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- EMDB-25572: Pseudomonas phage PaP3 portal protein, delta-C terminal homo-dodecamer -

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Basic information

Entry
Database: EMDB / ID: EMD-25572
TitlePseudomonas phage PaP3 portal protein, delta-C terminal homo-dodecamer
Map data
Sample
  • Complex: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant
    • Protein or peptide: Pseudomonas phage PaP3 portal protein
Biological speciesPseudomonas virus PaP3
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsHou C-FD / Swanson NA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 GM100888, R35 GM140733-0, P30 CA56036, HSSN261200800001E United States
CitationJournal: J Mol Biol / Year: 2022
Title: Cryo-EM Structure of a Kinetically Trapped Dodecameric Portal Protein from the Pseudomonas-phage PaP3.
Authors: Chun-Feng David Hou / Nicholas A Swanson / Fenglin Li / Ruoyu Yang / Ravi K Lokareddy / Gino Cingolani /
Abstract: Portal proteins are dodecameric assemblies that occupy a unique 5-fold vertex of the icosahedral capsid of tailed bacteriophages and herpesviruses. The portal vertex interrupts the icosahedral ...Portal proteins are dodecameric assemblies that occupy a unique 5-fold vertex of the icosahedral capsid of tailed bacteriophages and herpesviruses. The portal vertex interrupts the icosahedral symmetry, and in vivo, its assembly and incorporation in procapsid are controlled by the scaffolding protein. Ectopically expressed portal oligomers are polymorphic in solution, and portal rings built by a different number of subunits have been documented in the literature. In this paper, we describe the cryo-EM structure of the portal protein from the Pseudomonas-phage PaP3, which we determined at 3.4 Å resolution. Structural analysis revealed a dodecamer with helical rather than rotational symmetry, which we hypothesize is kinetically trapped. The helical assembly was stabilized by local mispairing of portal subunits caused by the slippage of crown and barrel helices that move like a lever with respect to the portal body. Removing the C-terminal barrel promoted assembly of undecameric and dodecameric rings with quasi-rotational symmetry, suggesting that the barrel contributes to subunits mispairing. However, ΔC-portal rings were intrinsically asymmetric, with most particles having one open portal subunit interface. Together, these data expand the structural repertoire of viral portal proteins to Pseudomonas-phages and shed light on the unexpected plasticity of the portal protein quaternary structure.
History
DepositionNov 29, 2021-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25572.png

Downloads & links

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Map

FileDownload / File: emd_25572.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 288 pix.
= 262.08 Å		0.91 Å/pix.
x 288 pix.
= 262.08 Å		0.91 Å/pix.
x 288 pix.
= 262.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.009021607 - 0.08554068
Average (Standard dev.)0.0026628312 (±0.009593176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 262.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25572_msk_1.map
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Half map: #1

Fileemd_25572_half_map_1.map
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Half map: #2

Fileemd_25572_half_map_2.map
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Sample components

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Entire : Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant

EntireName: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant
Components
  • Complex: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant
    • Protein or peptide: Pseudomonas phage PaP3 portal protein

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Supramolecule #1: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant

SupramoleculeName: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas virus PaP3
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Pseudomonas phage PaP3 portal protein

MacromoleculeName: Pseudomonas phage PaP3 portal protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus PaP3
SequenceString: MAKRRKIKPM DDEQVLRHLD QLVNDALDFN SSELSKQRSE ALKYYFGEPF GNERPGKSGI VSRDVQETVD WIMPSLMKV FTSGGQVVKY EPDTAEDVEQ AEQETEYVNY LFMRKNEGFK VMFDWFQDTL MMKTGVVKVY V EEVLKPTF ERFSGLSEDM VADILSDPDT ...String:
MAKRRKIKPM DDEQVLRHLD QLVNDALDFN SSELSKQRSE ALKYYFGEPF GNERPGKSGI VSRDVQETVD WIMPSLMKV FTSGGQVVKY EPDTAEDVEQ AEQETEYVNY LFMRKNEGFK VMFDWFQDTL MMKTGVVKVY V EEVLKPTF ERFSGLSEDM VADILSDPDT SILAQSVDDD GTYTIKIRKD KKKREIKVLC VKPENFLVDR LA TCIDDAR FLCHREKYTV SDLRLLGVPE DVIEELPYDE YEFSDSQPER LVRDNFDMTG QLQYNSGDDA EAN REVWAS ECYTLLDVDG DGISELRRIL YVGDYIISNE PWDCRPFADL NAYRIAHKFH GMSVYDKIRD IQEI RSVLM RNIMDNIYRT NQGRSVVLDG QVNLEDLLTN EAAGIVRVKS MNSITPLETP QLSGEVYGML DRLEA DRGK RTGITDRTRG LDQNTLHSNQ AAMSVNQLMT AAEQQIDLIA RMFAETGVKR LFQLLHDHAI KYQNQE EVF QLRGKWVAVN PANWRERSDL TVTVGIGNMN KDQQMLHLMR IWEMAQAVVG GGGLGVLVSE QNLYNIL KE VTENAGYKDP DRFWTNPNSP EALQAKAIRE QKEA

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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

Concentration3.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
20.0 mMTris-HCl
200.0 mMNaCl
5.0 mMEDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1200000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 129 / Target criteria: Correlation coefficient

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