[English] 日本語
![](img/lk-miru.gif)
- EMDB-26381: Cryo-EM structure of Shiga toxin 2 in complex with the native rib... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Shiga toxin 2 in complex with the native ribosomal P-stalk | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
Function / homology | ![]() rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Kulczyk AW | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo-EM structure of Shiga toxin 2 in complex with the native ribosomal P-stalk reveals residues involved in the binding interaction. Authors: Arkadiusz W Kulczyk / Carlos Oscar S Sorzano / Przemysław Grela / Marek Tchórzewski / Nilgun E Tumer / Xiao-Ping Li / ![]() ![]() ![]() Abstract: Shiga toxin 2a (Stx2a) is the virulence factor of enterohemorrhagic Escherichia coli. The catalytic A1 subunit of Stx2a (Stx2A1) interacts with the ribosomal P-stalk for loading onto the ribosome and ...Shiga toxin 2a (Stx2a) is the virulence factor of enterohemorrhagic Escherichia coli. The catalytic A1 subunit of Stx2a (Stx2A1) interacts with the ribosomal P-stalk for loading onto the ribosome and depurination of the sarcin-ricin loop, which halts protein synthesis. Because of the intrinsic flexibility of the P-stalk, a structure of the Stx2a-P-stalk complex is currently unknown. We demonstrated that the native P-stalk pentamer binds to Stx2a with nanomolar affinity, and we employed cryo-EM to determine a structure of the 72 kDa Stx2a complexed with the P-stalk. The structure identifies Stx2A1 residues involved in binding and reveals that Stx2a is anchored to the P-stalk via only the last six amino acids from the C-terminal domain of a single P-protein. For the first time, the cryo-EM structure shows the loop connecting Stx2A1 and Stx2A2, which is critical for activation of the toxin. Our principal component analysis of the cryo-EM data reveals the intrinsic dynamics of the Stx2a-P-stalk interaction, including conformational changes in the P-stalk binding site occurring upon complex formation. Our computational analysis unveils the propensity for structural rearrangements within the C-terminal domain, with its C-terminal six amino acids transitioning from a random coil to an α-helix upon binding to Stx2a. In conclusion, our cryo-EM structure sheds new light into the dynamics of the Stx2a-P-stalk interaction and indicates that the binding interface between Stx2a and the P-stalk is the potential target for drug discovery. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 61.7 KB | ||
Others | ![]() ![]() | 80.7 MB 80.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 565.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 564.8 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u6vMC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.8248 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_26381_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_26381_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Shiga toxin 2a in complex with the native ribosomal P-stalk
Entire | Name: Shiga toxin 2a in complex with the native ribosomal P-stalk |
---|---|
Components |
|
-Supramolecule #1: Shiga toxin 2a in complex with the native ribosomal P-stalk
Supramolecule | Name: Shiga toxin 2a in complex with the native ribosomal P-stalk type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Molecular weight | Theoretical: 100 KDa |
-Supramolecule #2: Shiga toxin 2a
Supramolecule | Name: Shiga toxin 2a / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1-#2 / Details: 72 KDa Stx2a holotoxin |
---|---|
Source (natural) | Organism: ![]() |
-Supramolecule #3: Native ribosomal P-stalk
Supramolecule | Name: Native ribosomal P-stalk / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #3 / Details: 56 kDa native ribosomal P-stalk |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Shiga toxin 2a subunit A (Stx2A)
Macromolecule | Name: Shiga toxin 2a subunit A (Stx2A) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: rRNA N-glycosylase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.214188 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: REFTIDFSTQ QSYVSSLNSI RTEISTPLEH ISQGTTSVSV INHTPPGSYF AVDIRGLDVY QARFDHLRLI IEQNNLYVAG FVNTATNTF YRFSDFTHIS VPGVTTVSMT TDSSYTTLQR VAALERSGMQ ISRHSLVSSY LALMEFSGNT MTRDASRAVL R FVTVTAEA ...String: REFTIDFSTQ QSYVSSLNSI RTEISTPLEH ISQGTTSVSV INHTPPGSYF AVDIRGLDVY QARFDHLRLI IEQNNLYVAG FVNTATNTF YRFSDFTHIS VPGVTTVSMT TDSSYTTLQR VAALERSGMQ ISRHSLVSSY LALMEFSGNT MTRDASRAVL R FVTVTAEA LRFRQIQREF RQALSETAPV YTMTPGDVDL TLNWGRISNV LPEYRGEDGV RVGRISFNNI SAILGTVAVI LN CHHQGAR SVRAVNEDSQ PECQITGDRP VIKINNTLWE SNTAAAFLNR KSQFLYTTGK |
-Macromolecule #2: Shiga toxin 2a subunit B (Stx2B)
Macromolecule | Name: Shiga toxin 2a subunit B (Stx2B) / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.82459 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: ADCAKGKIEF SKYNEDDTFT VKVDGKEYWT SRWNLQPLLQ SAQLTGMTVT IKSSTCESGS GFAEVQFNND |
-Macromolecule #3: C-terminal domain (CTD) from the Ribosomal P-stalk
Macromolecule | Name: C-terminal domain (CTD) from the Ribosomal P-stalk / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 654.712 Da |
Sequence | String: GFGLFD |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 23 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
---|---|
Output model | ![]() PDB-7u6v: |