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- PDB-3j92: Structure and assembly pathway of the ribosome quality control complex -

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Basic information

Entry
Database: PDB / ID: 3j92
TitleStructure and assembly pathway of the ribosome quality control complex
Components
  • (Listerin) x 2
  • (eL30) x 2
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • NEMFNew England Motor Freight
  • eL13
  • eL14
  • eL15List of Subaru engines
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL27
  • eL28
  • eL29
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL36
  • eL37
  • eL38
  • eL39
  • eL40
  • eL42
  • eL43
  • eL6
  • eL8
  • nascent chain
  • tRNATransfer RNA
  • uL10
  • uL11
  • uL13
  • uL14
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL23
  • uL24
  • uL29
  • uL3
  • uL4
  • uL5
  • uL6
KeywordsRIBOSOME/LIGASE / RWD / RING / quality control / RIBOSOME-LIGASE complex
Function / homology
Function and homology information


alpha-aminoacyl-tRNA binding / CAT tailing / RQC complex / nuclear export / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / protein autoubiquitination / rescue of stalled ribosome / cytosolic ribosome / RING-type E3 ubiquitin transferase ...alpha-aminoacyl-tRNA binding / CAT tailing / RQC complex / nuclear export / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / protein autoubiquitination / rescue of stalled ribosome / cytosolic ribosome / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein-containing complex assembly / tRNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
NFACT protein, C-terminal / NFACT protein C-terminal domain / E3 ubiquitin-protein ligase listerin / Listerin, zinc finger, RING-type / Zinc finger, RING-CH-type / The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Zinc finger RING-type profile. ...NFACT protein, C-terminal / NFACT protein C-terminal domain / E3 ubiquitin-protein ligase listerin / Listerin, zinc finger, RING-type / Zinc finger, RING-CH-type / The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosome quality control complex subunit NEMF / E3 ubiquitin-protein ligase listerin
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShao, S. / Brown, A. / Santhanam, B. / Hegde, R.S.
CitationJournal: Mol Cell / Year: 2015
Title: Structure and assembly pathway of the ribosome quality control complex.
Authors: Sichen Shao / Alan Brown / Balaji Santhanam / Ramanujan S Hegde /
Abstract: During ribosome-associated quality control, stalled ribosomes are split into subunits and the 60S-housed nascent polypeptides are poly-ubiquitinated by Listerin. How this low-abundance ubiquitin ...During ribosome-associated quality control, stalled ribosomes are split into subunits and the 60S-housed nascent polypeptides are poly-ubiquitinated by Listerin. How this low-abundance ubiquitin ligase targets rare stall-generated 60S among numerous empty 60S is unknown. Here, we show that Listerin specificity for nascent chain-60S complexes depends on nuclear export mediator factor (NEMF). The 3.6 Å cryo-EM structure of a nascent chain-containing 60S-Listerin-NEMF complex revealed that NEMF makes multiple simultaneous contacts with 60S and peptidyl-tRNA to sense nascent chain occupancy. Structural and mutational analyses showed that ribosome-bound NEMF recruits and stabilizes Listerin's N-terminal domain, while Listerin's C-terminal RWD domain directly contacts the ribosome to position the adjacent ligase domain near the nascent polypeptide exit tunnel. Thus, highly specific nascent chain targeting by Listerin is imparted by the avidity gained from a multivalent network of context-specific individually weak interactions, highlighting a new principle of client recognition during protein quality control.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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Structure viewerMolecule:
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Assembly

Deposited unit
A: uL2
B: uL3
C: uL4
D: uL18
E: eL6
F: eL30
G: eL8
H: uL6
I: uL16
J: uL5
L: eL13
M: eL14
N: eL15
O: uL13
P: uL22
Q: eL18
R: eL19
S: eL20
T: eL21
U: eL22
V: uL14
W: eL24
X: uL23
Y: uL24
Z: eL27
a: uL15
b: eL29
c: eL30
d: eL31
e: eL32
f: eL33
g: eL34
h: uL29
i: eL36
j: eL37
k: eL38
l: eL39
m: eL40
o: eL42
p: eL43
r: eL28
s: uL10
t: uL11
u: NEMF
v: NEMF
w: Listerin
x: Listerin
y: Listerin
z: Listerin
0: Listerin
1: nascent chain
2: tRNA
5: 28S rRNA
7: 5S rRNA
8: 5.8S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,945,310219
Polymers2,941,11855
Non-polymers4,192164
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 47 types, 51 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#1: Protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: Protein uL3


Mass: 44890.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: Protein uL4


Mass: 41766.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: Protein uL18


Mass: 34417.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein eL6


Mass: 32304.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#6: Protein eL30


Mass: 29521.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: Protein eL8


Mass: 30166.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#8: Protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: Protein uL16


Mass: 24596.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#10: Protein uL5


Mass: 20248.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein eL13


Mass: 24365.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein eL14


Mass: 23383.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#13: Protein eL15 / List of Subaru engines


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: Protein uL13


Mass: 23765.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein uL22


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#16: Protein eL18


Mass: 21588.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein eL19


Mass: 23567.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#18: Protein eL20


Mass: 26103.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#19: Protein eL21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#20: Protein eL22


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: Protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#23: Protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein uL15


Mass: 16631.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein eL29


Mass: 17545.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#28: Protein eL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: Protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#30: Protein eL32 / CD59


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#32: Protein eL34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#33: Protein uL29


Mass: 14591.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: Protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#35: Protein eL37


Mass: 11123.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: Protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: Protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: Protein eL40


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: Protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#40: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: Protein eL28


Mass: 15765.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#42: Protein uL10


Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein uL11


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein NEMF / New England Motor Freight / Nuclear export mediator factor


Mass: 57571.883 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEMF, SDCCAG1 / Plasmid: pcDNA3.1 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) / References: UniProt: O60524
#45: Protein Listerin / E3 ubiquitin-protein ligase


Mass: 200778.703 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: LTN1, C21orf10, C21orf98, KIAA0714, RNF160, ZNF294, HSPC087
Plasmid: pcDNA3.1 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
References: UniProt: O94822, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#46: Protein Listerin / E3 ubiquitin-protein ligase


Mass: 18570.826 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: LTN1, C21orf10, C21orf98, KIAA0714, RNF160, ZNF294, HSPC087
Plasmid: pcDNA3.1 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
References: Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#47: Protein nascent chain


Mass: 10901.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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RNA chain , 4 types, 4 molecules 2578

#48: RNA chain tRNA / Transfer RNA


Mass: 24816.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#49: RNA chain 28S rRNA / 28S ribosomal RNA


Mass: 1187230.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 2 types, 164 molecules

#52: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 159 / Source method: obtained synthetically / Formula: Mg
#53: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsALTHOUGH ONLY ONE INSTANCE EACH OF PROTEINS NEMF AND LISTERIN IS PRESENT WITHIN THE COMPLEX, EACH ...ALTHOUGH ONLY ONE INSTANCE EACH OF PROTEINS NEMF AND LISTERIN IS PRESENT WITHIN THE COMPLEX, EACH OF THESE PROTEINS IS REPRESENTED AS MULTIPLE CHAINS TO REFLECT THE DIFFERENT DEGREES OF ACCURACY OF PLACEMENT OF THE FRAGMENTS WITHIN THE EXPERIMENTAL EM DENSITY. THE NUMBERING OF RESIDUES LABELED AS UNK (UNKNOWN RESIDUE) IS ARBITRARY. THE RIBOSOME IN THE IMAGED SAMPLE WAS FROM ORYCTOLAGUS CUNICULUS, BUT THE MODELED RIBOSOMAL RNA AND PROTEIN SEQUENCES ARE FROM SUS SCROFA.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent-ID
1rabbit 60S ribosomal subunit housing an in vitro translated nascent chain attached to a P-site tRNA in complex with the E3 ligase Listerin and NEMFRIBOSOME0
260S ribosomal subunitRIBOSOME1
3tRNATransfer RNA1
4in vitro translated substrate1
5Listerin1
6NEMFNew England Motor Freight1
Buffer solutionName: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT
pH: 7.4
Details: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 on 400 mesh Cu grid with thin carbon support
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
Method: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Calibrated magnification: 104478 X / Details: Objective lens astigmatism was corrected at 59,000 times magnification. / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: FEI TITAN KRIOS / Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm / Nominal magnification: 59000 X / Specimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1

IDDate
1Apr 30, 2014
2Aug 18, 2014
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0091 2014/10/05 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2Cootmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63826 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-ID
14W1Z

4w1z
PDB Unreleased entry

1
24W20

4w20
PDB Unreleased entry

1
RefinementDetails: Hydrogens have been added in their riding positions
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms60263 85959 164 0 146386

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