+
Open data
-
Basic information
Entry | Database: PDB / ID: 5a9z | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Complex of Thermous thermophilus ribosome bound to BipA-GDPCP | |||||||||
![]() |
| |||||||||
![]() | RIBOSOME / BIPA / TRANSLATIONAL GTPASE FACTORS / X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY | |||||||||
Function / homology | ![]() guanosine tetraphosphate binding / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / protein folding chaperone / response to cold / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation ...guanosine tetraphosphate binding / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / protein folding chaperone / response to cold / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / response to heat / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
![]() | Kumar, V. / Chen, Y. / Ahmed, T. / Tan, J. / Ero, R. / Bhushan, S. / Gao, Y.-G. | |||||||||
![]() | ![]() Title: Structure of BipA in GTP form bound to the ratcheted ribosome. Authors: Veerendra Kumar / Yun Chen / Rya Ero / Tofayel Ahmed / Jackie Tan / Zhe Li / Andrew See Weng Wong / Shashi Bhushan / Yong-Gui Gao / ![]() Abstract: BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly ...BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation. | |||||||||
History |
| |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ...SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 3.7 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 234 KB | Display | |
Data in CIF | ![]() | 408.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6396MC ![]() 6397C ![]() 5a9vC ![]() 5a9wC ![]() 5a9xC ![]() 5a9yC ![]() 5aa0C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-RNA chain , 3 types, 3 molecules AAABBA
#1: RNA chain | Mass: 939567.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: RNA chain | Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#34: RNA chain | Mass: 491777.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 30 types, 30 molecules ACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAeAf
-Protein , 2 types, 2 molecules AgCA
#33: Protein | Mass: 10911.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#55: Protein | Mass: 65979.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-30S ribosomal protein ... , 20 types, 20 molecules BFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBY
#35: Protein | Mass: 26987.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#36: Protein | Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#37: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#38: Protein | Mass: 16331.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#39: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#41: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#42: Protein | Mass: 14279.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#43: Protein | Mass: 11299.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#44: Protein | Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#45: Protein | Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#46: Protein | Mass: 13037.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#47: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#48: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#49: Protein | Mass: 9924.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#50: Protein | Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#51: Protein | Mass: 8483.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#52: Protein | Mass: 9203.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#53: Protein | Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#54: Protein/peptide | Mass: 2960.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 2 types, 3 molecules ![](data/chem/img/NMY.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/GCP.gif)
#56: Chemical | #57: Chemical | ChemComp-GCP / | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: RIBOSOME / Type: RIBOSOME / Details: RIBOSOME AND BIPA |
---|---|
Buffer solution | Name: 5 MM HEPES PH 7.5, 10 MM MGAC, 50 MM KCL, 10 MM NH4CL, AND 6 MM 2- MERCAPTOETHANOL pH: 7.5 Details: 5 MM HEPES PH 7.5, 10 MM MGAC, 50 MM KCL, 10 MM NH4CL, AND 6 MM 2- MERCAPTOETHANOL |
Specimen | Conc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F20 / Date: Feb 5, 2015 |
Electron gun | Electron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal magnification: 53000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 658 |
-
Processing
EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: CTFFIND3 | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 4.7 Å / Num. of particles: 61165 / Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 4.7 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.7 Å
|