[English] 日本語
Yorodumi
- EMDB-0322: TnaC-stalled ribosome complex with the titin I27 domain folding c... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0322
TitleTnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel
Map dataTitin I27 domain folded at the exit of ribosomal tunnel
SampleTnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel:
ribosome / (Tryptophanase operon leader ...) x 2 / Titin nascent chain / (50S ribosomal protein ...) x 31 / (nucleic-acidNucleic acid) x 3 / Titin / (ligand) x 4
Function / homologyRibosomal protein L35, conserved site / 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 L35, conserved site / 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 L6, bacterial-type / 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
SourceEscherichia coli (E. coli) / Homo sapiens (human)
Methodsingle 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 ReportPDB-ID: 6i0y

SummaryFull reportAbout validation report
DateDeposition: Oct 26, 2018 / Header (metadata) release: Dec 5, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6i0y
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6i0y
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_0322.map.gz (map file in CCP4 format, 205916 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
372 pix
1.06 Å/pix.
= 394.32 Å
372 pix
1.06 Å/pix.
= 394.32 Å
372 pix
1.06 Å/pix.
= 394.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.019 (by author), 0.019 (movie #1):
Minimum - Maximum-0.17072792 - 0.2401755
Average (Standard dev.)0.00015069403 (0.011110076)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions372372372
Origin0.00.00.0
Limit371.0371.0371.0
Spacing372372372
CellA=B=C: 394.31998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z372372372
origin x/y/z0.0000.0000.000
length x/y/z394.320394.320394.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS372372372
D min/max/mean-0.1710.2400.000

-
Supplemental data

-
Sample components

+
Entire TnaC-stalled ribosome complex with the titin I27 domain folding c...

EntireName: TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel
Number of components: 44

+
Component #1: protein, TnaC-stalled ribosome complex with the titin I27 domain ...

ProteinName: TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel
Recombinant expression: No

+
Component #2: protein, ribosome

ProteinName: ribosome / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #3: protein, Tryptophanase operon leader peptide

ProteinName: Tryptophanase operon leader peptide / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: KC6

+
Component #4: protein, Titin nascent chain

ProteinName: Titin nascent chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: KC6

+
Component #5: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #6: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #7: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #8: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #9: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #10: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #11: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.736596 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #12: protein, 50S ribosomal protein L7/L12

ProteinName: 50S ribosomal protein L7/L12Ribosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.309155 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #13: protein, Tryptophanase operon leader peptide

ProteinName: Tryptophanase operon leader peptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.899416 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #14: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #15: nucleic-acid, 23S ribosomal RNA

Nucleic-acidName: 23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU UAAUGAGGCG AACCGGGGGA ACUGAAACAU CUAAGUACCC CGAGGAAAAG AAAUCAACCG AGAUUCCCCC AGUAGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGGCGCGCGA UACAGGGUGA CAGCCCCGUA CACAAAAAUG CACAUGCUGU GAGCUCGAUG AGUAGGGCGG GACACGUGGU AUCCUGUCUG AAUAUGGGGG GACCAUCCUC CAAGGCUAAA UACUCCUGAC UGACCGAUAG UGAACCAGUA CCGUGAGGGA AAGGCGAAAA GAACCCCGGC GAGGGGAGUG AAAAAGAACC UGAAACCGUG UACGUACAAG CAGUGGGAGC ACGCUUAGGC GUGUGACUGC GUACCUUUUG UAUAAUGGGU CAGCGACUUA UAUUCUGUAG CAAGGUUAAC CGAAUAGGGG AGCCGAAGGG AAACCGAGUC UUAACUGGGC GUUAAGUUGC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCAUGGGCAG GUUGAAGGUU GGGUAACACU AACUGGAGGA CCGAACCGAC UAAUGUUGAA AAAUUAGCGG AUGACUUGUG GCUGGGGGUG AAAGGCCAAU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAUCCC GACUUACCAA CCCGAUGCAA ACUGCGAAUA CCGGAGAAUG UUAUCACGGG AGACACACGG CGGGUGCUAA CGUCCGUCGU GAAGAGGGAA ACAACCCAGA CCGCCAGCUA AGGUCCCAAA GUCAUGGUUA AGUGGGAAAC GAUGUGGGAA GGCCCAGACA GCCAGGAUGU UGGCUUAGAA GCAGCCAUCA UUUAAAGAAA GCGUAAUAGC UCACUGGUCG AGUCGGCCUG CGCGGAAGAU GUAACGGGGC UAAACCAUGC ACCGAAGCUG CGGCAGCGAC GCUUAUGCGU UGUUGGGUAG GGGAGCGUUC UGUAAGCCUG CGAAGGUGUG CUGUGAGGCA UGCUGGAGGU AUCAGAAGUG CGAAUGCUGA CAUAAGUAAC GAUAAAGCGG GUGAAAAGCC CGCUCGCCGG AAGACCAAGG GUUCCUGUCC AACGUUAAUC GGGGCAGGGU GAGUCGACCC CUAAGGCGAG GCCGAAAGGC GUAGUCGAUG GGAAACAGGU UAAUAUUCCU GUACUUGGUG UUACUGCGAA GGGGGGACGG AGAAGGCUAU GUUGGCCGGG CGACGGUUGU CCCGGUUUAA GCGUGUAGGC UGGUUUUCCA GGCAAAUCCG GAAAAUCAAG GCUGAGGCGU GAUGACGAGG CACUACGGUG CUGAAGCAAC AAAUGCCCUG CUUCCAGGAA AAGCCUCUAA GCAUCAGGUA ACAUCAAAUC GUACCCCAAA CCGACACAGG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUAA CUUCGGGAGA AGGCACGCUG AUAUGUAGGU GAGGUCCCUC GCGGAUGGAG CUGAAAUCAG UCGAAGAUAC CAGCUGGCUG CAACUGUUUA UUAAAAACAC AGCACUGUGC AAACACGAAA GUGGACGUAU ACGGUGUGAC GCCUGCCCGG UGCCGGAAGG UUAAUUGAUG GGGUUAGCGC AAGCGAAGCU CUUGAUCGAA GCCCCGGUAA ACGGCGGCCG UAACUAUAAC GGUCCUAAGG UAGCGAAAUU CCUUGUCGGG UAAGUUCCGA CCUGCACGAA UGGCGUAAUG AUGGCCAGGC UGUCUCCACC CGAGACUCAG UGAAAUUGAA CUCGCUGUGA AGAUGCAGUG UACCCGCGGC AAGACGGAAA GACCCCGUGA ACCUUUACUA UAGCUUGACA CUGAACAUUG AGCCUUGAUG UGUAGGAUAG GUGGGAGGCU UUGAAGUGUG GACGCCAGUC UGCAUGGAGC CGACCUUGAA AUACCACCCU UUAAUGUUUG AUGUUCUAAC GUUGACCCGU AAUCCGGGUU GCGGACAGUG UCUGGUGGGU AGUUUGACUG GGGCGGUCUC CUCCUAAAGA GUAACGGAGG AGCACGAAGG UUGGCUAAUC CUGGUCGGAC AUCAGGAGGU UAGUGCAAUG GCAUAAGCCA GCUUGACUGC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCGGGGAUA ACAGGCUGAU ACCGCCCAAG AGUUCAUAUC GACGGCGGUG UUUGGCACCU CGAUGUCGGC UCAUCACAUC CUGGGGCUGA AGUAGGUCCC AAGGGUAUGG CUGUUCGCCA UUUAAAGUGG UACGCGAGCU GGGUUUAGAA CGUCGUGAGA CAGUUCGGUC CCUAUCUGCC GUGGGCGCUG GAGAACUGAG GGGGGCUGCU CCUAGUACGA GAGGACCGGA GUGGACGCAU CACUGGUGUU CGGGUUGUCA UGCCAAUGGC ACUGCCCGGU AGCUAAAUGC GGAAGAGAUA AGUGCUGAAA GCAUCUAAGC ACGAAACUUG CCCCGAGAUG AGUUCUCCCU GACCCUUUAA GGGUCCUGAA GGAACGUUGA AGACGACGAC GUUGAUAGGC CGGGUGUGUA AGCGCAGCGA UGCGUUGAGC UAACCGGUAC UAAUGAACCG UGAGGCUUAA CCU
MassTheoretical: 941.306188 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #16: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCCUGGCGGC CGUAGCGCGG UGGUCCCACC UGACCCCAUG CCGAACUCAG AAGUGAAACG CCGUAGCGCC GAUGGUAGUG UGGGGUCUCC CCAUGCGAGA GUAGGGAACU GCCAGGCA
MassTheoretical: 38.177762 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #17: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #18: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #19: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #20: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.073234 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #21: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.801598 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #22: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.467367 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #23: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.763165 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #24: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #25: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.45191 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #26: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.877273 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #27: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #28: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.721938 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #29: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.663471 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #30: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.028082 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #31: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.396828 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #32: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #33: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #34: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.546472 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #35: nucleic-acid, Proline tRNA

Nucleic-acidName: Proline tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGGCACGUAG CGCAGCCUGG UAGCGCACCG UCAUGGGGUG UCGGGGGUCG GAGGUUCAAA UCCUCUCGUG CCGACCA
MassTheoretical: 24.876777 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #36: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.47668 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #37: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.896354 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #38: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #39: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.423625 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: KC6

+
Component #40: protein, Titin

ProteinName: Titin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.794193 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #41: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 143 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #42: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #43: ligand, TRYPTOPHAN

LigandName: TRYPTOPHAN / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.204225 kDa

+
Component #44: ligand, water

LigandName: water / Number of Copies: 439 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.926 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 2613

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 301510
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more