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- PDB-4v48: Real space refined coordinates of the 30S and 50S subunits fitted... -

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Basic information

Entry
Database: PDB / ID: 4v48
TitleReal space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the initiation-like state of E. coli 70S ribosome
Components
  • (30S RIBOSOMAL PROTEIN ...) x 19
  • (50S ribosomal protein ...) x 25
  • 16S RIBOSOMAL RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • tRNA-PHE
KeywordsRIBOSOME / EF-G.GTP-bound state / ratchet-like movement / real-space refinement
Function / homology
Function and homology information


stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity ...stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / 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 DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / response to reactive oxygen species / DNA endonuclease activity / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / regulation of translation / transferase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit 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 / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L11, bacterial-type / 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 signature 2. / Ribosomal protein L16, conserved site ...Ribosomal protein L11, bacterial-type / 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 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 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 L36 signature. / 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 L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 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 L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / 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 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / 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 / Translation elongation factor EF1B/ribosomal protein S6
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S2 / 30S ribosomal protein S3 / 30S ribosomal protein S4 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S2 / 30S ribosomal protein S3 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / 30S ribosomal protein S8 / 30S ribosomal protein S9 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S16 / 30S ribosomal protein S17 / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 50S ribosomal protein L6 / 50S ribosomal protein L14 / Large ribosomal subunit protein uL15 / 50S ribosomal protein L16 / 50S ribosomal protein L17 / 50S ribosomal protein L23 / 50S ribosomal protein L30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / 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 bL36A / 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: 11.5 Å
AuthorsGao, H. / Sengupta, J. / Valle, M. / Korostelev, A. / Eswar, N. / Stagg, S.M. / Van Roey, P. / Agrawal, R.K. / Harvey, S.T. / Sali, A. ...Gao, H. / Sengupta, J. / Valle, M. / Korostelev, A. / Eswar, N. / Stagg, S.M. / Van Roey, P. / Agrawal, R.K. / Harvey, S.T. / Sali, A. / Chapman, M.S. / Frank, J.
Citation
Journal: Cell / Year: 2003
Title: Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
Authors: Haixiao Gao / Jayati Sengupta / Mikel Valle / Andrei Korostelev / Narayanan Eswar / Scott M Stagg / Patrick Van Roey / Rajendra K Agrawal / Stephen C Harvey / Andrej Sali / Michael S Chapman / Joachim Frank /
Abstract: Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting ...Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from a compact structure to a looser one, coupled with the rearrangement of many of the proteins. Furthermore, in contrast to the unchanged inter-subunit bridges formed wholly by RNA, the bridges involving proteins undergo large conformational changes following the ratchet-like motion, suggesting an important role of ribosomal proteins in facilitating the dynamics of translation.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Solution structure of the E. coli 70S ribosome at 11.5 A resolution
Authors: Gabashvili, I.S. / Agrawal, R.K. / Spahn, C.M.T. / Grassucci, R. / Svergun, D.I. / Frank, J. / Penczek, P.
#2: Journal: Nature / Year: 2000
Title: A ratchet-like inter-subunit reorganization of the ribosome during translocation
Authors: Frank, J. / Agrawal, R.K.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1P86, 1P87
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 18, 2015Group: Other
Revision 1.3Jan 24, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / em_image_scans / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 18, 2019Group: Database references / Other / Category: atom_sites / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A0: 23S ribosomal RNA
A9: 5S ribosomal RNA
A6: tRNA-PHE
AA: 50S ribosomal protein L2
AB: 50S ribosomal protein L3
AC: 50S ribosomal protein L4
AD: 50S ribosomal protein L5
AE: 50S ribosomal protein L6
AF: 50S ribosomal protein L9
AG: 50S ribosomal protein L11
AH: 50S ribosomal protein L13
AI: 50S ribosomal protein L14
AJ: 50S ribosomal protein L15
AK: 50S ribosomal protein L16
AL: 50S ribosomal protein L17
AM: 50S ribosomal protein L18
AN: 50S ribosomal protein L19
AO: 50S ribosomal protein L20
AQ: 50S ribosomal protein L22
AR: 50S ribosomal protein L23
AS: 50S ribosomal protein L24
AT: 50S ribosomal protein L25
AU: 50S ribosomal protein L27
AW: 50S ribosomal protein L29
AX: 50S ribosomal protein L30
AZ: 50S ribosomal protein L32
A1: 50S ribosomal protein L33
A4: 50S ribosomal protein L36
BA: 16S RIBOSOMAL RNA
BB: 30S RIBOSOMAL PROTEIN S2
BC: 30S RIBOSOMAL PROTEIN S3
BD: 30S RIBOSOMAL PROTEIN S4
BE: 30S RIBOSOMAL PROTEIN S5
BF: 30S RIBOSOMAL PROTEIN S6
BG: 30S RIBOSOMAL PROTEIN S7
BH: 30S RIBOSOMAL PROTEIN S8
BI: 30S RIBOSOMAL PROTEIN S9
BJ: 30S RIBOSOMAL PROTEIN S10
BK: 30S RIBOSOMAL PROTEIN S11
BL: 30S RIBOSOMAL PROTEIN S12
BM: 30S RIBOSOMAL PROTEIN S13
BN: 30S RIBOSOMAL PROTEIN S14
BO: 30S RIBOSOMAL PROTEIN S15
BP: 30S RIBOSOMAL PROTEIN S16
BQ: 30S RIBOSOMAL PROTEIN S17
BR: 30S RIBOSOMAL PROTEIN S18
BS: 30S RIBOSOMAL PROTEIN S19
BT: 30S RIBOSOMAL PROTEIN S20


Theoretical massNumber of molelcules
Total (without water)2,126,49848
Polymers2,126,49848
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, 4 molecules A0A9A6BA

#1: RNA chain 23S ribosomal RNA / Coordinate model: P atoms only


Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: EMBL: 2073407
#2: RNA chain 5S ribosomal RNA / Coordinate model: P atoms only


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: EMBL: 42753
#3: RNA chain tRNA-PHE / Coordinate model: P atoms only


Mass: 24518.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600
#29: RNA chain 16S RIBOSOMAL RNA / Coordinate model: P atoms only


Mass: 499995.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: EMBL: V00348

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50S ribosomal protein ... , 25 types, 25 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAQARASATAUAWAXAZA1A4

#4: Protein 50S ribosomal protein L2 / Coordinate model: Cα atoms only


Mass: 29792.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60422
#5: Protein 50S ribosomal protein L3 / Coordinate model: Cα atoms only


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60438
#6: Protein 50S ribosomal protein L4 / Coordinate model: Cα atoms only


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60723
#7: Protein 50S ribosomal protein L5 / Coordinate model: Cα atoms only


Mass: 20202.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P62399
#8: Protein 50S ribosomal protein L6 / Coordinate model: Cα atoms only


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02390, UniProt: P0AG56*PLUS
#9: Protein 50S ribosomal protein L9 / Coordinate model: Cα atoms only


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7R1
#10: Protein 50S ribosomal protein L11 / Coordinate model: Cα atoms only


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7J7
#11: Protein 50S ribosomal protein L13 / Coordinate model: Cα atoms only


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0AA10
#12: Protein 50S ribosomal protein L14 / Coordinate model: Cα atoms only


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02411, UniProt: P0ADY4*PLUS
#13: Protein 50S ribosomal protein L15 / Coordinate model: Cα atoms only


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02413
#14: Protein 50S ribosomal protein L16 / Coordinate model: Cα atoms only


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02414, UniProt: P0ADY7*PLUS
#15: Protein 50S ribosomal protein L17 / Coordinate model: Cα atoms only


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02416, UniProt: P0AG47*PLUS
#16: Protein 50S ribosomal protein L18 / Coordinate model: Cα atoms only


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0C018
#17: Protein 50S ribosomal protein L19 / Coordinate model: Cα atoms only


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7K6
#18: Protein 50S ribosomal protein L20 / Coordinate model: Cα atoms only


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7L3
#19: Protein 50S ribosomal protein L22 / Coordinate model: Cα atoms only


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P61175
#20: Protein 50S ribosomal protein L23 / Coordinate model: Cα atoms only


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02424, UniProt: P0ADZ2*PLUS
#21: Protein 50S ribosomal protein L24 / Coordinate model: Cα atoms only


Mass: 11208.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P60624
#22: Protein 50S ribosomal protein L25 / Coordinate model: Cα atoms only


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P68919
#23: Protein 50S ribosomal protein L27 / Coordinate model: Cα atoms only


Mass: 9015.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7L8
#24: Protein 50S ribosomal protein L29 / Coordinate model: Cα atoms only


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7M6
#25: Protein 50S ribosomal protein L30 / Coordinate model: Cα atoms only


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02430, UniProt: P0AG54*PLUS
#26: Protein 50S ribosomal protein L32 / Coordinate model: Cα atoms only


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7N4
#27: Protein 50S ribosomal protein L33 / Coordinate model: Cα atoms only


Mass: 6257.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7N9
#28: Protein/peptide 50S ribosomal protein L36 / Coordinate model: Cα atoms only


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7Q6

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30S RIBOSOMAL PROTEIN ... , 19 types, 19 molecules BBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBT

#30: Protein 30S RIBOSOMAL PROTEIN S2 / Coordinate model: Cα atoms only


Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02351, UniProt: P0A7V1*PLUS
#31: Protein 30S RIBOSOMAL PROTEIN S3 / Coordinate model: Cα atoms only


Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02352, UniProt: P0A7V5*PLUS
#32: Protein 30S RIBOSOMAL PROTEIN S4 / Coordinate model: Cα atoms only


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02354, UniProt: P0A7W0*PLUS
#33: Protein 30S RIBOSOMAL PROTEIN S5 / Coordinate model: Cα atoms only


Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02356, UniProt: P0A7W2*PLUS
#34: Protein 30S RIBOSOMAL PROTEIN S6 / Coordinate model: Cα atoms only


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02358
#35: Protein 30S RIBOSOMAL PROTEIN S7 / Coordinate model: Cα atoms only


Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02359
#36: Protein 30S RIBOSOMAL PROTEIN S8 / Coordinate model: Cα atoms only


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02361, UniProt: P0A7X0*PLUS
#37: Protein 30S RIBOSOMAL PROTEIN S9 / Coordinate model: Cα atoms only


Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02363, UniProt: P0A7X3*PLUS
#38: Protein 30S RIBOSOMAL PROTEIN S10 / Coordinate model: Cα atoms only


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02364, UniProt: P0A7R6*PLUS
#39: Protein 30S RIBOSOMAL PROTEIN S11 / Coordinate model: Cα atoms only


Mass: 13739.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02366, UniProt: P0A7S1*PLUS
#40: Protein 30S RIBOSOMAL PROTEIN S12 / Coordinate model: Cα atoms only


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02367, UniProt: P0A7S4*PLUS
#41: Protein 30S RIBOSOMAL PROTEIN S13 / Coordinate model: Cα atoms only


Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02369, UniProt: P0A7T0*PLUS
#42: Protein 30S RIBOSOMAL PROTEIN S14 / Coordinate model: Cα atoms only


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02370, UniProt: P0AG60*PLUS
#43: Protein 30S RIBOSOMAL PROTEIN S15 / Coordinate model: Cα atoms only


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02371, UniProt: P0ADZ4*PLUS
#44: Protein 30S RIBOSOMAL PROTEIN S16 / Coordinate model: Cα atoms only


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02372, UniProt: P0A7T3*PLUS
#45: Protein 30S RIBOSOMAL PROTEIN S17 / Coordinate model: Cα atoms only


Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02373, UniProt: P0AG66*PLUS
#46: Protein 30S RIBOSOMAL PROTEIN S18 / Coordinate model: Cα atoms only


Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02374, UniProt: P0A7U2*PLUS
#47: Protein 30S RIBOSOMAL PROTEIN S19 / Coordinate model: Cα atoms only


Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02375, UniProt: P0A7U3*PLUS
#48: Protein 30S RIBOSOMAL PROTEIN S20 / Coordinate model: Cα atoms only


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02378, UniProt: P0A7U8*PLUS

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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

ComponentName: E. coli 70S ribosome bound with formyl-methionyl initiator tRNA
Type: RIBOSOME
Buffer solutionName: hepes / pH: 7.5 / Details: hepes
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationDetails: 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, 1997
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 51200 X / Calibrated magnification: 51200 X / Nominal defocus max: 4340 nm / Nominal defocus min: 730 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
1RSRefmodel fitting
2RSRefmodel fittingTNT
CTF correctionDetails: CTF correction of 3D-maps
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Reference based alignment / Resolution: 11.5 Å / Nominal pixel size: 2.93 Å / Actual pixel size: 2.93 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: cross-correlation coefficient, real space R factor
Details: METHOD--auto REFINEMENT PROTOCOL--Multi-rigid body, real-space refinement
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11IBL

1ibl

11IBL1PDBexperimental model
21FJG

1fjg

11FJG2PDBexperimental model
31FFK

1ffk

11FFK3PDBexperimental model
41JJ2

1jj2

11JJ24PDBexperimental model
51LNR

1lnr
PDB Unreleased entry

11LNR5PDBexperimental model
61GIY

1giy
PDB Unreleased entry

11GIY6PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 2720 0 0 5410

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