[English] 日本語
Yorodumi
- EMDB-25521: Kinetically trapped Pseudomonas-phage PaP3 portal protein - Full ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25521
TitleKinetically trapped Pseudomonas-phage PaP3 portal protein - Full Length
Map data
Sample
  • Complex: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant
    • Protein or peptide: Portal protein
KeywordsPortal protein / Dodecamer / VIRAL PROTEIN
Function / homologyORF.04
Function and homology information
Biological speciesPseudomonas virus PaP3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHou CFD / 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 24, 2021-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25521.png

Downloads & links

-
Map

FileDownload / File: emd_25521.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.01798737 - 0.060080815
Average (Standard dev.)0.0022258377 (±0.0069928817)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_25521_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_25521_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_25521_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: Portal protein

-
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

-
Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus PaP3
Molecular weightTheoretical: 80.981344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKRRKIKPM DDEQVLRHLD QLVNDALDFN SSELSKQRSE ALKYYFGEPF GNERPGKSGI VSRDVQETVD WIMPSLMKVF TSGGQVVKY EPDTAEDVEQ AEQETEYVNY LFMRKNEGFK VMFDWFQDTL MMKTGVVKVY VEEVLKPTFE RFSGLSEDMV A DILSDPDT ...String:
MAKRRKIKPM DDEQVLRHLD QLVNDALDFN SSELSKQRSE ALKYYFGEPF GNERPGKSGI VSRDVQETVD WIMPSLMKVF TSGGQVVKY EPDTAEDVEQ AEQETEYVNY LFMRKNEGFK VMFDWFQDTL MMKTGVVKVY VEEVLKPTFE RFSGLSEDMV A DILSDPDT SILAQSVDDD GTYTIKIRKD KKKREIKVLC VKPENFLVDR LATCIDDARF LCHREKYTVS DLRLLGVPED VI EELPYDE YEFSDSQPER LVRDNFDMTG QLQYNSGDDA EANREVWASE CYTLLDVDGD GISELRRILY VGDYIISNEP WDC RPFADL NAYRIAHKFH GMSVYDKIRD IQEIRSVLMR NIMDNIYRTN QGRSVVLDGQ VNLEDLLTNE AAGIVRVKSM NSIT PLETP QLSGEVYGML DRLEADRGKR TGITDRTRGL DQNTLHSNQA AMSVNQLMTA AEQQIDLIAR MFAETGVKRL FQLLH DHAI KYQNQEEVFQ LRGKWVAVNP ANWRERSDLT VTVGIGNMNK DQQMLHLMRI WEMAQAVVGG GGLGVLVSEQ NLYNIL KEV TENAGYKDPD RFWTNPNSPE ALQAKAIREQ KEAQPKPEDI KAQADAQRAQ SDALAKQAEA QMKQVEAQIR LAEIELK KQ EAVLQQREMA LKEAELQLER DRFTWERARN EAEYHLEATQ ARAAYIGDGK VPETKKPTKA VRR

UniProtKB: ORF.04

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-hydrochloride
200.0 mMNaClSodium chloride
5.0 mMEDTAEDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
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

+
Image processing

Particle selectionNumber selected: 1200000
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

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

PDB-7sya:
Kinetically trapped Pseudomonas-phage PaP3 portal protein - Full Length

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more