+
Open data
-
Basic information
Entry | Database: PDB / ID: 8a3w | ||||||
---|---|---|---|---|---|---|---|
Title | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE | ||||||
![]() |
| ||||||
![]() | RIBOSOME / CRYO-EM LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE | ||||||
Function / homology | ![]() ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome ...ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / rRNA processing / ribosome biogenesis / ribosome binding / kinase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / phosphorylation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||
![]() | Rajan, K.S. / Yonath, A. / Bashan, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE Authors: Rajan, K.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 4.6 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 317.6 KB | Display | |
Data in CIF | ![]() | 548 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15124MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Putative 40S ribosomal protein ... , 15 types, 15 molecules SDSJSLSNSPSRSTSUSVSWSYScSdSCK
#1: Protein | Mass: 22188.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QIM3 |
---|---|
#7: Protein | Mass: 14719.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QGW3 |
#9: Protein | Mass: 16718.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q9A5 |
#11: Protein | Mass: 18681.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q1X7 |
#13: Protein | Mass: 15969.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QC89 |
#14: Protein | Mass: 17433.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q1Y2 |
#16: Protein | Mass: 17482.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q3M1 |
#17: Protein | Mass: 20023.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#18: Protein | Mass: 16551.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q806 |
#19: Protein | Mass: 17472.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QBV0 |
#21: Protein | Mass: 17035.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QH01 |
#25: Protein | Mass: 9819.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q140 |
#26: Protein | Mass: 9763.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q931 |
#32: Protein | Mass: 24511.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q4A0 |
#69: Protein | Mass: 19948.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QBJ1 |
-40S ribosomal protein ... , 14 types, 14 molecules SESFSGSHSISKSOSXSZSaSbSeSASB
#2: Protein | Mass: 30742.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QG31 |
---|---|
#3: Protein | Mass: 28791.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QDL5 |
#4: Protein | Mass: 28370.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q9NE83 |
#5: Protein | Mass: 21336.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q868B1 |
#6: Protein | Mass: 23765.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AC32 |
#8: Protein | Mass: 24984.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P25204 |
#12: Protein | Mass: 15623.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8H1 |
#20: Protein | Mass: 18158.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AEE8 |
#22: Protein | Mass: 15808.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q1D2 |
#23: Protein | Mass: 13071.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q9X4 |
#24: Protein | Mass: 12794.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8L6 |
#27: Protein | Mass: 7394.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q7P0 |
#30: Protein | Mass: 30062.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4FX73 |
#31: Protein | Mass: 27536.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q0Q0 |
-Putative ribosomal protein ... , 7 types, 7 molecules SMSSBCgXk
#10: Protein | Mass: 13031.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8G4 |
---|---|
#15: Protein | Mass: 6696.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q817 |
#43: Protein | Mass: 47593.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q2Q6 |
#44: Protein | Mass: 41096.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9ADW5 |
#62: Protein | Mass: 16492.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QHL3 |
#77: Protein | Mass: 14608.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q1W6 |
#79: Protein | Mass: 9479.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8X0 |
-Protein , 4 types, 4 molecules SgShcI
#28: Protein | Mass: 34441.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q7Y7 |
---|---|
#33: Protein | Mass: 25229.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q5K7 |
#46: Protein | Mass: 28900.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q9H4 |
#53: Protein | Mass: 24805.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AEA8 |
-RNA chain , 10 types, 10 molecules S1S486275431
#29: RNA chain | Mass: 710383.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
---|---|
#34: RNA chain | Mass: 6451.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#35: RNA chain | Mass: 39450.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321399712 |
#36: RNA chain | Mass: 23336.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
#37: RNA chain | Mass: 491219.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
#38: RNA chain | Mass: 54989.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 1207899567 |
#39: RNA chain | Mass: 43481.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
#40: RNA chain | Mass: 59160.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
#41: RNA chain | Mass: 69146.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
#42: RNA chain | Mass: 576984.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 321438308 |
-Putative 60S ... , 20 types, 20 molecules AOHQTSLFEaJWVhZiUple
#45: Protein | Mass: 28331.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4FWX5 |
---|---|
#47: Protein | Mass: 34058.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AF09 |
#49: Protein | Mass: 25509.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QFG2 |
#54: Protein | Mass: 28896.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QJ37 |
#55: Protein | Mass: 19124.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QAX6 |
#56: Protein | Mass: 18068.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QEX4 |
#57: Protein | Mass: 16135.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AFK0 |
#58: Protein | Mass: 21126.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q4D3 |
#59: Protein | Mass: 21594.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QC91 |
#63: Protein | Mass: 15262.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q8V7 |
#64: Protein | Mass: 14982.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AFK3 |
#65: Protein | Mass: 16217.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QAC5 |
#66: Protein | Mass: 16372.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QJ20 |
#67: Protein | Mass: 19335.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QDP9 |
#68: Protein | Mass: 16314.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QGW7 |
#71: Protein | Mass: 11975.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QCE1 |
#72: Protein | Mass: 15030.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q0X2 |
#73: Protein | Mass: 12302.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q3L3 |
#80: Protein | Mass: 6504.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QEQ0 |
#82: Protein | Mass: 21316.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AFF2 |
-Ribosomal protein ... , 2 types, 2 molecules Mj
#48: Protein | Mass: 24497.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q6S3 |
---|---|
#70: Protein | Mass: 9862.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AEH2 |
-60S ribosomal protein ... , 10 types, 10 molecules GPRYfoDdbn
#50: Protein | Mass: 29824.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QIP1 |
---|---|
#51: Protein | Mass: 22071.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QG98 |
#52: Protein | Mass: 20852.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q5J4 |
#60: Protein | Mass: 15469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q504 |
#61: Protein | Mass: 15458.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QC11 |
#74: Protein | Mass: 10337.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4QC01 |
#75: Protein | Mass: 21694.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P48157 |
#76: Protein | Mass: 11370.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E9AEK1 |
#78: Protein | Mass: 8001.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q4Q178 |
#81: Protein/peptide | Mass: 4390.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
-Non-polymers , 5 types, 875 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#83: Chemical | ChemComp-MG / #84: Chemical | ChemComp-NA / #85: Chemical | ChemComp-ZN / #86: Chemical | ChemComp-K / #87: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE Type: RIBOSOME Details: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE Entity ID: #1-#82 / Source: NATURAL | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 742580 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||
Refine LS restraints |
|