[English] 日本語
![](img/lk-miru.gif)
- EMDB-42442: CryoEM Structure of Allosterically Switchable De Novo Protein sr3... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM Structure of Allosterically Switchable De Novo Protein sr322, In Closed State without Effector Peptide | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Allosterically Switchable Protein / sr322 / closed state / DE NOVO PROTEIN | |||||||||
Biological species | unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.55 Å | |||||||||
![]() | Weidle C / Borst A | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: De Novo Design of Allosterically Switchable Protein Assemblies Authors: Pillai A / Idris A / Philomin A / Weidle C / Skotheim R / Leung P / Broerman A / Demakis C / Borst AJ / Praetorius F / Baker D | |||||||||
History |
|
-
Structure visualization
-
Downloads & links
-EMDB archive
Map data | ![]() | |||
---|---|---|---|---|
Header (meta data) | ![]() | |||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
Sample components
-Entire : sr322
Entire | Name: sr322 |
---|---|
Components |
|
-Supramolecule #1: sr322
Supramolecule | Name: sr322 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Complex is made up of 4 monomeric proteins, and is purified as a 4 sided multimer. |
---|---|
Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 163.296 MDa |
-Macromolecule #1: De Novo Protein sr322
Macromolecule | Name: De Novo Protein sr322 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 40.089242 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SGTVTFDITN ISHKAIDIIL KVVLGIAEHE GTEVTFHSER GQLQIEVKNL HEEDKRLIEQ AIEAARLADS PDPESVARAV ELLTKVAKA STNTELIQFI VKELLELARK LTDPKDLAKV LDSISELLTE LALKTGDPTA ALAAMVAHIA ELVVRLALMA E RTHPGSEI ...String: SGTVTFDITN ISHKAIDIIL KVVLGIAEHE GTEVTFHSER GQLQIEVKNL HEEDKRLIEQ AIEAARLADS PDPESVARAV ELLTKVAKA STNTELIQFI VKELLELARK LTDPKDLAKV LDSISELLTE LALKTGDPTA ALAAMVAHIA ELVVRLALMA E RTHPGSEI VKKAVKLVQE VAEEVLEAAQ LMLEKPNSDE VAKKLEEVAK KAIEACIELQ QILEAWAKER GDQDLLREVR EH KLQILTI AVAYKAAQMG VTVLKHTHGW VVFLVILGLH KQQAEQLLRF VHRVAHALGV TLSITFSGDI VVIAVTVGAS EEE KKEVRK IVKEIAKQLR HAETEEEAKE IVQRVIEEWQ EEGGSG |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.971 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
Details: 150 mM NaCl, 40 mM Tris pH 8.0 | |||||||||
Grid | Model: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 40 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa / Details: -15mA | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4213 / Average exposure time: 5.0 sec. / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Initial model | Chain - Initial model type: in silico model |
---|---|
Details | Initial fit was done using Chimera using Rigid body from In silico model. Then Isolde and Namdinator were used. Coot and Phenix were also used. |
Refinement | Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-8up1: |