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- EMDB-10891: Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms ... -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-10891

Title

Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms with modeled GBC SecM peptide

Map data

Sample

Complex: 50S ribosomal + GBC SecM peptide complex
- Complex: 50S ribosomal
  - Protein or peptide: x 28 types
  - RNA: x 3 types
- Complex: GBC SecM peptide complex
  - Protein or peptide: x 1 types

Keywords

translation 50S ribosome nascent peptide chain / RIBOSOME

Function / homology

Function and homology information

structural constituent of eye lens / lens development in camera-type eye / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...
Similarity search - Function

Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / : / Ribosomal protein L25, short-form / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site ...Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / : / Ribosomal protein L25, short-form / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / 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 L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / : / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site
Similarity search - Domain/homology

Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL5 ...Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL15 / Gamma-crystallin B / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component

Biological species

Escherichia coli BL21(DE3) (bacteria) /

Bos taurus (domestic cattle)

Method

single particle reconstruction / cryo EM / Resolution: 2.58 Å

Authors

Schulte L / Reitz J

Citation

Journal: Nat Commun / Year: 2020
Title: Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.
Authors: Linda Schulte / Jiafei Mao / Julian Reitz / Sridhar Sreeramulu / Denis Kudlinzki / Victor-Valentin Hodirnau / Jakob Meier-Credo / Krishna Saxena / Florian Buhr / Julian D Langer / Martin ...
Abstract: Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide ...

History

Deposition	Apr 20, 2020	-
Header (metadata) release	Sep 30, 2020	-
Map release	Sep 30, 2020	-
Update	Oct 16, 2024	-
Current status	Oct 16, 2024	Processing site: PDBe / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.01 Imaged by UCSF Chimera Download Surface view colored by height Surface level: 0.01 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-6ys3 Surface level: 0.01 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_10891.png

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Downloads & links

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EMDB archive

Map data	emd_10891.map.gz	337.8 MB		EMDB map data format
Header (meta data)	emd-10891-v30.xml emd-10891.xml	53 KB 53 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_10891_fsc.xml	16.9 KB	Display	FSC data file
Images	emd_10891.png	257.4 KB
Masks	emd_10891_msk_1.map	421.9 MB		Mask map
Filedesc metadata	emd-10891.cif.gz	10.6 KB
Others	emd_10891_half_map_1.map.gz emd_10891_half_map_2.map.gz	338.2 MB 338.3 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-10891 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10891	HTTPS FTP

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Validation report

Summary document	emd_10891_validation.pdf.gz	985.6 KB	Display	EMDB validaton report
Full document	emd_10891_full_validation.pdf.gz	985.1 KB	Display
Data in XML	emd_10891_validation.xml.gz	23.8 KB	Display
Data in CIF	emd_10891_validation.cif.gz	31.8 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10891 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10891	HTTPS FTP

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Related structure data

Related structure data	6ys3MC 4531C 6qdwC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	8114 21626 22465 21641 3285 22461 22468 22464 21631 4126 10683 4125 22459 8280 6584 8596 6485 6486 1003 8815 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource
Related items in Molecule of the Month	#253 - Jan 2021 Expressome similarity (42) #157 - Jan 2013 Transfer-Messenger RNA similarity (42) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (40) #127 - Jul 2010 Crystallins similarity (6) #121 - Jan 2010 70S Ribosomes similarity (8)

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Map

File

Download / File: emd_10891.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Projections & slices

Image control

Size
Brightness
Contrast
Others	InvertY flip

Axes	Z (Sec.)	Y (Row.)	X (Col.)
	1.05 Å/pix. x 480 pix. = 504. Å	1.05 Å/pix. x 480 pix. = 504. Å	1.05 Å/pix. x 480 pix. = 504. Å
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider.

Voxel size

X=Y=Z: 1.05 Å

Density

Histogram

Histogram (log scale)

Contour Level	By AUTHOR: 0.00741 / Movie #1: 0.01
Minimum - Maximum	-0.034037817 - 0.1089806
Average (Standard dev.)	-0.00003998832 (±0.0029740361)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	480	480	480
Spacing	480	480	480

Cell

A=B=C: 503.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.05	1.05	1.05
M x/y/z	480	480	480
origin x/y/z	0.000	0.000	0.000
length x/y/z	504.000	504.000	504.000
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	480	480	480
D min/max/mean	-0.034	0.109	-0.000

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Supplemental data

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Mask #1

File

emd_10891_msk_1.map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

File

emd_10891_half_map_1.map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

File

emd_10891_half_map_2.map

Projections & Slices

Axes	Z	Y	X
Projections
Slices (1/2)

Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 50S ribosomal + GBC SecM peptide complex

Entire	Name: 50S ribosomal + GBC SecM peptide complex
Components	Complex: 50S ribosomal + GBC SecM peptide complex Complex: 50S ribosomal Protein or peptide: 50S ribosomal protein L28 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 Protein or peptide: 50S ribosomal protein L34 Protein or peptide: 50S ribosomal protein L35 Protein or peptide: 50S ribosomal protein L36 RNA: 5S rRNA RNA: 23S rRNA 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 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 RNA: glycine-tRNA glyT Protein or peptide: 50S ribosomal protein L25 Protein or peptide: 50S ribosomal protein L27 Complex: GBC SecM peptide complex Protein or peptide: Gamma-crystallin B

Entire

Name: 50S ribosomal + GBC SecM peptide complex

Components

Complex: 50S ribosomal + GBC SecM peptide complex
- Complex: 50S ribosomal
  - Protein or peptide: 50S ribosomal protein L28
  - 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
  - Protein or peptide: 50S ribosomal protein L34
  - Protein or peptide: 50S ribosomal protein L35
  - Protein or peptide: 50S ribosomal protein L36
  - RNA: 5S rRNA
  - RNA: 23S rRNA
  - 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 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
  - RNA: glycine-tRNA glyT
  - Protein or peptide: 50S ribosomal protein L25
  - Protein or peptide: 50S ribosomal protein L27
- Complex: GBC SecM peptide complex
  - Protein or peptide: Gamma-crystallin B

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Supramolecule #1: 50S ribosomal + GBC SecM peptide complex

Supramolecule	Name: 50S ribosomal + GBC SecM peptide complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32

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Supramolecule #2: 50S ribosomal

Supramolecule	Name: 50S ribosomal / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#31
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #3: GBC SecM peptide complex

Supramolecule	Name: GBC SecM peptide complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #32
Source (natural)	Organism: Bos taurus (domestic cattle)

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Macromolecule #1: 50S ribosomal protein L28

Macromolecule	Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 9.027551 KDa
Sequence	String: MSRVCQVTGK RPVTGNNRSH ALNATKRRFL PNLHSHRFWV ESEKRFVTLR VSAKGMRVID KKGIDTVLAE LRARGEKY UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #2: 50S ribosomal protein L29

Macromolecule	Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 7.286464 KDa
Sequence	String: MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #3: 50S ribosomal protein L30

Macromolecule	Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 6.55482 KDa
Sequence	String: MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #4: 50S ribosomal protein L32

Macromolecule	Name: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 6.463445 KDa
Sequence	String: MAVQQNKPTR SKRGMRRSHD ALTAVTSLSV DKTSGEKHLR HHITADGYYR GRKVIAK UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #5: 50S ribosomal protein L33

Macromolecule	Name: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 6.388631 KDa
Sequence	String: MAKGIREKIK LVSSAGTGHF YTTTKNKRTK PEKLELKKFD PVVRQHVIYK EAKIK UniProtKB: Large ribosomal subunit protein bL33

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Macromolecule #6: 50S ribosomal protein L34

Macromolecule	Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 5.397463 KDa
Sequence	String: MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #7: 50S ribosomal protein L35

Macromolecule	Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 7.313032 KDa
Sequence	String: MPKIKTVRGA AKRFKKTGKG GFKHKHANLR HILTKKATKR KRHLRPKAMV SKGDLGLVIA CLPYA UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #8: 50S ribosomal protein L36

Macromolecule	Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 4.37739 KDa
Sequence	String: MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #11: 50S ribosomal protein L2

Macromolecule	Name: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 29.923619 KDa
Sequence	String: MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD ...String: MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD GAYVTLRLRS GEMRKVEADC RATLGEVGNA EHMLRVLGKA GAARWRGVRP TVRGTAMNPV DHPHGGGEGR NF GKHPVTP WGVQTKGKKT RSNKRTDKFI VRRRSK UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #12: 50S ribosomal protein L3

Macromolecule	Name: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 22.277535 KDa
Sequence	String: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE ...String: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #13: 50S ribosomal protein L4

Macromolecule	Name: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 22.121566 KDa
Sequence	String: MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD ...String: MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD VRDATGIDPV SLIAFDKVVM TADAVKQVEE MLA UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #14: 50S ribosomal protein L5

Macromolecule	Name: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 20.333611 KDa
Sequence	String: MAKLHDYYKD EVVKKLMTEF NYNSVMQVPR VEKITLNMGV GEAIADKKLL DNAAADLAAI SGQKPLITKA RKSVAGFKIR QGYPIGCKV TLRGERMWEF FERLITIAVP RIRDFRGLSA KSFDGRGNYS MGVREQIIFP EIDYDKVDRV RGLDITITTT A KSDEEGRA LLAAFDFPFR K UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #15: 50S ribosomal protein L6

Macromolecule	Name: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 18.932791 KDa
Sequence	String: MSRVAKAPVV VPAGVDVKIN GQVITIKGKN GELTRTLNDA VEVKHADNTL TFGPRDGYAD GWAQAGTARA LLNSMVIGVT EGFTKKLQL VGVGYRAAVK GNVINLSLGF SHPVDHQLPA GITAECPTQT EIVLKGADKQ VIGQVAADLR AYRRPEPYKG K GVRYADEV VRTKEAKKK UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #16: 50S ribosomal protein L9

Macromolecule	Name: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 15.78902 KDa
Sequence	String: MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #17: 50S ribosomal protein L13

Macromolecule	Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 16.050606 KDa
Sequence	String: MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #18: 50S ribosomal protein L14

Macromolecule	Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 13.565067 KDa
Sequence	String: MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEVL UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #19: 50S ribosomal protein L15

Macromolecule	Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 14.994443 KDa
Sequence	String: MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF EGGQMPLYRR LPKFGFTSRK AAITAEVRLS DLAKVEGGV VDLNTLKAAN IIGIQIEFAK VILAGEVTTP VTVRGLRVTK GARAAIEAAG GKIEE UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #20: 50S ribosomal protein L16

Macromolecule	Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 15.312269 KDa
Sequence	String: MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV RMGKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM UniProtKB: Large ribosomal subunit protein uL16

+
Macromolecule #21: 50S ribosomal protein L17

Macromolecule	Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 14.393657 KDa
Sequence	String: MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS EKAEAAAE UniProtKB: Large ribosomal subunit protein bL17

+
Macromolecule #22: 50S ribosomal protein L18

Macromolecule	Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 12.794668 KDa
Sequence	String: MDKKSARIRR ATRARRKLQE LGATRLVVHR TPRHIYAQVI APNGSEVLVA ASTVEKAIAE QLKYTGNKDA AAAVGKAVAE RALEKGIKD VSFDRSGFQY HGRVQALADA AREAGLQF UniProtKB: Large ribosomal subunit protein uL18

+
Macromolecule #23: 50S ribosomal protein L19

Macromolecule	Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 13.159278 KDa
Sequence	String: MSNIIKQLEQ EQMKQDVPSF RPGDTVEVKV WVVEGSKKRL QAFEGVVIAI RNRGLHSAFT VRKISNGEGV ERVFQTHSPV VDSISVKRR GAVRKAKLYY LRERTGKAAR IKERLN UniProtKB: Large ribosomal subunit protein bL19

+
Macromolecule #24: 50S ribosomal protein L20

Macromolecule	Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 13.528024 KDa
Sequence	String: MARVKRGVIA RARHKKILKQ AKGYYGARSR VYRVAFQAVI KAGQYAYRDR RQRKRQFRQL WIARINAAAR QNGISYSKFI NGLKKASVE IDRKILADIA VFDKVAFTAL VEKAKAALA UniProtKB: Large ribosomal subunit protein bL20

+
Macromolecule #25: 50S ribosomal protein L21

Macromolecule	Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 11.586374 KDa
Sequence	String: MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA UniProtKB: Large ribosomal subunit protein bL21

+
Macromolecule #26: 50S ribosomal protein L22

Macromolecule	Name: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 12.253359 KDa
Sequence	String: METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #27: 50S ribosomal protein L23

Macromolecule	Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 11.22216 KDa
Sequence	String: MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNLDFVGGA E UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #28: 50S ribosomal protein L24

Macromolecule	Name: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 11.33925 KDa
Sequence	String: MAAKIRRDDE VIVLTGKDKG KRGKVKNVLS SGKVIVEGIN LVKKHQKPVP ALNQPGGIVE KEAAIQVSNV AIFNAATGKA DRVGFRFED GKKVRFFKSN SETIK UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #30: 50S ribosomal protein L25

Macromolecule	Name: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 10.713465 KDa
Sequence	String: MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA UniProtKB: Large ribosomal subunit protein bL25

+
Macromolecule #31: 50S ribosomal protein L27

Macromolecule	Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 9.14654 KDa
Sequence	String: MAHKKAGGST RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #32: Gamma-crystallin B

Macromolecule	Name: Gamma-crystallin B / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Bos taurus (domestic cattle)
Molecular weight	Theoretical: 7.15797 KDa
Recombinant expression	Organism: Escherichia coli BL21(DE3) (bacteria)
Sequence	String: MGHHHHHHHH HHMGKITFYE DRGFQGHCYE CSSDCPNLQP YFSRCFSTPV WISQAQGIRA G UniProtKB: Gamma-crystallin B

+
Macromolecule #9: 5S rRNA

Macromolecule	Name: 5S rRNA / type: rna / ID: 9 / Number of copies: 1
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 38.79009 KDa
Sequence	String: UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCU CCCCAUGCGA GAGUAGGGAA CUGCCAGGCA U

+
Macromolecule #10: 23S rRNA

Macromolecule	Name: 23S rRNA / type: rna / ID: 10 / Number of copies: 1
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 942.342938 KDa
Sequence	String: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG ...String: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACAG AGCAAUCUGU GUGACU GCG UACCUUUUGU AUAAUGGGUC AGCGACUUAU AUUCUGUAGC AAGGUUAACC GAAUAGGGGA GCCGAAGGGA AACCGAG UC UUAACUGGGC GUUAAGUUGC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCAUGGGCAG GUUGAAGGUU GGGUAACA C UAACUGGAGG ACCGAACCGA CUAAUGUUGA AAAAUUAGCG GAUGACUUGU GGCUGGGGGU GAAAGGCCAA UCAAACCGG GAGAUAGCUG GUUCUCCCCG AAAGCUAUUU AGGUAGCGCC UCGUGAAUUC AUCUCCGGGG GUAGAGCACU GUUUCGGCAA GGGGGUCAU CCCGACUUAC CAACCCGAUG CAAACUGCGA AUACCGGAGA AUGUUAUCAC GGGAGACACA CGGCGGGUGC U AACGUCCG UCGUGAAGAG GGAAACAACC CAGACCGCCA GCUAAGGUCC CAAAGUCAUG GUUAAGUGGG AAACGAUGUG GG AAGGCCC AGACAGCCAG GAUGUUGGCU UAGAAGCAGC CAUCAUUUAA AGAAAGCGUA AUAGCUCACU GGUCGAGUCG GCC UGCGCG GAAGAUGUAA CGGGGCUAAA CCAUGCACCG AAGCUGCGGC AGCGACGCUU AUGCGUUGUU GGGUAGGGGA GCGU UCUGU AAGCCUGUGA AGGUGUGCUG UGAGGCAUGC UGGAGGUAUC AGAAGUGCGA AUGCUGACAU AAGUAACGAU AAAGC GGGU GAAAAGCCCG CUCGCCGGAA GACCAAGGGU UCCUGUCCAA CGUUAAUCGG GGCAGGGUGA GUCGACCCCU AAGGCG AGG CCGAAAGGCG UAGUCGAUGG GAAACAGGUU AAUAUUCCUG UACUUGGUGU UACUGCGAAG GGGGGACGGA GAAGGCU AU GUUGGCCGGG CGACGGUUGU CCCGGUUUAA GCGUGUAGGC UGGUUUUCCA GGCAAAUCCG GAAAAUCAAG GCUGAGGC G UGAUGACGAG GCACUACGGU GCUGAAGCAA CAAAUGCCCU GCUUCCAGGA AAAGCCUCUA AGCAUCAGGU AACAUCAAA UCGUACCCCA AACCGACACA GGUGGUCAGG UAGAGAAUAC CAAGGCGCUU GAGAGAACUC GGGUGAAGGA ACUAGGCAAA AUGGUGCCG UAACUUCGGG AGAAGGCACG CUGAUAUGUA GGUGAGGUCC CUCGCGGAUG GAGCUGAAAU CAGUCGAAGA U ACCAGCUG GCUGCAACUG UUUAUUAAAA ACACAGCACU GUGCAAACAC GAAAGUGGAC GUAUACGGUG UGACGCCUGC CC GGUGCCG GAAGGUUAAU UGAUGGGGUU AGCGGUAACG CGAAGCUCUU GAUCGAAGCC CCGGUAAACG GCGGCCGUAA CUA UAACGG UCCUAAGGUA GCGAAAUUCC UUGUCGGGUA AGUUCCGACC UGCACGAAUG GCGUAAUGAU GGCCAGGCUG UCUC CACCC GAGACUCAGU GAAAUUGAAC UCGCUGUGAA GAUGCAGUGU ACCCGCGGCA AGACGGAAAG ACCCCGUGAA CCUUU ACUA UAGCUUGACA CUGAACAUUG AGCCUUGAUG UGUAGGAUAG GUGGGAGGCU UUGAAGUGUG GACGCCAGUC UGCAUG GAG CCGGCCUUGA AAUACCACCC UUUAAUGUUU GAUGUUCUAA CGUUGGCCCC UGAUCGGGGU UGCGGACAGU GUCUGGU GG GUAGUUUGAC UGGGGCGGUC UCCUCCUAAA GAGUAACGGA GGAGCACGAA GGUUGGCUAA UCCUGGUCGG ACAUCAGG A GGUUAGUGCA AUGGCAUAAG CCAGCUUGAC UGCGAGCGUG ACGGCGCGAG CAGGUGCGAA AGCAGGUCAU AGUGAUCCG GUGGUUCUGA AUGGAAGGGC CAUCGCUCAA CGGAUAAAAG GUACUCCGGG GAUAACAGGC UGAUACCGCC CAAGAGUUCA UAUCGACGG CGGUGUUUGG CACCUCGAUG UCGGCUCAUC ACAUCCUGGG GCUGAAGUAG GUCCCAAGGG UAUGGCUGUU C GCCAUUUA AAGUGGUACG CGAGCUGGGU UUAGAACGUC GUGAGACAGU UCGGUCCCUA UCUGCCGUGG GCGCUGGAGA AC UGAGGGG GGCUGCUCCU AGUACGAGAG GACCGGAGUG GACGCAUCAC UGGUGUUCGG GUUGUCAUGC CAAUGGCACU GCC CGGUAG CUAAAUGCGG AAGAGAUAAG UGCUGAAAGC AUCUAAGCAC GAAACUUGCC CCGAGAUGAG UUCUCCCUGA CUCC UUGAG AGUCCUGAAG GAACGUUGAA GACGACGACG UUGAUAGGCC GGGUGUGUAA GCGCAGCGAU GCGUUGAGCU AACCG GUAC UAAUGAACCG UGAGGCUUAA CC GENBANK: GENBANK: CP001509.3

+
Macromolecule #29: glycine-tRNA glyT

Macromolecule	Name: glycine-tRNA glyT / type: rna / ID: 29 / Number of copies: 1
Source (natural)	Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weight	Theoretical: 23.935143 KDa
Sequence	String: GCGGGCAUCG UAUAAUGGCU AUUACCUCAG CCUUCCAAGC UGAUGAUGCG GGUUCGAUUC CCGCUGCCCG CUCCA

-
Experimental details

-
Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

-
Sample preparation

Concentration

0.12 mg/mL

Buffer

pH: 7.5
Component:

Concentration	Formula	Name
10.0 mM	C₈H₁₈N₂O₄S	HEPES
30.0 mM	NH₄CL	Ammonium chloride
12.0 mM	MgCl₂	magnesium chloride
1.0 mM	C₁₀H₁₆N₂O₈	Ethylenediaminetetraacetic acid (EDTA)

Grid

Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.

Vitrification

Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

Microscope	FEI TITAN KRIOS
Image recording	Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 7.2 sec. / Average electron dose: 60.0 e/Å²
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stage	Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selection	Number selected: 436999
Startup model	Type of model: PDB ENTRY PDB model - PDB ID: 3jbu
Final reconstruction	Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196254
Initial angle assignment	Type: RANDOM ASSIGNMENT
Final angle assignment	Type: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model	PDB ID: 3jbu Chain - Source name: PDB / Chain - Initial model type: experimental model
Refinement	Space: REAL / Protocol: RIGID BODY FIT
Output model	PDB-6ys3: Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms with modeled GBC SecM peptide

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-Supplemental data

-Mask #1

-Half map: #2

-Half map: #1

-Sample components

+Entire : 50S ribosomal + GBC SecM peptide complex

+Supramolecule #1: 50S ribosomal + GBC SecM peptide complex

+Supramolecule #2: 50S ribosomal

+Supramolecule #3: GBC SecM peptide complex

+Macromolecule #1: 50S ribosomal protein L28

+Macromolecule #2: 50S ribosomal protein L29

+Macromolecule #3: 50S ribosomal protein L30

+Macromolecule #4: 50S ribosomal protein L32

+Macromolecule #5: 50S ribosomal protein L33

+Macromolecule #6: 50S ribosomal protein L34

+Macromolecule #7: 50S ribosomal protein L35

+Macromolecule #8: 50S ribosomal protein L36

+Macromolecule #11: 50S ribosomal protein L2

+Macromolecule #12: 50S ribosomal protein L3

+Macromolecule #13: 50S ribosomal protein L4

+Macromolecule #14: 50S ribosomal protein L5

+Macromolecule #15: 50S ribosomal protein L6

+Macromolecule #16: 50S ribosomal protein L9

+Macromolecule #17: 50S ribosomal protein L13

+Macromolecule #18: 50S ribosomal protein L14

+Macromolecule #19: 50S ribosomal protein L15

+Macromolecule #20: 50S ribosomal protein L16

+Macromolecule #21: 50S ribosomal protein L17

+Macromolecule #22: 50S ribosomal protein L18

+Macromolecule #23: 50S ribosomal protein L19

+Macromolecule #24: 50S ribosomal protein L20

+Macromolecule #25: 50S ribosomal protein L21

+Macromolecule #26: 50S ribosomal protein L22

+Macromolecule #27: 50S ribosomal protein L23

+Macromolecule #28: 50S ribosomal protein L24

+Macromolecule #30: 50S ribosomal protein L25

+Macromolecule #31: 50S ribosomal protein L27

+Macromolecule #32: Gamma-crystallin B

+Macromolecule #9: 5S rRNA

+Macromolecule #10: 23S rRNA

+Macromolecule #29: glycine-tRNA glyT

-Experimental details

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Downloads & links

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Related structure data

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Links

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Map

Image control

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Supplemental data

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Mask #1

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Half map: #2

-
Half map: #1

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Sample components

+
Entire : 50S ribosomal + GBC SecM peptide complex

+
Supramolecule #1: 50S ribosomal + GBC SecM peptide complex

+
Supramolecule #2: 50S ribosomal

+
Supramolecule #3: GBC SecM peptide complex

+
Macromolecule #1: 50S ribosomal protein L28

+
Macromolecule #2: 50S ribosomal protein L29

+
Macromolecule #3: 50S ribosomal protein L30

+
Macromolecule #4: 50S ribosomal protein L32

+
Macromolecule #5: 50S ribosomal protein L33

+
Macromolecule #6: 50S ribosomal protein L34

+
Macromolecule #7: 50S ribosomal protein L35

+
Macromolecule #8: 50S ribosomal protein L36

+
Macromolecule #11: 50S ribosomal protein L2

+
Macromolecule #12: 50S ribosomal protein L3

+
Macromolecule #13: 50S ribosomal protein L4

+
Macromolecule #14: 50S ribosomal protein L5

+
Macromolecule #15: 50S ribosomal protein L6

+
Macromolecule #16: 50S ribosomal protein L9

+
Macromolecule #17: 50S ribosomal protein L13

+
Macromolecule #18: 50S ribosomal protein L14

+
Macromolecule #19: 50S ribosomal protein L15

+
Macromolecule #20: 50S ribosomal protein L16

+
Macromolecule #21: 50S ribosomal protein L17

+
Macromolecule #22: 50S ribosomal protein L18

+
Macromolecule #23: 50S ribosomal protein L19

+
Macromolecule #24: 50S ribosomal protein L20

+
Macromolecule #25: 50S ribosomal protein L21

+
Macromolecule #26: 50S ribosomal protein L22

+
Macromolecule #27: 50S ribosomal protein L23

+
Macromolecule #28: 50S ribosomal protein L24

+
Macromolecule #30: 50S ribosomal protein L25

+
Macromolecule #31: 50S ribosomal protein L27

+
Macromolecule #32: Gamma-crystallin B

+
Macromolecule #9: 5S rRNA

+
Macromolecule #10: 23S rRNA

+
Macromolecule #29: glycine-tRNA glyT

-
Experimental details

-
Structure determination

-
Sample preparation

-
Electron microscopy

+
Image processing

-
Atomic model buiding 1

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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