDGIS GITPTQRAAW RYIRELIIAT TLFASVYRCG ELELRRPDCS RPTSEGRY R YPPGVYLTYD SDCPLVAIVE SAPDGCIGPR SVVVYDRDVF SILYSVLQHL APR UniProtKB: Tripartite terminase subunit 1 |
-Macromolecule #3: Tripartite terminase subunit 2
Macromolecule | Name: Tripartite terminase subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human herpesvirus 1 (strain 17) / Strain: 17 |
Molecular weight | Theoretical: 13.182892 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: TLRDTIPDCA LRSQTLESLD ARYVSRDGAH DAAVWFEDMT PAELEVVFPT TDAKLNYLSR TQRLASLLTY AGPIKAPDDA AAPQTPDTA CVHGELLARK RERFAAVINR FLDLHQILR UniProtKB: DNA packaging protein UL33 |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106572 |