[English] 日本語
![](img/lk-miru.gif)
- EMDB-25572: Pseudomonas phage PaP3 portal protein, delta-C terminal homo-dodecamer -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Pseudomonas phage PaP3 portal protein, delta-C terminal homo-dodecamer | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Hou C-FD / Swanson NA | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 70.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.3 KB | Display | ![]() |
Images | ![]() | 69.3 KB | ||
Masks | ![]() | 91.1 MB | ![]() | |
Others | ![]() ![]() | 70.9 MB 70.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 552.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 552.2 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_25572_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_25572_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant
Entire | Name: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant |
---|---|
Components |
|
-Supramolecule #1: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant
Supramolecule | Name: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Pseudomonas phage PaP3 portal protein
Macromolecule | Name: Pseudomonas phage PaP3 portal protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 3.5 mg/mL | ||||||||
---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Image recording | Film 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 beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Cooling holder cryogen: NITROGEN |
+
Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL / Overall B value: 129 / Target criteria: Correlation coefficient |
---|