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- EMDB-23539: Cfr-modified 50S subunit from Escherichia coli -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-23539

Title

Cfr-modified 50S subunit from Escherichia coli

Map data

Sample

Complex: Escherichia coli 50S subunit
- RNA: x 2 types
- Protein or peptide: x 28 types
Ligand: x 4 types

Keywords

Cfr-modified 50S subunit /

RIBOSOME

Function / homology

Function and homology information

positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly /

regulation of cell growth /

ribosomal large subunit assembly /

ribosome binding / large ribosomal subunit /

5S rRNA binding ...
Similarity search - Function

Ribosomal protein L25, short-form /

Ribosomal protein L21, conserved site /

Ribosomal protein L21 signature. /

Ribosomal protein L16 signature 1. /

Ribosomal protein L6, conserved site /

Ribosomal protein L6 signature 1. /

Ribosomal protein L16, conserved site /

Ribosomal protein L16 signature 2. /

Ribosomal protein L17 signature. /

Ribosomal protein L9 signature. ...

Ribosomal protein L25, short-form /

Ribosomal protein L21, conserved site /

Ribosomal protein L21 signature. /

Ribosomal protein L16 signature 1. /

Ribosomal protein L6, conserved site /

Ribosomal protein L6 signature 1. /

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 L25p family /

Ribosomal protein L25 /

Ribosomal protein L28/L24 superfamily /

Ribosomal protein L36 signature. /

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 L28 /

Ribosomal protein L35, conserved site /

Ribosomal protein L35 signature. /

Ribosomal protein L33, conserved site /

Ribosomal protein L33 signature. /

Ribosomal protein L35, non-mitochondrial /

Ribosomal protein L5, bacterial-type /

Ribosomal protein L6, bacterial-type /

Ribosomal protein L18, bacterial-type /

Ribosomal protein L19, conserved site /

Ribosomal protein L19 signature. /

Ribosomal protein L36 /

Ribosomal protein L36 superfamily /

Ribosomal protein L36 /

Ribosomal protein L9/RNase H1, N-terminal /

Ribosomal protein L20 signature. /

Ribosomal protein L27, conserved site /

Ribosomal protein L27 signature. /

Ribosomal protein L14P, bacterial-type /

Ribosomal protein L34, conserved site /

Ribosomal protein L34 signature. /

Ribosomal protein L22, bacterial/chloroplast-type /

Ribosomal protein L35 /

Ribosomal protein L35 superfamily /

Ribosomal protein L2, bacterial/organellar-type /

Ribosomal protein L35 / Ribosomal L28 family /

Ribosomal protein L33 /

Ribosomal protein L28/L24 /

Ribosomal protein L33 superfamily /

Ribosomal protein L30, bacterial-type /

Ribosomal protein L16 /

Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like /

Ribosomal protein L20 /

Ribosomal protein L20, C-terminal /

Ribosomal protein L21 /

Ribosomal protein L27 / Ribosomal L27 protein /

Ribosomal protein L19 /

Ribosomal protein L19 superfamily /

Ribosomal protein L19 /

Ribosomal proteins 50S L24/mitochondrial 39S L24 /

Ribosomal protein L17 /

Ribosomal protein L17 superfamily /

Ribosomal protein L17 /

Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family /

Ribosomal protein L24 /

Ribosomal protein L32p /

Ribosomal protein L34 /

Ribosomal protein L13, bacterial-type /

Ribosomal protein L23/L25, conserved site /

Ribosomal protein L3, bacterial/organelle-type /

Ribosomal protein L15, bacterial-type /

50S ribosomal protein uL4 /

Ribosomal protein L23 signature. /

Ribosomal protein L30, conserved site /

Ribosomal protein L5, conserved site /

Ribosomal protein L29, conserved site /

Ribosomal protein L30 signature. /

Ribosomal protein L5, N-terminal /

Ribosomal protein L5 signature. /

Ribosomal protein L15, conserved site /

Ribosomal protein L5, C-terminal /

Ribosomal protein L5 /

Ribosomal protein L5 domain superfamily /

Ribosomal protein L2, conserved site /

Ribosomal protein L2 signature. /

Ribosomal protein L10e/L16
Similarity search - Domain/homology

Biological species

Escherichia coli (E. coli)

Method

single particle reconstruction /

cryo EM / Resolution: 2.2 Å

Authors

Stojkovic V / Myasnikov AG

Funding support

United States, 1 items

Citation

Journal: To Be Published
Title: Investigating antibiotic resistance of a ribosomal-RNA methylating enzyme through directed evolution
Authors: Tsai K / Stojkovic V / Noda-Garcia L / Myasnikov AG / Young ID / Palla A / Venkataramanan S / Floor S / Fraser JS / Frost A / Tawfik DS / Fujimori DG

History

Deposition	Feb 25, 2021	-
Header (metadata) release	Dec 15, 2021	-
Map release	Dec 15, 2021	-
Update	Nov 15, 2023	-
Current status	Nov 15, 2023	Processing site: RCSB / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.015 Imaged by UCSF Chimera Download Surface view colored by height Surface level: 0.015 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-7lvk Surface level: 0.015 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_23539.png

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Downloads & links

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EMDB archive

Map data	emd_23539.map.gz	19.6 MB		EMDB map data format
Header (meta data)	emd-23539-v30.xml emd-23539.xml	45 KB 45 KB	Display Display	EMDB header
Images	emd_23539.png	141.4 KB
Filedesc metadata	emd-23539.cif.gz	10.9 KB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-23539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23539	HTTPS FTP

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Related structure data

Related structure data	7lvkMC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	21873 21872 11918 23667 20353 3525 10655 4638 11862 10809 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 (41) #157 - Jan 2013 Transfer-Messenger RNA similarity (18) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (17) #10 - Oct 2000 Ribosome similarity (1) #121 - Jan 2010 70S Ribosomes similarity (7)

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Map

File

Download / File: emd_23539.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Voxel size

X=Y=Z: 0.822 Å

Density

Contour Level	By AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum	-0.114439964 - 0.22561929
Average (Standard dev.)	0.000028785347 (±0.004007534)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	512	512	512
Spacing	512	512	512

Cell

A=B=C: 420.864 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	0.822	0.822	0.822
M x/y/z	512	512	512
origin x/y/z	0.000	0.000	0.000
length x/y/z	420.864	420.864	420.864
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	450	450	450
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	512	512	512
D min/max/mean	-0.114	0.226	0.000

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Supplemental data

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Sample components

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Entire : Escherichia coli 50S subunit

Entire	Name: Escherichia coli 50S subunit
Components	Complex: Escherichia coli 50S subunit RNA: 23S rRNA23S ribosomal RNA RNA: 5S rRNA5S ribosomal RNA 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 Protein or peptide: 50S ribosomal protein L25 Protein or peptide: 50S ribosomal protein L27 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 Ligand: MAGNESIUM ION Ligand: SODIUM IONSodium Ligand: ZINC ION Ligand: water

Entire

Name: Escherichia coli 50S subunit

Components

Complex: Escherichia coli 50S subunit
- RNA: 23S rRNA23S ribosomal RNA
- RNA: 5S rRNA5S ribosomal RNA
- 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
- Protein or peptide: 50S ribosomal protein L25
- Protein or peptide: 50S ribosomal protein L27
- 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
Ligand: MAGNESIUM ION
Ligand: SODIUM IONSodium
Ligand: ZINC ION
Ligand: water

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Supramolecule #1: Escherichia coli 50S subunit

Supramolecule	Name: Escherichia coli 50S subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)	Organism: Escherichia coli (E. coli)

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Macromolecule #1: 23S rRNA

Macromolecule	Name: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 941.823562 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 GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAU(1MG)(PSU)(5MU)GAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCA AU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACU G UUUCGGCAAG GGGGUCAUCC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACAC GGCGGG(PSU)GCU AACGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUG GGA AACGAUGUGG GAAGGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCAC UG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUU G GGUAGGGGAG CGUUCUGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUA AGUAACGAUA AAGCGGGUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUA AGGCGAGGCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG G GGACGGAG AAGGCUAUGU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AA AUCAAGG CUGAGGCGUG AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAU CAGGUA ACAUCAAAUC GUACCCCAAA CCGACAC(6MZ)GG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAA CUAGGCAAAA UGGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCCU CGCGGAUGGA G CUGAAAUC AGUCGAAGAU ACCAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AU ACGGUGU GACGCCU(2MG)CC CGGUGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCG GUAAACGGCG GCCG(PSU)AAC(3TD)A (PSU)AACGGUCCU AAGGUAGCGA AA(5MU)UCCUUGU CGGGUAAGUU CCGA C(5MC)UGC ACGAAUGGCG UAAUGAUGGC CAGGCUGUCU CCACCCGAGA CUCAGUGAAA UUGAACUCGC UGUG(6MZ)AG AU GCAGUGUACC CGCGGCAAGA CGGAAAGACC CCGU(G7M)AACCU UUACUAUAGC UUGACACUGA ACAUUGAGCC UUGA UGUGU AGGAUAGGUG GGAGGCUUUG AAGUGUGGAC GCCAGUCUGC AUGGAGCCGA CCUUGAAAUA CCACCCUUUA AUGUU UGAU GUUCUAACGU UGACCCGUAA UCCGGGUUGC GGACAGUGUC UGGUGGGUAG UUUGACUG(OMG)G GCGGUCUCCU CC UAAAGAG UAACGGAGGA GCACGAAGGU UGGCUAAUCC UGGUCGGACA UCAGGAGGUU AGUGCAAUGG CAUAAGCCAG CUU GACUGC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUC AACGG AUAAAAGGUA CUCCG(2MG)GGAU AACAGGC(PSU)GA UACCGCCCAA GAGUUCAUAU CGACGGCGGU GUUUGGC A(OMC) CUCG(8AH)(PSU)GUCG GCUCAUCACA UCCUGGGGCU GAAGUAGGUC CCAAGGGUAU GGC(OMU)GUUCGC CA UUUAAAG UGGUACGCGA GC(PSU)GGGUUUA GAACGUCGUG AGACAGU(PSU)CG GUCCCUAUCU GCCGUGGGCG CUGGA GAAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCCAA UGGCAC UGC CCGGUAGCUA AAUGCGGAAG AGAUAAGUGC UGAAAGCAUC UAAGCACGAA ACUUGCCCCG AGAUGAGUUC UCCCUGA CC CUUUAAGGGU CCUGAAGGAA CGUUGAAGAC GACGACGUUG AUAGGCCGGG UGUGUAAGCG CAGCGAUGCG UUGAGCUA A CCGGUACUAA UGAACCGUGA GGCUUAACCU U

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Macromolecule #2: 5S rRNA

Macromolecule	Name: 5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 38.79009 KDa
Sequence	String: UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCU CCCCAUGCGA GAGUAGGGAA CUGCCAGGCA U GENBANK: GENBANK: CP024273.1

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Macromolecule #3: 50S ribosomal protein L2

Macromolecule	Name: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
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 #4: 50S ribosomal protein L3

Macromolecule	Name: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
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 #5: 50S ribosomal protein L4

Macromolecule	Name: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
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: 50S ribosomal protein L4

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Macromolecule #6: 50S ribosomal protein L5

Macromolecule	Name: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
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: 50S ribosomal protein L5

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Macromolecule #7: 50S ribosomal protein L6

Macromolecule	Name: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
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: 50S ribosomal protein L6

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Macromolecule #8: 50S ribosomal protein L9

Macromolecule	Name: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weight	Theoretical: 15.78902 KDa
Sequence	String: MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE UniProtKB: 50S ribosomal protein L9

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Macromolecule #9: 50S ribosomal protein L13

Macromolecule	Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 16.050606 KDa
Sequence	String: MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI UniProtKB: 50S ribosomal protein L13

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Macromolecule #10: 50S ribosomal protein L14

Macromolecule	Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 13.565067 KDa
Sequence	String: MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEVL UniProtKB: 50S ribosomal protein L14

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Macromolecule #11: 50S ribosomal protein L15

Macromolecule	Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 15.008471 KDa
Sequence	String: MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF EGGQMPLYRR LPKFGFTSRK AAITAEIRLS DLAKVEGGV VDLNTLKAAN IIGIQIEFAK VILAGEVTTP VTVRGLRVTK GARAAIEAAG GKIEE UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #12: 50S ribosomal protein L16

Macromolecule	Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 15.327261 KDa
Sequence	String: MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV (4D4)MGKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM UniProtKB: 50S ribosomal protein L16

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Macromolecule #13: 50S ribosomal protein L17

Macromolecule	Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 14.393657 KDa
Sequence	String: MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS EKAEAAAE UniProtKB: 50S ribosomal protein L17

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Macromolecule #14: 50S ribosomal protein L18

Macromolecule	Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 12.794668 KDa
Sequence	String: MDKKSARIRR ATRARRKLQE LGATRLVVHR TPRHIYAQVI APNGSEVLVA ASTVEKAIAE QLKYTGNKDA AAAVGKAVAE RALEKGIKD VSFDRSGFQY HGRVQALADA AREAGLQF UniProtKB: 50S ribosomal protein L18

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Macromolecule #15: 50S ribosomal protein L19

Macromolecule	Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 13.159278 KDa
Sequence	String: MSNIIKQLEQ EQMKQDVPSF RPGDTVEVKV WVVEGSKKRL QAFEGVVIAI RNRGLHSAFT VRKISNGEGV ERVFQTHSPV VDSISVKRR GAVRKAKLYY LRERTGKAAR IKERLN UniProtKB: 50S ribosomal protein L19

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Macromolecule #16: 50S ribosomal protein L20

Macromolecule	Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
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

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Macromolecule #17: 50S ribosomal protein L21

Macromolecule	Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 11.586374 KDa
Sequence	String: MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA UniProtKB: 50S ribosomal protein L21

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Macromolecule #18: 50S ribosomal protein L22

Macromolecule	Name: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 12.253359 KDa
Sequence	String: METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R UniProtKB: 50S ribosomal protein L22

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Macromolecule #19: 50S ribosomal protein L23

Macromolecule	Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 11.22216 KDa
Sequence	String: MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNLDFVGGA E UniProtKB: 50S ribosomal protein L23

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Macromolecule #20: 50S ribosomal protein L24

Macromolecule	Name: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 11.33925 KDa
Sequence	String: MAAKIRRDDE VIVLTGKDKG KRGKVKNVLS SGKVIVEGIN LVKKHQKPVP ALNQPGGIVE KEAAIQVSNV AIFNAATGKA DRVGFRFED GKKVRFFKSN SETIK UniProtKB: 50S ribosomal protein L24

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Macromolecule #21: 50S ribosomal protein L25

Macromolecule	Name: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 10.713465 KDa
Sequence	String: MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #22: 50S ribosomal protein L27

Macromolecule	Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 9.14654 KDa
Sequence	String: MAHKKAGGST RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #23: 50S ribosomal protein L28

Macromolecule	Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 9.027551 KDa
Sequence	String: MSRVCQVTGK RPVTGNNRSH ALNATKRRFL PNLHSHRFWV ESEKRFVTLR VSAKGMRVID KKGIDTVLAE LRARGEKY UniProtKB: 50S ribosomal protein L28

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Macromolecule #24: 50S ribosomal protein L29

Macromolecule	Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 7.286464 KDa
Sequence	String: MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA UniProtKB: 50S ribosomal protein L29

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Macromolecule #25: 50S ribosomal protein L30

Macromolecule	Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 6.55482 KDa
Sequence	String: MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE UniProtKB: 50S ribosomal protein L30

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Macromolecule #26: 50S ribosomal protein L32

Macromolecule	Name: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 6.463445 KDa
Sequence	String: MAVQQNKPTR SKRGMRRSHD ALTAVTSLSV DKTSGEKHLR HHITADGYYR GRKVIAK UniProtKB: 50S ribosomal protein L32

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Macromolecule #27: 50S ribosomal protein L33

Macromolecule	Name: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 6.388631 KDa
Sequence	String: MAKGIREKIK LVSSAGTGHF YTTTKNKRTK PEKLELKKFD PVVRQHVIYK EAKIK UniProtKB: 50S ribosomal protein L33

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Macromolecule #28: 50S ribosomal protein L34

Macromolecule	Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 5.397463 KDa
Sequence	String: MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #29: 50S ribosomal protein L35

Macromolecule	Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 7.313032 KDa
Sequence	String: MPKIKTVRGA AKRFKKTGKG GFKHKHANLR HILTKKATKR KRHLRPKAMV SKGDLGLVIA CLPYA UniProtKB: 50S ribosomal protein L35

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Macromolecule #30: 50S ribosomal protein L36

Macromolecule	Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Escherichia coli (E. coli)
Molecular weight	Theoretical: 4.37739 KDa
Sequence	String: MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #31: MAGNESIUM ION

Macromolecule	Name: MAGNESIUM ION / type: ligand / ID: 31 / Number of copies: 179 / Formula: MG
Molecular weight	Theoretical: 24.305 Da

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Macromolecule #32: SODIUM ION

Macromolecule	Name: SODIUM ION / type: ligand / ID: 32 / Number of copies: 1
Molecular weight	Theoretical: 22.99 Da

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Macromolecule #33: ZINC ION

Macromolecule	Name: ZINC ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: ZN
Molecular weight	Theoretical: 65.409 Da

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Macromolecule #34: water

Macromolecule	Name: water / type: ligand / ID: 34 / Number of copies: 2716 / Formula: HOH
Molecular weight	Theoretical: 18.015 Da
Chemical component information	ChemComp-HOH: WATER / Water

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Experimental details

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Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

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Sample preparation

Concentration	1 mg/mL
Buffer	pH: 7.5 / Component - Concentration: 10.0 mM / Component - Formula: TRIS / Component - Name: TRIS / Details: Buffer A
Grid	Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
Vitrification	Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV Details: Blot Force 5 Blot Time 10sec Hum 95% Temperature 10C Waiting time 1 min.
Details	50S ribosomal subunit was purified from E. coli MRE600 using modified version of previously published protocol (Mehta et al. 2012)

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Electron microscopy

Microscope	FEI TITAN KRIOS
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	C2 aperture diameter: 70.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 29000
Sample stage	Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Temperature	Min: 86.0 K / Max: 130.0 K
Alignment procedure	Coma free - Residual tilt: 10.0 mrad
Image recording	Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 0-80 / Number grids imaged: 1 / Number real images: 2055 / Average exposure time: 8.0 sec. / Average electron dose: 80.0 e/Å²
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selection	Number selected: 162713
Startup model	Type of model: OTHER / Details: CryoSPARC
Initial angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.0)
Final reconstruction	Number classes used: 1 / Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Number images used: 141549

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Atomic model buiding 1

Refinement	Space: REAL / Protocol: FLEXIBLE FIT
Output model	PDB-7lvk: Cfr-modified 50S subunit from Escherichia coli

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+Entire : Escherichia coli 50S subunit

+Supramolecule #1: Escherichia coli 50S subunit

+Macromolecule #1: 23S rRNA

+Macromolecule #2: 5S rRNA

+Macromolecule #3: 50S ribosomal protein L2

+Macromolecule #4: 50S ribosomal protein L3

+Macromolecule #5: 50S ribosomal protein L4

+Macromolecule #6: 50S ribosomal protein L5

+Macromolecule #7: 50S ribosomal protein L6

+Macromolecule #8: 50S ribosomal protein L9

+Macromolecule #9: 50S ribosomal protein L13

+Macromolecule #10: 50S ribosomal protein L14

+Macromolecule #11: 50S ribosomal protein L15

+Macromolecule #12: 50S ribosomal protein L16

+Macromolecule #13: 50S ribosomal protein L17

+Macromolecule #14: 50S ribosomal protein L18

+Macromolecule #15: 50S ribosomal protein L19

+Macromolecule #16: 50S ribosomal protein L20

+Macromolecule #17: 50S ribosomal protein L21

+Macromolecule #18: 50S ribosomal protein L22

+Macromolecule #19: 50S ribosomal protein L23

+Macromolecule #20: 50S ribosomal protein L24

+Macromolecule #21: 50S ribosomal protein L25

+Macromolecule #22: 50S ribosomal protein L27

+Macromolecule #23: 50S ribosomal protein L28

+Macromolecule #24: 50S ribosomal protein L29

+Macromolecule #25: 50S ribosomal protein L30

+Macromolecule #26: 50S ribosomal protein L32

+Macromolecule #27: 50S ribosomal protein L33

+Macromolecule #28: 50S ribosomal protein L34

+Macromolecule #29: 50S ribosomal protein L35

+Macromolecule #30: 50S ribosomal protein L36

+Macromolecule #31: MAGNESIUM ION

+Macromolecule #32: SODIUM ION

+Macromolecule #33: ZINC ION

+Macromolecule #34: water

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

-Image processing

-Atomic model buiding 1

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-Aug 12, 2020. Covid-19 info

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