[English] 日本語
Yorodumi
- EMDB-8932: Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8932
TitleCryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex
Map dataCryo-EM structure of Mycobacterium smegmatis Cminus ribosome 70S-MPY complex
Sample
  • Complex: 70S-MPY complex
    • RNA: x 3 types
    • Protein or peptide: x 52 types
  • Protein or peptide: x 1 types
Function / homology
Function and homology information


primary metabolic process / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / ribosome ...primary metabolic process / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / cytoplasm
Similarity search - Function
Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosome hibernation promoting factor/RaiA / Ribosomal protein L10 signature. / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 ...Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosome hibernation promoting factor/RaiA / Ribosomal protein L10 signature. / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 / Ribosomal protein L25, long-form / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein L11, bacterial-type / Ribosomal protein S16 signature. / Ribosomal protein S16, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10 / Ribosomal protein L10P / Ribosomal protein L11 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L16 signature 1. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L19 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S20 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S4, bacterial-type / Ribosomal protein L33 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L33 / Ribosomal protein L33 superfamily
Similarity search - Domain/homology
30S ribosomal protein S20 / 50S ribosomal protein L13 / 30S ribosomal protein S9 / Ribosome hibernation promoting factor / Uncharacterized protein / 30S ribosomal protein S16 / 50S ribosomal protein L19 / 30S ribosomal protein S2 / 30S ribosomal protein S15 / 50S ribosomal protein L20 ...30S ribosomal protein S20 / 50S ribosomal protein L13 / 30S ribosomal protein S9 / Ribosome hibernation promoting factor / Uncharacterized protein / 30S ribosomal protein S16 / 50S ribosomal protein L19 / 30S ribosomal protein S2 / 30S ribosomal protein S15 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L18 / 50S ribosomal protein L27 / 50S ribosomal protein L21 / 50S ribosomal protein L25 / 50S ribosomal protein L32 / 30S ribosomal protein S18 1 / 30S ribosomal protein S14 / 50S ribosomal protein L33 2 / 50S ribosomal protein L31 / 50S ribosomal protein L9 / 50S ribosomal protein L34 / 30S ribosomal protein S4 / 50S ribosomal protein L17 / 50S ribosomal protein L3 / 30S ribosomal protein S11 / 50S ribosomal protein L22 / 30S ribosomal protein S6 / 50S ribosomal protein L11 / 50S ribosomal protein L10 / 30S ribosomal protein S12 / 30S ribosomal protein S7 / 30S ribosomal protein S10 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 50S ribosomal protein L2 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 30S ribosomal protein S13 / 50S ribosomal protein L16 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 30S ribosomal protein S5 / 50S ribosomal protein L30 / 50S ribosomal protein L36 / 50S ribosomal protein L15
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) / Mycobacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsLi Y / Sharma MR / Koripella RK / Yang Y / Kaushal PS / Lin Q / Wade JT / Gray TA / Derbyshire KM / Agrawal RK / Ojha AK
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM061576 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI097191 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI107595 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Zinc depletion induces ribosome hibernation in mycobacteria.
Authors: Yunlong Li / Manjuli R Sharma / Ravi K Koripella / Yong Yang / Prem S Kaushal / Qishan Lin / Joseph T Wade / Todd A Gray / Keith M Derbyshire / Rajendra K Agrawal / Anil K Ojha /
Abstract: Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc ...Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc homeostasis are unknown. Here, we show that the C- ribosome in is the exclusive target of a bacterial protein Y homolog, referred to as mycobacterial-specific protein Y (MPY), which binds to the decoding region of the 30S subunit, thereby inactivating the ribosome. MPY binding is dependent on another mycobacterial protein, MPY recruitment factor (MRF), which is induced on zinc depletion, and interacts with C- ribosomes. MPY binding confers structural stability to C- ribosomes, promoting survival of growth-arrested cells under zinc-limiting conditions. Binding of MPY also has direct influence on the dynamics of aminoglycoside-binding pockets of the C- ribosome to inhibit binding of these antibiotics. Together, our data suggest that zinc limitation leads to ribosome hibernation and aminoglycoside resistance in mycobacteria. Furthermore, our observation of the expression of the proteins of C- ribosomes in in a mouse model of infection suggests that ribosome hibernation could be relevant in our understanding of persistence and drug tolerance of the pathogen encountered during chemotherapy of TB.
History
DepositionJul 5, 2018-
Header (metadata) releaseSep 26, 2018-
Map releaseSep 26, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6dzi
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_8932.map.gz / Format: CCP4 / Size: 357 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Mycobacterium smegmatis Cminus ribosome 70S-MPY complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 454 pix.
= 485.78 Å
1.07 Å/pix.
x 454 pix.
= 485.78 Å
1.07 Å/pix.
x 454 pix.
= 485.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.03
Minimum - Maximum-0.17540994 - 0.31266665
Average (Standard dev.)0.0007398391 (±0.008653646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions454454454
Spacing454454454
CellA=B=C: 485.78003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z454454454
origin x/y/z0.0000.0000.000
length x/y/z485.780485.780485.780
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS454454454
D min/max/mean-0.1750.3130.001

-
Supplemental data

-
Sample components

+
Entire : 70S-MPY complex

EntireName: 70S-MPY complex
Components
  • Complex: 70S-MPY complex
    • RNA: 16S rRNA
    • Protein or peptide: CONSERVED PROTEIN DOMAINConservation
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S19
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S18 1Ribosome
    • Protein or peptide: Ribosome hibernation promoting factor
    • Protein or peptide: 30S ribosomal protein S14
    • RNA: 23 S rRNA (3119-MER)
    • RNA: 5S RNA (118-MER)
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L10
    • Protein or peptide: 50S ribosomal protein L11
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33 2Ribosome
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: Uncharacterized protein
  • Protein or peptide: 50S ribosomal protein L31

+
Supramolecule #1: 70S-MPY complex

SupramoleculeName: 70S-MPY complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#53, #55-#56
Details: Mycobacterium smegmatis ribosome (Cminus) 70S-MPY complex
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)

+
Macromolecule #1: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 1 / Details: 16 S RNA / Number of copies: 1
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 490.111719 KDa
SequenceString: UUUGGAGAGU UUGAUCCUGG CUCAGGACGA ACGCUGGCGG CGUGCUUAAC ACAUGCAAGU CGAACGGAAA GGCCCUUUCG GGGGUACUC GAGUGGCGAA CGGGUGAGUA ACACGUGGGU GAUCUGCCCU GCACUUUGGG AUAAGCCUGG GAAACUGGGU C UAAUACCG ...String:
UUUGGAGAGU UUGAUCCUGG CUCAGGACGA ACGCUGGCGG CGUGCUUAAC ACAUGCAAGU CGAACGGAAA GGCCCUUUCG GGGGUACUC GAGUGGCGAA CGGGUGAGUA ACACGUGGGU GAUCUGCCCU GCACUUUGGG AUAAGCCUGG GAAACUGGGU C UAAUACCG AAUACACCCU GCUGGUCGCA UGGCCUGGUA GGGGAAAGCU UUUGCGGUGU GGGAUGGGCC CGCGGCCUAU CA GCUUGUU GGUGGGGUGA UGGCCUACCA AGGCGACGAC GGGUAGCCGG CCUGAGAGGG UGACCGGCCA CACUGGGACU GAG AUACGG CCCAGACUCC UACGGGAGGC AGCAGUGGGG AAUAUUGCAC AAUGGGCGCA AGCCUGAUGC AGCGACGCCG CGUG AGGGA UGACGGCCUU CGGGUUGUAA ACCUCUUUCA GCACAGACGA AGCGCAAGUG ACGGUAUGUG CAGAAGAAGG ACCGG CCAA CUACGUGCCA GCAGCCGCGG UAAUACGUAG GGUCCGAGCG UUGUCCGGAA UUACUGGGCG UAAAGAGCUC GUAGGU GGU UUGUCGCGUU GUUCGUGAAA ACUCACAGCU UAACUGUGGG CGUGCGGGCG AUACGGGCAG ACUAGAGUAC UGCAGGG GA GACUGGAAUU CCUGGUGUAG CGGUGGAAUG CGCAGAUAUC AGGAGGAACA CCGGUGGCGA AGGCGGGUCU CUGGGCAG U AACUGACGCU GAGGAGCGAA AGCGUGGGGA GCGAACAGGA UUAGAUACCC UGGUAGUCCA CGCCGUAAAC GGUGGGUAC UAGGUGUGGG UUUCCUUCCU UGGGAUCCGU GCCGUAGCUA ACGCAUUAAG UACCCCGCCU GGGGAGUACG GCCGCAAGGC UAAAACUCA AAGGAAUUGA CGGGGGCCCG CACAAGCGGC GGAGCAUGUG GAUUAAUUCG AUGCAACGCG AAGAACCUUA C CUGGGUUU GACAUGCACA GGACGCCGGC AGAGAUGUCG GUUCCCUUGU GGCCUGUGUG CAGGUGGUGC AUGGCUGUCG UC AGCUCGU GUCGUGAGAU GUUGGGUUAA GUCCCGCAAC GAGCGCAACC CUUGUCUCAU GUUGCCAGCA CGUUAUGGUG GGG ACUCGU GAGAGACUGC CGGGGUCAAC UCGGAGGAAG GUGGGGAUGA CGUCAAGUCA UCAUGCCCCU UAUGUCCAGG GCUU CACAC AUGCUACAAU GGCCGGUACA AAGGGCUGCG AUGCCGUGAG GUGGAGCGAA UCCUUUCAAA GCCGGUCUCA GUUCG GAUC GGGGUCUGCA ACUCGACCCC GUGAAGUCGG AGUCGCUAGU AAUCGCAGAU CAGCAACGCU GCGGUGAAUA CGUUCC CGG GCCUUGUACA CACCGCCCGU CACGUCAUGA AAGUCGGUAA CACCCGAAGC CGGUGGCCUA ACCCUUGUGG AGGGAGC CG UCGAAGGUGG GAUCGGCGAU UGGGACGAAG UCGUAACAAG GUAGCCGUAC CGGAAGGUGC GGCUGGAUC

+
Macromolecule #23: 23 S rRNA (3119-MER)

MacromoleculeName: 23 S rRNA (3119-MER) / type: rna / ID: 23 / Number of copies: 1
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 1.01183475 MDa
SequenceString: AAGUGUUUAA GGGCGCAUGG UGGAUGCCUU GGCACUGGGA GCCGAUGAAG GACGUAGGAG GCUGCGAUAA GCCUCGGGGA GCUGUCAAC CGAGCGUUGA UCCGAGGAUG UCCGAAUGGG GAAACCCGGC ACGAGUGAUG UCGUGUCACC AGGCGCUGAA U AUAUAGGC ...String:
AAGUGUUUAA GGGCGCAUGG UGGAUGCCUU GGCACUGGGA GCCGAUGAAG GACGUAGGAG GCUGCGAUAA GCCUCGGGGA GCUGUCAAC CGAGCGUUGA UCCGAGGAUG UCCGAAUGGG GAAACCCGGC ACGAGUGAUG UCGUGUCACC AGGCGCUGAA U AUAUAGGC GUCUGGGGGG AACGCGGGGA AGUGAAACAU CUCAGUACCC GUAGGAAGAG AAAACAAAAU GUGAUUCCGU GA GUAGUGG CGAGCGAAAG CGGAGGAUGG CUAAACCGUA UGCAUGUGAU ACCGGGUAGG GGUUGUGUGU GCGGGGUUGU GGG ACCUAU CUUUCCGGCU CUACCUGGCU GGAGGGCAGU GAGAAAAUGU UGUGGUUAGC GGAAAUGGCU UGGGAUGGCC UGCC GUAGA CGGUGAGAGC CCGGUACGUG AAAACCCGAC GUCUGUCUUG AUGGUGUUCC CGAGUAGCAG CGGGCCCGUG GAAUC UGCU GUGAAUCUGC CGGGACCACC CGGUAAGCCU GAAUACUUCC CAGUGACCGA UAGCGGAUUA GUACCGUGAG GGAAUG GUG AAAAGUACCC CGGGAGGGGA GUGAAAGAGU ACCUGAAACC GUGCGCUUAC AAUCCGUCAG AGCCCUCGAC GUGUCGU GG GGUGAUGGCG UGCCUUUUGA AGAAUGAGCC UGCGAGUCAG GGACAUGUCG CGAGGUUAAC CCGGGUGGGG UAGCCGCA G CGAAAGCGAG UCUGAAUAGG GCGUAUCCAC ACAAGAGUGU GUGGUGUAGU GGUGUGUUCU GGACCCGAAG CGGAGUGAU CUACCCAUGG CCAGGGUGAA GCGCGGGUAA GACCGCGUGG AGGCCCGAAC CCACUUAGGU UGAAGACUGA GGGGAUGAGC UGUGGGUAG GGGUGAAAGG CCAAUCAAAC UCCGUGAUAG CUGGUUCUCC CCGAAAUGCA UUUAGGUGCA GCGUCGCAUG U UUCUUGCC GGAGGUAGAG CUACUGGAUG GCCGAUGGGC CCCACAGGGU UACUGACGUC AGCCAAACUC CGAAUGCCGG UA AGUCCAA GAGUGCGGCA GUGAGACGGC GGGGGAUAAG CUCCGUGCGU CGAGAGGGAA ACAGCCCAGA UCGCCGGCUA AGG CCCCUA AGCGUGUGCU AAGUGGAAAA GGAUGUGCAG UCGCGAAGAC AACCAGGAGG UUGGCUUAGA AGCAGCCACC CUUG AAAGA GUGCGUAAUA GCUCACUGGU CAAGUGAUUG UGCGCCGAUA AUGUAGCGGG GCUCAAGCAC ACCGCCGAAG CCGCG GCAG CCAACGUGUU GGCUGGGUAG GGGAGCGUCC UGCAUCCGGU GAAGCCGCCG AGUGAUCGAG UGGUGGAGGG UGUGGG AGU GAGAAUGCAG GCAUGAGUAG CGAUUAGGCA AGUGAGAACC UUGCCCGCCG AAAGACCAAG GGUUCCUGGG CCAGGCC AG UCCGCCCAGG GUGAGUCGGG ACCUAAGGCG AGGCCGACAG GCGUAGUCGA UGGACAACGG GUUGAUAUUC CCGUACCC G UGUAUGUGCG UCCAUGAUGA AUCAGCGGUA CUAACCAUCC AAAACCACCG UGACCGCACC UUUCGGGGUG UGGCGUUGG UGGGGCUGCA UGGGACCUUC GUUGGUAGUA GUCAAGCGAU GGGGUGACGC AGGAAGGUAG CCGUACCGGU CAGUGGUAAU ACCGGGGUA AGCCUGUAGG GAGUCAGAUA GGUAAAUCCG UCUGGCAUAU AUCCUGAGAG GUGAUGCAUA GCCGAGUGAG G CGAAUUCG GUGAUCCUAU GCUGCCGAGA AAAGCCUCUA GCGAGGACAU ACACGGCCCG UACCCCAAAC CAACACAGGU GG UCAGGUA GAGAAUACUA AGGCGUACGA GUGAACUAUG GUUAAGGAAC UCGGCAAAAU GCCCCCGUAA CUUCGGGAGA AGG GGGACC CACAUGGCGU GUAAGCCUUU ACGGCCCAAG CGUGAGUGGG UGGCACAAAC CAGUGAGAAG CGACUGUUUA CUAA AAACA CAGGUCCGUG CGAAGUCGCA AGACGAUGUA UACGGACUGA CGCCUGCCCG GUGCUGGAAG GUUAAGAGGA CCCGU UAAC UCCCUUUGGG GGUGAAGCGG AGAAUUUAAG CCCCAGUAAA CGGCGGUGGU AACUAUAACC AUCCUAAGGU AGCGAA AUU CCUUGUCGGG UAAGUUCCGA CCUGCACGAA UGGCGUAACG ACUUCUCAAC UGUCUCAACC AUAGACUCGG CGAAAUU GC ACUACGAGUA AAGAUGCUCG UUACGCGCGG CAGGACGAAA AGACCCCGGG ACCUUCACUA CAACUUGGUA UUGGUGCU C GAUACGGUUU GUGUAGGAUA GGUGGGAGAC UGUGAAGCUC ACACGCCAGU GUGGGUGGAG UCGUUGUUGA AAUACCACU CUGAUCGUAU UGGGCCUCUA ACCUCGGACC GUAUAUCCGG UUCAGGGACA GUGCCUGGUG GGUAGUUUAA CUGGGGCGGU UGCCUCCUA AAAUGUAACG GAGGCGCCCA AAGGUUCCCU CAACCUGGAC GGCAAUCAGG UGUUGAGUGU AAGUGCACAA G GGAGCUUG ACUGCGAGAC GGACAUGUCG AGCAGGGACG AAAGUCGGGA CUAGUGAUCC GGCACCUCUG AGUGGAAGGG GU GUCGCUC AACGGAUAAA AGGUACCCCG GGGAUAACAG GCUGAUCUUC CCCAAGAGUC CAUAUCGACG GGAUGGUUUG GCA CCUCGA UGUCGGCUCG UCGCAUCCUG GGGCUGGAGC AGGUCCCAAG GGUUGGGCUG UUCGCCCAUU AAAGCGGCAC GCGA GCUGG GUUUAGAACG UCGUGAGACA GUUCGGUCUC UAUCCGCCGC GCGCGUCAGA AGCUUGAGGA AACCUGUCCC UAGUA CGAG AGGACCGGGA CGGACGAACC UCUGGUAUAC CAGUUGUCCC ACCAGGGGCA CGGCUGGAUA GCCACGUUCG GACAGG AUA ACCGCUGAAA GCAUCUAAGC GGGAAACCUC UUCCAAGACC AGGCUUCUCA CCCUCUAGGA GGGAUAAGGC CCCCCGC AG ACCACGGGAU UGAUAGACCA GACCUGGAAG CCUAGUAAUA GGUGCAGGGA ACUGGCACUA ACCGGCCGAA AACUUAC

+
Macromolecule #24: 5S RNA (118-MER)

MacromoleculeName: 5S RNA (118-MER) / type: rna / ID: 24 / Number of copies: 1
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 38.061816 KDa
SequenceString:
GUUACGGCGG UCCAUAGCGG CAGGGAAACG CCCGGUCCCA UCCCGAACCC GGAAGCUAAG CCUGCCAGCG CCGAUGAUAC UACCCAUCC GGGUGGAAAA GUAGGACACC GCCGAACAC

+
Macromolecule #2: CONSERVED PROTEIN DOMAIN

MacromoleculeName: CONSERVED PROTEIN DOMAIN / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 4.033104 KDa
SequenceString:
GSVIKKRRKR MSKKKHRKLL RRTRVQRRKL GK

+
Macromolecule #3: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 23.61715 KDa
SequenceString: GQKINPHGFR LGITTEWKSR WYADKQYKDY VKEDVAIRKL LATGLERAGI ADVEIERTRD RVRVDIHTAR PGIVIGRRGT EADRIRADL EKLTGKQVQL NILEVKNPES QAQLVAQGVA EQLSNRVAFR RAMRKAIQSA MRQPNVKGIR VQCSGRLGGA E MSRSEFYR ...String:
GQKINPHGFR LGITTEWKSR WYADKQYKDY VKEDVAIRKL LATGLERAGI ADVEIERTRD RVRVDIHTAR PGIVIGRRGT EADRIRADL EKLTGKQVQL NILEVKNPES QAQLVAQGVA EQLSNRVAFR RAMRKAIQSA MRQPNVKGIR VQCSGRLGGA E MSRSEFYR EGRVPLHTLR ADIDYGLYEA KTTFGRIGVK VWIYKGDIVG

+
Macromolecule #4: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 23.28459 KDa
SequenceString: ARYTGPATRK SRRLGVDLVG GDQSFEKRPY PPGQHGRARI KESEYRQQLQ EKQKARFSYG VMEKQFRRYY EEANRQPGKT GDNLLRILE SRLDNVVYRA GLARTRRMAR QLVSHGHFLV NGVKVDIPSY RVSQYDIIDV KEKSLNTLPF QIARETAGER P IPSWLQVV ...String:
ARYTGPATRK SRRLGVDLVG GDQSFEKRPY PPGQHGRARI KESEYRQQLQ EKQKARFSYG VMEKQFRRYY EEANRQPGKT GDNLLRILE SRLDNVVYRA GLARTRRMAR QLVSHGHFLV NGVKVDIPSY RVSQYDIIDV KEKSLNTLPF QIARETAGER P IPSWLQVV GERQRILVHQ LPERAQIDVP LTEQLIVELY SK

+
Macromolecule #5: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 18.481439 KDa
SequenceString:
NYIERVVSIN RVSKVVKGGR RFSFTALVIV GDGKGMVGVG YGKAKEVPAA IAKGVEEARK NFFRVPLIGS TITHPVQGEA AAGVVMLRP ASPGTGVIAG GAARAVLECA GVHDILAKSL GSDNAINVVH ATVAALKLLQ RPEEVAARRG LPIEDVAPAG M LKARRESE ALAAAAAREG SA

+
Macromolecule #6: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (bacteria)
Molecular weightTheoretical: 10.991637 KDa
SequenceString:
MRPYEIMVIL DPTLDERTVA PSLETFLNVI RKDGGTVDKV DIWGRRRLAY EIAKHAEGIY AVIDVKAEPA TVSELDRQLN LNESVLRTK VLRTDKH

+
Macromolecule #7: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 17.52918 KDa
SequenceString:
PRKGPAPKRP LVNDPVYGSQ LVTQLVNKVL LEGKKSLAER IVYGALEQAR EKTGTDPVVT LKRALDNVKP ALEVRSRRVG GATYQVPVE VRPDRSTTLA LRWLVNFSRQ RREKTMVERL ANEILDASNG LGASVKRRED THKMAEANRA FAHYRW

+
Macromolecule #8: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.361442 KDa
SequenceString:
TMTDPIADFL TRLRNANSAY HDEVTLPHSK LKANIAEILK REGYISDYRT EDARVGKSLV VQLKYGPSRE RSIAGLRRVS KPGLRVYAK STNLPRVLGG LGVAIISTSS GLLTDRQAAR QGVGGEVLAY VW

+
Macromolecule #9: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.093392 KDa
SequenceString:
PIQTVGRRKE AVVRVRLVPG TGQFNLDGRT LENYFPNKVH QQLIKAPLVT VDRVDQFDIY AHLDGGGPSG QAGALRLAIA RALILVQPE DRPALKKAGF LTRDPRAIER KKYGLKKARK APQYSKR

+
Macromolecule #10: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.252039 KDa
SequenceString:
GQKIRIRLKA YDHEAIDASA RKIVETVTRT GASVVGPVPL PTEKNVYCVI RSPHKYKDSR EHFEMRTHKR LIDILDPTPK TVDALMRID LPASVDVNIQ

+
Macromolecule #11: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 12.151729 KDa
SequenceString:
KNVPHGAAHI KSTFNNTIVS ITDPQGNVIA WASSGHVGFK GSRKSTPFAA QLAAENAARK AQEHGVKKVD VFVKGPGSGR ETAIRSLQA AGLEVGTISD VTPQPHNGCR PPKRRR

+
Macromolecule #12: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.678093 KDa
SequenceString:
PTIQQLVRKG RRDKIAKVKT AALKGSPQRR GVCTRVYTTT PKKPNSALRK VARVKLTSQV EVTAYIPGEG HNLQEHSMVL VRGGRVKDL PGVRYKIIRG SLDTQGVKNR KQARSRYGAK KEK

+
Macromolecule #13: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.374481 KDa
SequenceString:
ARLVGVDLPR DKRMEIALTY IYGIGRTRSN EILAATGIDK NMRTKDLTDD QVTVLRDYIE GNLKVEGDLR REVQADIRRK IEIGCYQGL RHRRGLPVRG QRTKTNARTR KGPKRTI

+
Macromolecule #14: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 10.2369 KDa
SequenceString:
ALTAEQKKEI LGQYGLHDTD TGSPEAQVAL LTKRIQDLTE HLKVHKHDHH SRRGLLLLVG RRRRLLKYVA QVDVARYRSL IERLGLRR

+
Macromolecule #15: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 12.635652 KDa
SequenceString:
AVKIKLTRLG KIRNPQYRII VADARTRRDG RAIEVIGRYH PKEEPSLIQI DSERAQYWLG VGAQPTEPVL ALLKITGDWQ KFKGLPGAE GTLKVKEPKP SKLDLFNAAL AEAE

+
Macromolecule #16: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 10.680461 KDa
SequenceString:
QKGPKYTPAA EKPRGRRKTA IGYVVSDKMQ KTIVVELEDR KSHPLYGKII RTTKKVKAHD ENGEAGIGDR VSLMETRPLS ATKRWRLVE ILEKA

+
Macromolecule #17: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.379874 KDa
SequenceString:
PRSLKKGPFV DDHLLKKVDV QNEKNTKQVI KTWSRRSTII PDFIGHTFAV HDGRKHVPVF VTEAMVGHKL GEFAPTRTFK GH

+
Macromolecule #18: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.424908 KDa
SequenceString:
ANIKSQIKRI RTNERRRLRN QSVKSSLRTA IRGFREAVDA GDKDKASELL HATSRKLDKA ASKGVIHPNQ AANKKSALAL ALNKL

+
Macromolecule #19: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 25.576547 KDa
SequenceString: MAVVTMKQLL DSGAHFGHQT RRWNPKMKRF IFTDRNGIYI IDLQQTLTYI DKAYEFVKET VAHGGTVLFV GTKKQAQESI AEEATRVGM PYVNQRWLGG MLTNFSTVHK RLQRLKELEA MEQTGGFEGR TKKEILMLTR EKNKLERSLG GIRDMQKVPS A VWVVDTNK ...String:
MAVVTMKQLL DSGAHFGHQT RRWNPKMKRF IFTDRNGIYI IDLQQTLTYI DKAYEFVKET VAHGGTVLFV GTKKQAQESI AEEATRVGM PYVNQRWLGG MLTNFSTVHK RLQRLKELEA MEQTGGFEGR TKKEILMLTR EKNKLERSLG GIRDMQKVPS A VWVVDTNK EHIAVGEARK LGIPVIAILD TNCDPDVVDY PIPGNDDAIR SAALLTKVIA SAVAEGLQAR

+
Macromolecule #20: 30S ribosomal protein S18 1

MacromoleculeName: 30S ribosomal protein S18 1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.449175 KDa
SequenceString:
MMAVKKSRKR TAATELKKPR RNQLEALGVT TIDYKDVAVL RTFLSERGKI RSRHVTGLTP QQQRQVATAI KNAREMALLP MAGP

+
Macromolecule #21: Ribosome hibernation promoting factor

MacromoleculeName: Ribosome hibernation promoting factor / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 12.238882 KDa
SequenceString:
ERPHAEVVVK GRNVEVPDHF RTYVSEKLSR LERFDKTIYL FDVELDHERN RRQRKNCQHV EITARGRGPV VRGEACADSF YTAFESAVQ KLEGRLRRAK DRRK

+
Macromolecule #22: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.66153 KDa
SequenceString:
AKKSKIVKNE QRRELVQRYA ERRAELKRTI RDPASSPERR AAAVSALQRL PRDSSPVRLR NRDVVDGRPR GHLRKFGLSR VRVREMAHR GELPGVRKAS W

+
Macromolecule #25: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 30.008379 KDa
SequenceString: GIRKYKPTTP GRRGASVSDF AEITRSTPEK SLVRPLHGKG GRNAHGRITT RHKGGGHKRA YRVIDFRRHD KDGVNAKVAH IEYDPNRTA NIALLHYLDG EKRYIIAPQG LKQGDVIESG ANADIKPGNN LPLRNIPAGT VIHAVELRPG GGAKLARSAG V SIQLLGKE ...String:
GIRKYKPTTP GRRGASVSDF AEITRSTPEK SLVRPLHGKG GRNAHGRITT RHKGGGHKRA YRVIDFRRHD KDGVNAKVAH IEYDPNRTA NIALLHYLDG EKRYIIAPQG LKQGDVIESG ANADIKPGNN LPLRNIPAGT VIHAVELRPG GGAKLARSAG V SIQLLGKE GTYAALRMPS GEIRRVDVRC RATVGEVGNA EQSNINWGKA GRMRWKGKRP TVRGVVMNPV DHPHGGGEGK TS GGRHPVS PWGKPEGRTR KPNKPSDKLI VRRRRTGK

+
Macromolecule #26: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 22.621902 KDa
SequenceString: ARKGILGTKL GMTQVFDENN KVVPVTVVKA GPNVVTRIRT TERDGYSAVQ LAYGEISPRK VIKPVAGQFA AAGVNPRRHV AELRLDDEA AVAEYEVGQE LTAEIFSDGA YVDVTGTSKG KGFAGTMKRH GFRGQGAAHG AQAVHRRPGS IGGCATPGRV F KGTRMSGR ...String:
ARKGILGTKL GMTQVFDENN KVVPVTVVKA GPNVVTRIRT TERDGYSAVQ LAYGEISPRK VIKPVAGQFA AAGVNPRRHV AELRLDDEA AVAEYEVGQE LTAEIFSDGA YVDVTGTSKG KGFAGTMKRH GFRGQGAAHG AQAVHRRPGS IGGCATPGRV F KGTRMSGR MGNDRVTTQN LKVHKVDAEN GVLLIKGAIP GRNGGLVVVR SAIKRG

+
Macromolecule #27: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 22.346301 KDa
SequenceString: TLKVDVKTPA GKTDGSVELP AELFDVEPNI ALMHQVVTAQ LAAKRQGTHS TKTRGEVSGG GKKPYRQKGT GRARQGSTRA PQFTGGGTV HGPKPRDYSQ RTPKKMIAAA LRGALSDRAR NDRIHAVTEL VEGQTPSTKS AKTFLGTLTE NKKVLVVIGR T DEVGAKSV ...String:
TLKVDVKTPA GKTDGSVELP AELFDVEPNI ALMHQVVTAQ LAAKRQGTHS TKTRGEVSGG GKKPYRQKGT GRARQGSTRA PQFTGGGTV HGPKPRDYSQ RTPKKMIAAA LRGALSDRAR NDRIHAVTEL VEGQTPSTKS AKTFLGTLTE NKKVLVVIGR T DEVGAKSV RNLPGVHVIS PDQLNTYDVL NADDVVFSVE ALNAYISANS K

+
Macromolecule #28: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 20.588701 KDa
SequenceString:
KALPRLKQRY REEIREALQQ EFNYANVMQI PGVVKVVVNM GVGDAARDAK LINGAINDLA LITGQKPEVR RARKSIAQFK LREGMPIGA RVTLRGDRMW EFLDRLISIA LPRIRDFRGL SPKQFDGTGN YTFGLNEQSM FHEIDVDSID RPRGMDITVV T TATNDAEG RALLRALGFP FKEN

+
Macromolecule #29: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 19.165934 KDa
SequenceString:
SRIGKQPVPV PSGVDVTING QNLSVKGPKG TLTLDVAEPI SVSRAEDGAI VVTRPDDERR SRSLHGLSRT LIANLVTGVT EGYTQKMEI FGVGYRVQLK GQNLEFALGY SHPVLIEAPE GITFAVESPT KFSVSGIDKQ KVGQISAVIR RLRRPDPYKG K GVRYEGEQ IRRKVGKT

+
Macromolecule #30: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 15.949253 KDa
SequenceString:
MKLILTAEVE HLGAAGDTVE VKDGYGRNYL LPRGLAIVAS RGAERQAEEI RRARESKVIR DIEHANELKT ALEGLGDVTL SVNAAGDTG KLFGSVTAAD VVNAIKKAGG PNLDKRTVQL AKAHIKSVGT HPVTVKLHTG VEAKVSLNVV AQ

+
Macromolecule #31: 50S ribosomal protein L10

MacromoleculeName: 50S ribosomal protein L10 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.095021 KDa
SequenceString:
MAKADKATAV ADIAEQFKAS TATVVTEYRG LTVANLAELR RALGDSATYT VAKNTLVKRA ASEAGIEGLD ELFAGPTAIA FVKGEAVDA AKAIKKFAKD NKALVIKGGY MDGKALSVAD VEKIADL

+
Macromolecule #32: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.109185 KDa
SequenceString:
LIKLQIQAGQ ANPAPPVGPA LGQHGVNIME FCKAYNAATE SQRGNVIPVE ITVYEDRSFT FALKTPPAAK LLLKAAGVQK GSGEPHKTK VAKVTWDQVR EIAETKKADL NANDIDAAAK IIAGTARSMG ITVE

+
Macromolecule #33: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 16.015493 KDa
SequenceString:
PTYTPKAGDT TRSWYVIDAS DVVLGRLASA AATLLRGKHK PTFTPNVDGG DFVIVINADK IAVSGDKLTK KFAYRHSGYP GGLRKRTIG ELLEKHPTRV VENAIIGMLP HNKLGRQIQK KLKVYAGPDH PHAAQQPIPF EIKQVAQ

+
Macromolecule #34: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.400625 KDa
SequenceString:
MIQQESRLKV ADNTGAKEIL CIRVLGGSSR RYAGIGDVIV ATVKDAIPGG NVKRGDVVKA VVVRTVKERR RADGSYIKFD ENAAVIIKN DNDPRGTRIF GPVGRELREK KFMKIVSLAP EVL

+
Macromolecule #35: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 15.383968 KDa
SequenceString:
VIKLHDLKPA PGEKKAKTRV GRGEGSKGKT AGRGTKGTKA RKNVPVMFEG GQMPIHMRLP KLKGFKNRFR TEYQVVNVGD INKAFPQGG TVGVDELVAK GLVRKNSLVK VLGDGKLTVK VDVTANKFSG SAREAITAAG GSATEL

+
Macromolecule #36: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 15.498937 KDa
SequenceString:
MLIPRKVKHR KQHHPEQRGI ASGGTSVSFG DYGIQALEHA YITNRQIESA RIAINRHIKR GGKVWINIFP DRPLTKKPAE TRMGSGKGS PEWWVANVKP GRVLFELSYP DEKTARDALT RAIHKLPIKA RIVTREE

+
Macromolecule #37: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.210346 KDa
SequenceString:
PKPTKGPRLG GSSSHQSALL ANLATSLFEH GRIKTTEPKA RALRPYAEKL ITHAKKGALH NRREVMKKIR DKDVVHTLFA EIGPFYADR NGGYTRIIKV ENRKGDNAPM AVIELVREK

+
Macromolecule #38: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.580531 KDa
SequenceString:
AHKPVGQNIS EVRRNARLRR HARLRKKVAG TAEVPRLVVN RSARHIHVQL VNDLNGTTLA AASSIEADVR AIDGDKKAHS VRVGQLIAE RAKAAGVETV VFDRGGYTYG GRIAALADAA REAGLKF

+
Macromolecule #39: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 12.892806 KDa
SequenceString:
MNTLDFVDQA SLRDDIPTFS PGDTVNVHVK VIEGSKERIQ VFKGVVIRRQ GGGISETFTV RKESYGVGVE RTFPVHSPNI DHIDVLTRG DVRRAKLYYL RELRGKKAKI KEKR

+
Macromolecule #40: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 14.035175 KDa
SequenceString:
ARVKRALNAQ KKRRTVLKAS KGYRGQRSRL YRKAKEQQLH SLTYAYRDRR ARKGEFRKLW ISRINAAARA NDITYNRLIQ GLKAAGVEV DRKNLAELAV SDPAAFTALV DVARAALPED VNAPS

+
Macromolecule #41: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 10.72444 KDa
SequenceString:
TYAIVKTGGK QYKVAAGDVV KVEKLDSEPG ASVSLPVALV VDGANVTSKA DDLAKVAVTA EVLEHTKGPK IRIHKFKNKT GYHKRQGHR QQLTVLKVTG I

+
Macromolecule #42: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 12.408192 KDa
SequenceString:
EFPSATAKAR YVRVSATKAR RVIDLVRGKS VEEALDILRW APQAASEPVA KVIASAAANA QNNEGLDPST LVVATVYADE GPTAKRIRP RAQGRAFRIR KRTSHITVIV ESRPP

+
Macromolecule #43: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 43 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 10.748448 KDa
SequenceString:
ATITDPRDII LAPVISEKSY GLIEDNVYTF VVHPDSNKTQ IKIAIEKIFD VKVDSVNTAN RQGKRKRTRT GFGKRKSTKR AIVKLAAGS KPIDLFGA

+
Macromolecule #44: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 44 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.228946 KDa
SequenceString:
MKVHKGDTVL VISGKDKGAK GKVLVAYPDR NKVLVEGVNR IKKHTAVSAN ERGASSGGIV TQEAPIHVSN VMVVDSDGKP TRVGYRIDD ETGKKVRIAK TNGKDI

+
Macromolecule #45: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 45 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 20.331725 KDa
SequenceString: TANIPNKLTA NVRTRTGKGA SRQARRDGKV PAVLYGHGTD PQHLELNARD FAAVLRSHGT NAILTLDIEG TEQLALTKAL DVHPIRRNI QHADLLVVQR GEKVTVEVTV LVEGDATPGT LVTQDANTIE IEAEALSIPE QLTVSVEGVE AGTQITAGQI S LPEGVNLI ...String:
TANIPNKLTA NVRTRTGKGA SRQARRDGKV PAVLYGHGTD PQHLELNARD FAAVLRSHGT NAILTLDIEG TEQLALTKAL DVHPIRRNI QHADLLVVQR GEKVTVEVTV LVEGDATPGT LVTQDANTIE IEAEALSIPE QLTVSVEGVE AGTQITAGQI S LPEGVNLI SDPELLVVNV VEAPSAEALE EEGA

+
Macromolecule #46: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 46 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 8.322479 KDa
SequenceString:
SSSRNGRDSA AQRLGVKRFG GQVVKAGEIL VRQRGTHFHP GVNVGRGGDD TLFALAPGAV EFGAKRGRKT VNIVPVARP

+
Macromolecule #47: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 47 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 7.590576 KDa
SequenceString:
GTTPGELREL TDDELKDKLR ESKEELFNLR FQMATGQLSN NRRLRTVRQE IARVYTVLRE RELG

+
Macromolecule #48: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 48 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 6.761772 KDa
SequenceString:
AELKITQVRS TIGARWKQRE SLRTLGLKKI RQSVVREDNA QTRGLINTVH HLVEVEEVG

+
Macromolecule #49: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 49 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 6.050149 KDa
SequenceString:
AVPKRRMSRA NTRSRRAQWK AEAPGLVTVS VAGQQRKVPR RLLKAARLGL VDLD

+
Macromolecule #50: 50S ribosomal protein L33 2

MacromoleculeName: 50S ribosomal protein L33 2 / type: protein_or_peptide / ID: 50 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 6.484445 KDa
SequenceString:
ARNEIRPIVK LRSTAGTGYT YVTRKNRRND PDRIVLRKYD PVLRRHVEFR EER

+
Macromolecule #51: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 51 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 5.391384 KDa
SequenceString:
AKGKRTFQPN NRRRARVHGF RLRMRTRAGR AIVANRRSKG RRALTA

+
Macromolecule #52: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 52 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 7.16731 KDa
SequenceString:
PKAKTHSGAS KRFRRTGTGK IVRQKANRRH LLEHKPTKRT RRLDGRTTVS AADNSRINKL LNG

+
Macromolecule #53: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 53 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 4.341277 KDa
SequenceString:
MKVNPSVKPI CDKCRVIRRH GRVMVICSDP RHKQRQG

+
Macromolecule #54: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 54 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 9.141198 KDa
SequenceString:
MKPGIHPDYH PVVFQDAATG AQFLTRSTAT STRTIEWPTP SGPKTYPLIV VDVTSDSHPF WTGSARHIDS AGQVEKFRRR YG

+
Macromolecule #55: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 55 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 8.794038 KDa
SequenceString:
SAHCQVTGRG PGFGNSVSHS HRRTPRRWDP NIQNKTYYLP SEGRRIRLRV SAKGIKVIDR DGIEAVVARM RARGEKY

+
Macromolecule #56: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 56 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 2.710179 KDa
SequenceString:
AKRGRKKRDR KHSKANHGKR PNA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 67.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 205510
CTF correctionSoftware - Name: RELION (ver. 2.01)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 10 / Avg.num./class: 66840 / Software - Name: RELION (ver. 2.01)
Software - details: Relion used for image processing and Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 66840
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6dzi:
Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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