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- EMDB-30092: The coordinate of the nuclease domain of the apo terminase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30092
TitleThe coordinate of the nuclease domain of the apo terminase complex
Map data
Sample
  • Complex: HSV-1 nuclease domain of terminase complex
    • Protein or peptide: Tripartite terminase subunit 3
KeywordsHSV-1 / nuclease domain / apo terminase complex / VIRAL PROTEIN
Function / homology
Function and homology information


chromosome organization / Hydrolases; Acting on ester bonds / hydrolase activity / host cell nucleus / DNA binding
Similarity search - Function
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
Tripartite terminase subunit 3
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1) / Human alphaherpesvirus 1 strain 17
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0259
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0259
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m5t
  • Surface level: 0.0259
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6m5t
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30092.png

Downloads & links

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Map

FileDownload / File: emd_30092.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.)
1.05 Å/pix.
x 250 pix.
= 262.5 Å		1.05 Å/pix.
x 250 pix.
= 262.5 Å		1.05 Å/pix.
x 250 pix.
= 262.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0259 / Movie #1: 0.0259
Minimum - Maximum-0.073416196 - 0.1105791
Average (Standard dev.)0.00037746475 (±0.0030653093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 262.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z262.500262.500262.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0730.1110.000

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Supplemental data

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Sample components

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Entire : HSV-1 nuclease domain of terminase complex

EntireName: HSV-1 nuclease domain of terminase complex
Components
  • Complex: HSV-1 nuclease domain of terminase complex
    • Protein or peptide: Tripartite terminase subunit 3

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Supramolecule #1: HSV-1 nuclease domain of terminase complex

SupramoleculeName: HSV-1 nuclease domain of terminase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 alphaherpesvirus 1 strain 17 / Strain: 17
Molecular weightTheoretical: 30.918906 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SSGLVPRGSH MTGDDRPVLT KSAGERFLLY RPSTTTNSGL MAPDLYVYVD PAFTANTRAS GTGVAVVGRY RDDYIIFAL EHFFLRALTG SAPADIARCV VHSLTQVLAL HPGAFRGVRV AVEGNSSQDS AVAIATHVHT EMHRLLASEG A DAGSGPEL ...String:
MGSSHHHHHH SSGLVPRGSH MTGDDRPVLT KSAGERFLLY RPSTTTNSGL MAPDLYVYVD PAFTANTRAS GTGVAVVGRY RDDYIIFAL EHFFLRALTG SAPADIARCV VHSLTQVLAL HPGAFRGVRV AVEGNSSQDS AVAIATHVHT EMHRLLASEG A DAGSGPEL LFYHCEPPGS AVLYPFFLLN KQKTPAFEHF IKKFNSGGVM ASQEIVSATV RLQTDPVEYL LEQLNNLTET VS PNTDVRT YSGKRNGASD DLMVAVIMAI YLAAQAGPPH TFAPITRVS

UniProtKB: Tripartite terminase subunit 3

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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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42053
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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