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- EMDB-53128: In situ subtomogram average of the Vaccinia virus (WR) portal com... -

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Basic information

Entry
Database: EMDB / ID: EMD-53128
TitleIn situ subtomogram average of the Vaccinia virus (WR) portal complex in mature virions
Map data
Sample
  • Complex: Portal complex with surrounding palisade trimers
    • Complex: Portal complex
      • Protein or peptide: Portal protein E8
      • Protein or peptide: Portal Protein E6
      • Protein or peptide: Portal Protein L3
    • Complex: Palisade trimers
      • Protein or peptide: Core protein A10
      • Protein or peptide: Core protein A4
Keywordsportal complex / morphogenesis / assembly / translation / VIRAL PROTEIN
Function / homology
Function and homology information


virion assembly / virion component / host cell cytoplasm / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell endoplasmic reticulum membrane / structural molecule activity
Similarity search - Function
Poxvirus L3/FP4 / Poxvirus E8 / Pox virus E6 protein / Poxvirus L3/FP4 protein / Poxvirus E8 protein / Pox virus E6 protein / Orthopoxvirus A5 / Orthopoxvirus A5L protein-like / Poxvirus P4A / Poxvirus P4A protein
Similarity search - Domain/homology
Protein OPG097 / Major core protein OPG136 precursor / Protein OPG068 / Protein OPG070 / 39kDa core protein OPG130
Similarity search - Component
Biological speciesVaccinia virus WR
Methodsubtomogram averaging / cryo EM / Resolution: 8.21 Å
AuthorsCalcraft T / Hernandez-Gonzalez M / Nans A / Rosenthal PB / Way M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: To Be Published
Title: In situ structure of the poxvirus portal complex
Authors: Calcraft T / Hernandez-Gonzalez M / Nans A / Rosenthal PB / Way M
History
DepositionMar 13, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53128.png

Downloads & links

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Map

FileDownload / File: emd_53128.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 200 pix.
= 312. Å		1.56 Å/pix.
x 200 pix.
= 312. Å		1.56 Å/pix.
x 200 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0559
Minimum - Maximum-0.1506441 - 0.22988655
Average (Standard dev.)-0.000000000000407 (±0.021858541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53128_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53128_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53128_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Portal complex with surrounding palisade trimers

EntireName: Portal complex with surrounding palisade trimers
Components
  • Complex: Portal complex with surrounding palisade trimers
    • Complex: Portal complex
      • Protein or peptide: Portal protein E8
      • Protein or peptide: Portal Protein E6
      • Protein or peptide: Portal Protein L3
    • Complex: Palisade trimers
      • Protein or peptide: Core protein A10
      • Protein or peptide: Core protein A4

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Supramolecule #1: Portal complex with surrounding palisade trimers

SupramoleculeName: Portal complex with surrounding palisade trimers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vaccinia virus WR / Strain: A36-YdF

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Supramolecule #2: Portal complex

SupramoleculeName: Portal complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Vaccinia virus WR

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Supramolecule #3: Palisade trimers

SupramoleculeName: Palisade trimers / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Vaccinia virus WR

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Macromolecule #1: Portal protein E8

MacromoleculeName: Portal protein E8 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus WR
Molecular weightTheoretical: 31.791479 KDa
SequenceString: AATVPRFDDV YKNAQRRILD QETFFSRGLS RPLMKNTYLF DNYAYGWIPE TAIWSSRYAN LDASDYYPIS LGLLKKFEFL MSLYKGPIP VYEEKVNTEF IANGSFSGRY VSYLRKFSAL PTNEFISFLL LTSIPIYNIL FWFKNTQFDI TKHTLFRYVY T DNAKHLAL ...String:
AATVPRFDDV YKNAQRRILD QETFFSRGLS RPLMKNTYLF DNYAYGWIPE TAIWSSRYAN LDASDYYPIS LGLLKKFEFL MSLYKGPIP VYEEKVNTEF IANGSFSGRY VSYLRKFSAL PTNEFISFLL LTSIPIYNIL FWFKNTQFDI TKHTLFRYVY T DNAKHLAL ARYMHQTGDY KPLFSRLKEN YIFTGPVPIG IKDINHPNLS RARSPSDYET LANISTILYF TKYDPVLMFL LF YVPGYSI TTKITPAVEY LMDKLNLTKS DVQLL

UniProtKB: Protein OPG070

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Macromolecule #2: Portal Protein E6

MacromoleculeName: Portal Protein E6 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus WR
Molecular weightTheoretical: 66.812773 KDa
SequenceString: MDFIRRKYLI YTVENNIDFL KDDTLSKVNN FTLNHVLALK YLVSNFPQHV ITKDVLANTN FFVFIHMVRC CKVYEAVLRH AFDAPTLYV KALTKNYLSF SNTIQSYKET VHKLTQDEKF LEVAKYMDEL GELIGVNYDL VLNPLFHGGE PIKDMEIIFL K LFKKTDFK ...String:
MDFIRRKYLI YTVENNIDFL KDDTLSKVNN FTLNHVLALK YLVSNFPQHV ITKDVLANTN FFVFIHMVRC CKVYEAVLRH AFDAPTLYV KALTKNYLSF SNTIQSYKET VHKLTQDEKF LEVAKYMDEL GELIGVNYDL VLNPLFHGGE PIKDMEIIFL K LFKKTDFK VVKKLSVIRL LIWAYLSKKD TGIEFADNDR QDIYTLFQQT GRIVHSNLTE TFRDYIFPGD KTSYWVWLNE SI ANDADIV LNRHAITMYD KILSYIYSEI KQGRVNKNML KLVYIFEPEK DIRELLLEII YDIPGDILSI IDAKNDDWKK YFI SFYKAN FINGNTFISD RTFNEDLFRV VVQIDPEYFD NERIMSLFST SAADIKRFDE LDINNSYISN IIYEVNDITL DTMD DMKKC QIFNEDTSYY VKEYNTYLFL HESDPMVIEN GILKKLSSIK SKSRRLNLFS KNILKYYLDG QLARLGLVLD DYKGD LLVK MINHLKSVED VSAFVRFSTD KNPSILPSLI KTILASYNIS IIVLFQRFLR DNLYHVEEFL DKSIHLTKTD KKYILQ LIR HGRS

UniProtKB: Protein OPG068

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Macromolecule #3: Portal Protein L3

MacromoleculeName: Portal Protein L3 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus WR
Molecular weightTheoretical: 33.045363 KDa
SequenceString: DFINIRLCAY EKEYCNDGYL SPAYYMLKQV DDEEMSCWSE LSSLVRSRKA VGFPLLKAAK RISHGSMLYF EQFKNSKVVR LTPQVKCLN DTVIFQTVVI LYSMYKRGIY SNEFCFDLVS IPRTNIVFSV NQLMFNICTD ILVVLSICGN RLYRTNLPQS C YLNFIHGH ...String:
DFINIRLCAY EKEYCNDGYL SPAYYMLKQV DDEEMSCWSE LSSLVRSRKA VGFPLLKAAK RISHGSMLYF EQFKNSKVVR LTPQVKCLN DTVIFQTVVI LYSMYKRGIY SNEFCFDLVS IPRTNIVFSV NQLMFNICTD ILVVLSICGN RLYRTNLPQS C YLNFIHGH ETIARRGYEH SNYFFEWLIK NHISLLTKQT MDILKVKKKY AIGAPVNRLL EPGTLVYVPK EDYYFIGISL TD VSISDNV RVLFSTDGIV LEIEDFNIKH LFMAGEMFVR SQSSTIIV

UniProtKB: Protein OPG097

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Macromolecule #4: Core protein A10

MacromoleculeName: Core protein A10 / type: protein_or_peptide / ID: 4 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus WR
Molecular weightTheoretical: 68.417578 KDa
SequenceString: MMPIKSIVTL DQLEDSEYLF RIVSTVLPHL CLDYKVCDQL KTTFVHPFDI LLNNSLGSVT KQDELQAAIS KLGINYLIDT TSRELKLFN VTLNAGNIDI INTPINISSE TNPIINTHSF YDLPPFTQHL LNIRLTDTEY RARFIGGYIK PDGSDSMDVL A EKKYPDLN ...String:
MMPIKSIVTL DQLEDSEYLF RIVSTVLPHL CLDYKVCDQL KTTFVHPFDI LLNNSLGSVT KQDELQAAIS KLGINYLIDT TSRELKLFN VTLNAGNIDI INTPINISSE TNPIINTHSF YDLPPFTQHL LNIRLTDTEY RARFIGGYIK PDGSDSMDVL A EKKYPDLN FDNTYLFNIL YKDVINAPIK EFKAKIVNGV LSRQDFDNLI GVRQYITIQD RPRFDDAYNI ADAARHYGVN LN TLPLPNV DLTTMPTYKH LIMFEQYFIY TYDRVDIYYN GNKMLFDDEI INFTISMRYQ SLIPRLVDFF PDIPVNNNIV LHT RDPQNA AVNVTVALPN VQFVDINRNN KFFINFFNLL AKEQRSTAIK VTKSMFWDGM DYEEYKSKNL QDMMFINSTC YVFG LYNHN NTTYCSILSD IISAEKTPIR VCLLPRVVGG KTVTNLISET LKSISSMTIR EFPRKDKSIM HIGLSETGFM RFFQL LRLM ADKPHETAIK EVVMAYVGIK LGDKGSPYYI RKESYQDFIY LLFASMGFKV TTRRSIMGSN NISIISIRPR VTKQYI VAT LMKTSCSKNE AEKLITSAFD LLNFMVSVSD F

UniProtKB: Major core protein OPG136 precursor

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Macromolecule #5: Core protein A4

MacromoleculeName: Core protein A4 / type: protein_or_peptide / ID: 5 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus WR
Molecular weightTheoretical: 5.065543 KDa
SequenceString:
SEEKDPDTKK DEAIEIGLKS QESYYQRQLR EQLARDNMTV ASR

UniProtKB: 39kDa core protein OPG130

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Details: 45mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 2075
ExtractionNumber tomograms: 100 / Number images used: 5369 / Reference model: EMD-18917 / Method: Template matching / Software:
Namedetails
PyTom
EMAN2
UCSF ChimeraXArtiaX
RELION
/ Details: Template matching and interactive curation
CTF correctionSoftware: (Name: Gctf, RELION) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainPDB ID
source_name: AlphaFold, initial_model_type: in silico model
source_name: AlphaFold, initial_model_type: in silico model
source_name: AlphaFold, initial_model_type: in silico model
source_name: PDB, initial_model_type: experimental model

8r5i

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qg7:
In situ structure of the Vaccinia virus (WR) portal complex in mature virions

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