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- EMDB-30093: The coordinates of the monomeric terminase complex in the presenc... -

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Basic information

Entry
Database: EMDB / ID: EMD-30093
TitleThe coordinates of the monomeric terminase complex in the presence of the ADP-BeF3
Map data
Sample
  • Complex: HSV-1 terminase complex in presence of ADP-BeF3
    • Protein or peptide: Tripartite terminase subunit 3
    • Protein or peptide: Tripartite terminase subunit 1
    • Protein or peptide: Tripartite terminase subunit 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsHSV-1 / terminase complex / ADP-BeF3 / monomer / VIRAL PROTEIN
Function / homology
Function and homology information


viral DNA genome packaging / chromosome organization / Hydrolases; Acting on ester bonds / hydrolase activity / host cell nucleus / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Tripartite terminase subunit 1 / Herpesvirus tripartite terminase subunit 2 / Herpesvirus processing and transport protein / Herpesvirus UL33-like protein / Probable DNA packing protein, C-terminal / Probable DNA packing protein, N-terminal / Tripartite terminase subunit 3 / Probable DNA packing protein, C-terminal domain superfamily / Probable DNA packing protein, C-terminus / Probable DNA packing protein, N-terminus / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA packaging protein UL33 / Tripartite terminase subunit 3 / Tripartite terminase subunit 1 / Tripartite terminase subunit 2
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1) / Human herpesvirus 1 (strain 17) / Human alphaherpesvirus 1 strain 17
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYang YX / Yang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800145 and 31570717 China
CitationJournal: 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
DepositionMar 11, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0239
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0239
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m5u
  • Surface level: 0.0239
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6m5u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30093.png

Downloads & links

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Map

FileDownload / File: emd_30093.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 250 pix.
= 265.5 Å		1.06 Å/pix.
x 250 pix.
= 265.5 Å		1.06 Å/pix.
x 250 pix.
= 265.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.062 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0239 / Movie #1: 0.0239
Minimum - Maximum-0.1042764 - 0.1605052
Average (Standard dev.)0.00023045707 (±0.005693249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0621.0621.062
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z265.500265.500265.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.1040.1610.000

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Supplemental data

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Sample components

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Entire : HSV-1 terminase complex in presence of ADP-BeF3

EntireName: HSV-1 terminase complex in presence of ADP-BeF3
Components
  • Complex: HSV-1 terminase complex in presence of ADP-BeF3
    • Protein or peptide: Tripartite terminase subunit 3
    • Protein or peptide: Tripartite terminase subunit 1
    • Protein or peptide: Tripartite terminase subunit 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: HSV-1 terminase complex in presence of ADP-BeF3

SupramoleculeName: HSV-1 terminase complex in presence of ADP-BeF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human herpesvirus 1 (Herpes simplex virus type 1)

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Macromolecule #1: Tripartite terminase subunit 3

MacromoleculeName: Tripartite terminase subunit 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Human herpesvirus 1 (strain 17) / Strain: 17
Molecular weightTheoretical: 76.501266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: Tripartite terminase subunit 1

MacromoleculeName: Tripartite terminase subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17 / Strain: 17
Molecular weightTheoretical: 84.51275 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #3: Tripartite terminase subunit 2

MacromoleculeName: Tripartite terminase subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 (strain 17) / Strain: 17
Molecular weightTheoretical: 13.182892 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
TLRDTIPDCA LRSQTLESLD ARYVSRDGAH DAAVWFEDMT PAELEVVFPT TDAKLNYLSR TQRLASLLTY AGPIKAPDDA AAPQTPDTA CVHGELLARK RERFAAVINR FLDLHQILR

UniProtKB: DNA packaging protein UL33

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106572
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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