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- PDB-6i0y: TnaC-stalled ribosome complex with the titin I27 domain folding c... -

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Basic information

Entry
Database: PDB / ID: 6i0y
TitleTnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel
Components
  • (50S ribosomal protein ...) x 31
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Proline tRNA
  • Titin
  • Tryptophanase operon leader peptide
KeywordsRIBOSOME / Protein folding / ribosomal exit tunnel / nascent chain / titin I27 domain
Function / homologyRibosomal protein L6, bacterial-type / Ribosomal protein L21-like / Ribosomal protein L16, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal ...Ribosomal protein L6, bacterial-type / Ribosomal protein L21-like / Ribosomal protein L16, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L10 / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L28/L24 / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / L21-like superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal L18e/L15P superfamily / Immunoglobulin-like domain superfamily / Fibronectin type III superfamily / Ribosomal protein L15 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L10e/L16 / Tryptophanese operon leader peptide / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / 50S ribosomal protein uL4 / Ribosomal protein L25/L23 / Immunoglobulin I-set / Immunoglobulin V-set domain / Immunoglobulin-like fold / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Titin, Z repeat / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L14P, conserved site / Ribosomal protein L3, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L34 signature. / Ribosomal protein L7/L12 dimerisation domain / Ribosomal L27 protein / Ribosomal protein L17 / Ribosomal protein L19 / Ribosomal protein L9, N-terminal domain / Ribosomal L25p family / Ribosomal protein L35 / Ribosomal L32p protein family / PPAK motif / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L9, C-terminal domain / Immunoglobulin I-set domain / Tryptophanase operon leader peptide / Titin Z / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal L29 protein / Ribosomal protein L6 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L30 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L33 signature. / Ribosomal protein L29 signature. / Ribosomal protein L15 signature. / Ribosomal protein L14 signature. / Ribosomal protein L3 signature. / Ribosomal protein L2 signature. / Ribosomal protein L22 signature.
Function and homology information
Specimen sourceEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsSu, T. / Kudva, R. / von Heijne, G. / Beckmann, R.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Folding pathway of an Ig domain is conserved on and off the ribosome.
Authors: Pengfei Tian / Annette Steward / Renuka Kudva / Ting Su / Patrick J Shilling / Adrian A Nickson / Jeffrey J Hollins / Roland Beckmann / Gunnar von Heijne / Jane Clarke / Robert B Best
Abstract: Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ...Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-β Ig domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force dependence of escape from arrest accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations-which also reproduce experiments on mutant forms of I27-show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 26, 2018 / Release: Dec 5, 2018

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Assembly

Deposited unit
h: 50S ribosomal protein L24
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
5: 50S ribosomal protein L10
6: 50S ribosomal protein L7/L12
7: Tryptophanase operon leader peptide
8: 50S ribosomal protein L25
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L11
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
V: Proline tRNA
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
z: Titin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,414,238181
Polyers1,410,49336
Non-polymers3,745145
Water7,909439
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 31 types, 31 molecules h01234568CDEFGHIJKLMNOPQRSTWXYZ

#1: Protein/peptide 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11339.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P60624
#2: Protein/peptide 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6463.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7N4
#3: Protein/peptide 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 6388.631 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7N9
#4: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7P5
#5: Protein/peptide 50S ribosomal protein L35 / / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7Q1
#6: Protein/peptide 50S ribosomal protein L36 / / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7Q6
#7: Protein/peptide 50S ribosomal protein L10 / / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 17736.596 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7J3
#8: Protein/peptide 50S ribosomal protein L7/L12 / Ribosome / L8 / Large ribosomal subunit protein bL12


Mass: 12309.155 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7K2
#10: Protein/peptide 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P68919
#13: Protein/peptide 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29923.619 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P60422
#14: Protein/peptide 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P60438
#15: Protein/peptide 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P60723
#16: Protein/peptide 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P62399
#17: Protein/peptide 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0AG55
#18: Protein/peptide 50S ribosomal protein L9 / / Large ribosomal subunit protein bL9


Mass: 5467.367 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7R1
#19: Protein/peptide 50S ribosomal protein L11 / / Large ribosomal subunit protein uL11


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7J7
#20: Protein/peptide 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0AA10
#21: Protein/peptide 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0ADY3
#22: Protein/peptide 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P02413
#23: Protein/peptide 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0ADY7
#24: Protein/peptide 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0AG44
#25: Protein/peptide 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0C018
#26: Protein/peptide 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7K6
#27: Protein/peptide 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7L3
#28: Protein/peptide 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0AG48
#29: Protein/peptide 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P61175
#30: Protein/peptide 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0ADZ0
#32: Protein/peptide 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 8476.680 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7L8
#33: Protein/peptide 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7M2
#34: Protein/peptide 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0A7M6
#35: Protein/peptide 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: KC6 / References: UniProt: P0AG51

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Protein/peptide , 2 types, 2 molecules 7z

#9: Protein/peptide Tryptophanase operon leader peptide


Mass: 2899.416 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: KC6 / Gene: tnaC, tnaL, b3707, JW3685 / Production host: Escherichia coli (E. coli) / Strain (production host): KC6 / References: UniProt: P0AD89
#36: Protein/peptide Titin / / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 9794.193 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli) / Strain (production host): KC6
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase

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RNA chain , 3 types, 3 molecules ABV

#11: RNA chain 23S ribosomal RNA /


Mass: 941306.188 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1109114233
#12: RNA chain 5S ribosomal RNA /


Mass: 38177.762 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1430654817
#31: RNA chain Proline tRNA


Mass: 24876.777 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1476611766

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Non-polymers , 4 types, 584 molecules

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


Mass: 24.305 Da / Num. of mol.: 143 / Formula: Mg / Magnesium
#38: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#39: Chemical ChemComp-TRP / TRYPTOPHAN


Mass: 204.225 Da / Num. of mol.: 1 / Formula: C11H12N2O2 / Tryptophan
#40: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Formula: H2O / Water

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnelRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,360MULTIPLE SOURCES
2ribosomeRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,361NATURAL
3Tryptophanase operon leader peptideCOMPLEX91RECOMBINANT
4Titin nascent chainCOMPLEX361RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganismStrain
22562Escherichia coli (E. coli)KC6
33562Escherichia coli (E. coli)KC6
449606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganismStrain
13562Escherichia coli (E. coli)KC6
24562Escherichia coli (E. coli)KC6
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 0.926 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2613
Image scansMovie frames/image: 30

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Processing

EM software
IDNameVersionCategory
4GctfCTF correction
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 468015
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 301510 / Symmetry type: POINT

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