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- PDB-4v4v: Structure of a pre-translocational E. coli ribosome obtained by f... -

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Basic information

Entry
Database: PDB / ID: 4v4v
TitleStructure of a pre-translocational E. coli ribosome obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1056
Components
  • (30S ribosomal subunit protein ...) x 19
  • (50S ribosomal protein ...) x 26
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • tRNA
KeywordsRIBOSOME / SecM / nascent chain / signal transduction / RNA world / polypeptide exit tunnel / translocation / elongation arrest
Function / homology
Function and homology information


stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / ribosome assembly / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / ribosome biogenesis / large ribosomal subunit / ribosome binding / transferase activity / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. ...Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L11, bacterial-type / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / 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 L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal protein S18, conserved site / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein bL19 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / 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 speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 Å
AuthorsMitra, K. / Frank, J.
Citation
Journal: Mol Cell / Year: 2006
Title: Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
Authors: Kakoli Mitra / Christiane Schaffitzel / Felcy Fabiola / Michael S Chapman / Nenad Ban / Joachim Frank /
Abstract: In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models ...In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron microscopy reconstructions of a pretranslocational and SecM-stalled E. coli ribosome complex. A cascade of RNA rearrangements propagates from the exit tunnel throughout the large subunit, affecting intersubunit bridges and tRNA positions, which in turn reorient small subunit RNA elements. Elongation arrest could result from the inhibition of mRNA.(tRNAs) translocation, E site tRNA egress, and perhaps translation factor activation at the GTPase-associated center. Our study suggests that the specific secondary and tertiary arrangement of ribosomal RNA provides the basis for internal signal transduction within the ribosome. Thus, the ribosome may itself have the ability to regulate its progression through translation by modulating its structure and consequently its receptivity to activation by cofactors.
#1: Journal: Nature / Year: 2005
Title: Structure of the E. coli protein-conducting channel bound to a translating ribosome
Authors: Mitra, K. / Schaffitzel, C. / Shaikh, T. / Tama, F. / Jenni, S. / Brooks III, C.L. / Ban, N. / Frank, J.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Locking and unlocking of ribosomal motions
Authors: Valle, M. / Zavialov, A.V. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J.
#3: Journal: FEBS Lett / Year: 2006
Title: A model for co-translational translocation: ribosome-regulated nascent polypeptide translocation at the protein-conducting channel.
Authors: Kakoli Mitra / Joachim Frank /
Abstract: The protein-conducting channel (PCC) must allow both the translocation of soluble polypeptide regions across, and the lateral partitioning of hydrophobic transmembrane helices (TMHs) into, the ...The protein-conducting channel (PCC) must allow both the translocation of soluble polypeptide regions across, and the lateral partitioning of hydrophobic transmembrane helices (TMHs) into, the membrane. We have analyzed existing structures of ribosomes and ribosome-PCC complexes and observe conformational changes suggesting that the ribosome may sense and orient the nascent polypeptide and also facilitate conformational changes in the PCC, subsequently directing the nascent polypeptide into the appropriate PCC-mediated translocation mode. The PCC is predicted to be able to accommodate one central, consolidated channel or two segregated pores with different lipid accessibilities, which may enable the lipid-mediated partitioning of a TMH from one pore, while the other, aqueous, pore allows translocation of a hydrophilic polypeptide segment. Our hypothesis suggests a plausible mechanism for the transitioning of the PCC between different configurations.
History
DepositionMay 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2GY9, 2GYA
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 18, 2015Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND THIS FILE, 2GY9, CONTAINS THE 30S SUBUNIT OF THE WHOLE RIBOSOMAL COMPLEX. THE ENTIRE CRYO- ...COMPOUND THIS FILE, 2GY9, CONTAINS THE 30S SUBUNIT OF THE WHOLE RIBOSOMAL COMPLEX. THE ENTIRE CRYO-EM STRUCTURE CONTAINS ONE 70S RIBOSOME AND ARE DEPOSITED UNDER 2GY9 (30S SUBUNIT) AND 2GYA (50S SUBUNIT).
Remark 999SEQUENCE THIS PDB FILE WAS OBTAINED UPON RIGID BODY REFINEMENT OF A STARTING PDB FILE INTO A CRYO- ...SEQUENCE THIS PDB FILE WAS OBTAINED UPON RIGID BODY REFINEMENT OF A STARTING PDB FILE INTO A CRYO-EM MAP. THE E. COLI RIBOSOMES ARE OBTAINED NATURALLY, BUT FOR THE MODELING OF THE PROTEINS INTO THE EM MAP, AUTHORS SOMETIMES DID NOT MODEL IN THE ENTIRE PROTEIN. RESIDUE (B TRP 95) AND RESIDUE (B LEU 96) ARE NOT LINKED. RESIDUE (B LEU 156) AND RESIDUE (B PRO 157) ARE NOT LINKED. RESIDUE (M ARG 97) AND RESIDUE (M GLY 98) ARE NOT LINKED.

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1056
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 16S ribosomal RNA
AU: tRNA
AV: tRNA
AW: tRNA
AB: 30S ribosomal subunit protein S2
AC: 30S ribosomal subunit protein S3
AD: 30S ribosomal subunit protein S4
AE: 30S ribosomal subunit protein S5
AF: 30S ribosomal subunit protein S6
AG: 30S ribosomal subunit protein S7
AH: 30S ribosomal subunit protein S8
AI: 30S ribosomal subunit protein S9
AJ: 30S ribosomal subunit protein S10
AK: 30S ribosomal subunit protein S11
AL: 30S ribosomal subunit protein S12
AM: 30S ribosomal subunit protein S13
AN: 30S ribosomal subunit protein S14
AO: 30S ribosomal subunit protein S15
AP: 30S ribosomal subunit protein S16
AQ: 30S ribosomal subunit protein S17
AR: 30S ribosomal subunit protein S18
AS: 30S ribosomal subunit protein S19
AT: 30S ribosomal subunit protein S20
B0: 23S ribosomal RNA
B9: 5S ribosomal RNA
B2: 50S ribosomal protein L1
B3: 50S ribosomal protein L7/L12
B5: 50S ribosomal protein L7/L12
BA: 50S ribosomal protein L2
BB: 50S ribosomal protein L3
BC: 50S ribosomal protein L4
BD: 50S ribosomal protein L5
BE: 50S ribosomal protein L6
BF: 50S ribosomal protein L9
BG: 50S ribosomal protein L11
BH: 50S ribosomal protein L13
BI: 50S ribosomal protein L14
BJ: 50S ribosomal protein L15
BK: 50S ribosomal protein L16
BL: 50S ribosomal protein L17
BM: 50S ribosomal protein L18
BN: 50S ribosomal protein L19
BO: 50S RIBOSOMAL PROTEIN L20
BQ: 50S ribosomal protein L22
BR: 50S ribosomal protein L23
BS: 50S ribosomal protein L24
BT: 50S ribosomal protein L25
BU: 50S ribosomal protein L27
BW: 50S ribosomal protein L29
BX: 50S ribosomal protein L30
BZ: 50S ribosomal protein L32
B1: 50S ribosomal protein L33


Theoretical massNumber of molelcules
Total (without water)2,102,33252
Polymers2,102,33252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 6 molecules AAAUAVAWB0B9

#1: RNA chain 16S ribosomal RNA


Mass: 482285.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain tRNA


Mass: 24518.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: A-site, P-site, E-site / Source: (natural) Escherichia coli (E. coli)
#22: RNA chain 23S ribosomal RNA


Mass: 888503.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#23: RNA chain 5S ribosomal RNA


Mass: 34916.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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30S ribosomal subunit protein ... , 19 types, 19 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASAT

#3: Protein 30S ribosomal subunit protein S2


Mass: 26292.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#4: Protein 30S ribosomal subunit protein S3


Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#5: Protein 30S ribosomal subunit protein S4


Mass: 23311.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#6: Protein 30S ribosomal subunit protein S5


Mass: 15618.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#7: Protein 30S ribosomal subunit protein S6


Mass: 11181.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#8: Protein 30S ribosomal subunit protein S7


Mass: 15384.665 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#9: Protein 30S ribosomal subunit protein S8


Mass: 13857.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#10: Protein 30S ribosomal subunit protein S9


Mass: 14440.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3
#11: Protein 30S ribosomal subunit protein S10


Mass: 10996.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5
#12: Protein 30S ribosomal subunit protein S11


Mass: 12388.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#13: Protein 30S ribosomal subunit protein S12


Mass: 11245.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#14: Protein 30S ribosomal subunit protein S13


Mass: 12738.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9
#15: Protein 30S ribosomal subunit protein S14


Mass: 7117.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59
#16: Protein 30S ribosomal subunit protein S15


Mass: 9915.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#17: Protein 30S ribosomal subunit protein S16


Mass: 8822.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3
#18: Protein 30S ribosomal subunit protein S17


Mass: 9134.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#19: Protein 30S ribosomal subunit protein S18


Mass: 8178.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7
#20: Protein 30S ribosomal subunit protein S19


Mass: 9865.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3
#21: Protein 30S ribosomal subunit protein S20


Mass: 9278.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7

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50S ribosomal protein ... , 26 types, 27 molecules B2B3B5BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBQBRBSBTBUBWBXBZB1

#24: Protein 50S ribosomal protein L1


Mass: 23591.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L0
#25: Protein 50S ribosomal protein L7/L12


Mass: 12090.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K2
#26: Protein 50S ribosomal protein L2


Mass: 24691.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#27: Protein 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#28: Protein 50S ribosomal protein L4


Mass: 21806.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#29: Protein 50S ribosomal protein L5


Mass: 20131.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#30: Protein 50S ribosomal protein L6


Mass: 17799.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#31: Protein 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#32: Protein 50S ribosomal protein L11


Mass: 14577.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#33: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#34: Protein 50S ribosomal protein L14


Mass: 13433.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#35: Protein 50S ribosomal protein L15


Mass: 14477.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#36: Protein 50S ribosomal protein L16


Mass: 14736.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#37: Protein 50S ribosomal protein L17


Mass: 12945.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#38: Protein 50S ribosomal protein L18


Mass: 12273.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#39: Protein 50S ribosomal protein L19


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#40: Protein 50S RIBOSOMAL PROTEIN L20


Mass: 13254.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#41: Protein 50S ribosomal protein L22


Mass: 11778.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#42: Protein 50S ribosomal protein L23


Mass: 10205.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#43: Protein 50S ribosomal protein L24


Mass: 10823.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#44: Protein 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#45: Protein 50S ribosomal protein L27


Mass: 9015.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#46: Protein 50S ribosomal protein L29


Mass: 7087.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#47: Protein 50S ribosomal protein L30


Mass: 6223.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#48: Protein/peptide 50S ribosomal protein L32


Mass: 3317.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#49: Protein 50S ribosomal protein L33


Mass: 6015.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent-IDDetails
1pre-translocational E. coli ribosomeRIBOSOME0
230S ribosomal protein S21structural constituent of ribosome
330S ribosomal subunit protein S31structural constituent of ribosome
430S ribosomal subunit protein S41structural constituent of ribosome
530S ribosomal subunit protein S51structural constituent of ribosome
630S ribosomal subunit protein S61structural constituent of ribosome
730S ribosomal subunit protein S71structural constituent of ribosome
830S ribosomal subunit protein S81structural constituent of ribosome
930S ribosomal subunit protein S91structural constituent of ribosome
1030S ribosomal subunit protein S101structural constituent of ribosome
1130S ribosomal subunit protein S111structural constituent of ribosome
1230S ribosomal subunit protein S121structural constituent of ribosome
1330S ribosomal subunit protein S131structural constituent of ribosome
1430S ribosomal subunit protein S141structural constituent of ribosome
1530S ribosomal subunit protein S151structural constituent of ribosome
1630S ribosomal subunit protein S161structural constituent of ribosome
1730S ribosomal subunit protein S171structural constituent of ribosome
1830S ribosomal subunit protein S181structural constituent of ribosome
1930S ribosomal subunit protein S191structural constituent of ribosome
2030S ribosomal subunit protein S201structural constituent of ribosome
Buffer solutionpH: 7.5
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey-Carbon film grids
VitrificationCryogen name: ETHANE / Details: rapid-freezing in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jul 1, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 3.8 nm / Nominal defocus min: 1.1 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1CNSmodel fittingCNS implementation of RSRef
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction of 3D-maps by Wiener filtration
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D projection matching; conjugate gradients with regularization
Resolution: 15 Å / Num. of particles: 52181 / Nominal pixel size: 2.82 Å / Actual pixel size: 2.82 Å / Magnification calibration: TMV
Details: WITH THE USE OF APPROPRIATE STEREOCHEMICAL CONSTRAINTS, AN ATOMIC MODEL FITTED INTO AN EM MAP YIELDS AN ACCURACY OF 5-FOLD BETTER THAN THE NOMINAL RESOLUTION OF THE EM MAP. THE RESOLUTION OF ...Details: WITH THE USE OF APPROPRIATE STEREOCHEMICAL CONSTRAINTS, AN ATOMIC MODEL FITTED INTO AN EM MAP YIELDS AN ACCURACY OF 5-FOLD BETTER THAN THE NOMINAL RESOLUTION OF THE EM MAP. THE RESOLUTION OF THE ATOMIC MODEL FITTED INTO EMD-1056 (NOMINAL RESOLUTION 15.0 ANGSTROMS) IS THUS ESTIMATED TO BE BETWEEN 2-3 ANGSTROMS. REAL-SPACE REFINEMENT USING RIGID BODIES INTO EM MAP EMD-1056 (FILTERED TO A NOMINAL RESOLUTION OF 15 ANGSTROMS). RIGID BODY DEFINITION: AN AUTONOMOUS SECONDARY STRUCTURE UNIT (E.G. HELIX SEGMENT, HAIRPIN) OF THE RIBOSOMAL RNA; AN AUTONOMOUS RIBOSOMAL PROTEIN DOMAIN. THE ATOMIC MODEL USED WAS GENERATED FROM E. COLI MODELS OF X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS. IN THE ABSENCE OF E. COLI MODELS, STRUCTURES WERE DERIVED DIRECTLY FROM THE X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Target criteria: Minimization of number of poor van der Waals contacts and maximation of correlation coefficient
Details: REFINEMENT PROTOCOL--CNS implementation of RSRef
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms17749 36790 0 0 54539

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