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- PDB-4v5n: tRNA translocation on the 70S ribosome: the post- translocational... -

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Basic information

Entry
Database: PDB / ID: 4v5n
TitletRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST)
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 31
  • 16S RRNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • ELONGATION FACTOR GEF-G
  • MRNAMessenger RNA
  • TRNATransfer RNA
KeywordsRIBOSOME / TRANSLATION / ELONGATION CYCLE / TRNA TRANSLOCATION
Function / homology
Function and homology information


translation elongation factor activity / large ribosomal subunit rRNA binding / regulation of translation / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation ...translation elongation factor activity / large ribosomal subunit rRNA binding / regulation of translation / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / protein homodimerization activity / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / 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 ...: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L1, bacterial-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal L25p family / Ribosomal protein L25 / 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, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / 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 S14/S29 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type
Similarity search - Domain/homology
FUSIDIC ACID / GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...FUSIDIC ACID / GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Elongation factor G / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
ESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsRatje, A.H. / Loerke, J. / Mikolajka, A. / Bruenner, M. / Hildebrand, P.W. / Starosta, A.L. / Doenhoefer, A. / Connell, S.R. / Fucini, P. / Mielke, T. ...Ratje, A.H. / Loerke, J. / Mikolajka, A. / Bruenner, M. / Hildebrand, P.W. / Starosta, A.L. / Doenhoefer, A. / Connell, S.R. / Fucini, P. / Mielke, T. / Whitford, P.C. / Onuchic, J.N. / Yu, Y. / Sanbonmatsu, K.Y. / Hartmann, R.K. / Penczek, P.A. / Wilson, D.N. / Spahn, C.M.T.
CitationJournal: Nature / Year: 2010
Title: Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
Authors: Andreas H Ratje / Justus Loerke / Aleksandra Mikolajka / Matthias Brünner / Peter W Hildebrand / Agata L Starosta / Alexandra Dönhöfer / Sean R Connell / Paola Fucini / Thorsten Mielke / ...Authors: Andreas H Ratje / Justus Loerke / Aleksandra Mikolajka / Matthias Brünner / Peter W Hildebrand / Agata L Starosta / Alexandra Dönhöfer / Sean R Connell / Paola Fucini / Thorsten Mielke / Paul C Whitford / José N Onuchic / Yanan Yu / Karissa Y Sanbonmatsu / Roland K Hartmann / Pawel A Penczek / Daniel N Wilson / Christian M T Spahn /
Abstract: The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and ...The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A site. The translocation reaction is catalysed by elongation factor G (EF-G) in a GTP-dependent manner. Despite the availability of structures of various EF-G-ribosome complexes, the precise mechanism by which tRNAs move through the ribosome still remains unclear. Here we use multiparticle cryoelectron microscopy analysis to resolve two previously unseen subpopulations within Thermus thermophilus EF-G-ribosome complexes at subnanometre resolution, one of them with a partly translocated tRNA. Comparison of these substates reveals that translocation of tRNA on the 30S subunit parallels the swivelling of the 30S head and is coupled to unratcheting of the 30S body. Because the tRNA maintains contact with the peptidyl-tRNA-binding site (P site) on the 30S head and simultaneously establishes interaction with the exit site (E site) on the 30S platform, a novel intra-subunit 'pe/E' hybrid state is formed. This state is stabilized by domain IV of EF-G, which interacts with the swivelled 30S-head conformation. These findings provide direct structural and mechanistic insight into the 'missing link' in terms of tRNA intermediates involved in the universally conserved translocation process.
History
DepositionOct 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2XUX, 2XUY
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 18, 2015Group: Other
Revision 2.0Aug 2, 2017Group: Atomic model / Data collection / Derived calculations
Category: atom_site / em_software / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.fitting_id / _em_software.image_processing_id
Revision 2.1Dec 11, 2019Group: Other / Category: atom_sites / pdbx_database_status
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] / _pdbx_database_status.process_site
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Assembly

Deposited unit
AA: 16S RRNA
AB: 30S RIBOSOMAL PROTEIN S2
AC: 30S RIBOSOMAL PROTEIN S3
AD: 30S RIBOSOMAL PROTEIN S4
AE: 30S RIBOSOMAL PROTEIN S5
AF: 30S RIBOSOMAL PROTEIN S6
AG: 30S RIBOSOMAL PROTEIN S7
AH: 30S RIBOSOMAL PROTEIN S8
AI: 30S RIBOSOMAL PROTEIN S9
AJ: 30S RIBOSOMAL PROTEIN S10
AK: 30S RIBOSOMAL PROTEIN S11
AL: 30S RIBOSOMAL PROTEIN S12
AM: 30S RIBOSOMAL PROTEIN S13
AN: 30S RIBOSOMAL PROTEIN S14 TYPE Z
AO: 30S RIBOSOMAL PROTEIN S15
AP: 30S RIBOSOMAL PROTEIN S16
AQ: 30S RIBOSOMAL PROTEIN S17
AR: 30S RIBOSOMAL PROTEIN S18
AS: 30S RIBOSOMAL PROTEIN S19
AT: 30S RIBOSOMAL PROTEIN S20
AU: 30S RIBOSOMAL PROTEIN THX
AV: TRNA
AX: MRNA
AY: ELONGATION FACTOR G
B0: 50S RIBOSOMAL PROTEIN L27
B1: 50S RIBOSOMAL PROTEIN L28
B2: 50S RIBOSOMAL PROTEIN L29
B3: 50S RIBOSOMAL PROTEIN L30
B4: 50S RIBOSOMAL PROTEIN L31
B5: 50S RIBOSOMAL PROTEIN L32
B6: 50S RIBOSOMAL PROTEIN L33
B7: 50S RIBOSOMAL PROTEIN L34
B8: 50S RIBOSOMAL PROTEIN L35
B9: 50S RIBOSOMAL PROTEIN L36
BA: 23S RIBOSOMAL RNA
BB: 5S RIBOSOMAL RNA
BC: 50S RIBOSOMAL PROTEIN L1
BD: 50S RIBOSOMAL PROTEIN L2
BE: 50S RIBOSOMAL PROTEIN L3
BF: 50S RIBOSOMAL PROTEIN L4
BG: 50S RIBOSOMAL PROTEIN L5
BH: 50S RIBOSOMAL PROTEIN L6
BK: 50S RIBOSOMAL PROTEIN L11
BL: 50S RIBOSOMAL PROTEIN L7/L12
BN: 50S RIBOSOMAL PROTEIN L13
BO: 50S RIBOSOMAL PROTEIN L14
BP: 50S RIBOSOMAL PROTEIN L15
BQ: 50S RIBOSOMAL PROTEIN L16
BR: 50S RIBOSOMAL PROTEIN L17
BS: 50S RIBOSOMAL PROTEIN L18
BT: 50S RIBOSOMAL PROTEIN L19
BU: 50S RIBOSOMAL PROTEIN L20
BV: 50S RIBOSOMAL PROTEIN L21
BW: 50S RIBOSOMAL PROTEIN L22
BX: 50S RIBOSOMAL PROTEIN L23
BY: 50S RIBOSOMAL PROTEIN L24
BZ: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,311,29659
Polymers2,310,33657
Non-polymers9602
Water0
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 , 5 types, 5 molecules AAAVAXBABB

#1: RNA chain 16S RRNA /


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55979969
#22: RNA chain TRNA / Transfer RNA


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRNA WAS COPURIFIED WITH 70S RIBOSOMES / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8
#23: RNA chain MRNA / Messenger RNA


Mass: 3476.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MRNA WAS COPURIFIED WITH 70S RIBOSOMES / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8
#35: RNA chain 23S RIBOSOMAL RNA /


Mass: 947935.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969
#36: RNA chain 5S RIBOSOMAL RNA /


Mass: 39540.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU

#2: Protein 30S RIBOSOMAL PROTEIN S2 /


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80371
#3: Protein 30S RIBOSOMAL PROTEIN S3 /


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80372
#4: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80373
#5: Protein 30S RIBOSOMAL PROTEIN S5 /


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#6: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#7: Protein 30S RIBOSOMAL PROTEIN S7 /


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P17291
#8: Protein 30S RIBOSOMAL PROTEIN S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80374
#10: Protein 30S RIBOSOMAL PROTEIN S10 /


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#11: Protein 30S RIBOSOMAL PROTEIN S11 /


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80376
#12: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3
#13: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80377
#14: Protein 30S RIBOSOMAL PROTEIN S14 TYPE Z / Ribosome


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#16: Protein 30S RIBOSOMAL PROTEIN S16 /


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#17: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0
#19: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#20: Protein 30S RIBOSOMAL PROTEIN S20 /


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80380
#21: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Ribosome


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

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Protein , 1 types, 1 molecules AY

#24: Protein ELONGATION FACTOR G / EF-G


Mass: 76977.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET-46 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHN5

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50S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules B0B1B2B3B4B5B6B7B8B9BCBDBEBFBGBHBKBLBNBOBPBQBRBSBTBUBVBWBXBYBZ

#25: Protein 50S RIBOSOMAL PROTEIN L27 /


Mass: 9529.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60493
#26: Protein 50S RIBOSOMAL PROTEIN L28 /


Mass: 11004.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60494
#27: Protein 50S RIBOSOMAL PROTEIN L29 / / TL5


Mass: 8670.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP6
#28: Protein 50S RIBOSOMAL PROTEIN L30 /


Mass: 6799.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ6
#29: Protein 50S RIBOSOMAL PROTEIN L31 /


Mass: 8300.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SJE1
#30: Protein 50S RIBOSOMAL PROTEIN L32 /


Mass: 6722.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80339
#31: Protein 50S RIBOSOMAL PROTEIN L33 /


Mass: 6632.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P35871
#32: Protein/peptide 50S RIBOSOMAL PROTEIN L34 /


Mass: 6132.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80340
#33: Protein 50S RIBOSOMAL PROTEIN L35 /


Mass: 7506.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SKU1
#34: Protein/peptide 50S RIBOSOMAL PROTEIN L36 / / RIBOSOMAL PROTEIN B


Mass: 4435.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHR2
#37: Protein 50S RIBOSOMAL PROTEIN L1 /


Mass: 24872.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SLP7
#38: Protein 50S RIBOSOMAL PROTEIN L2 /


Mass: 30532.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60405
#39: Protein 50S RIBOSOMAL PROTEIN L3 /


Mass: 22450.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN8
#40: Protein 50S RIBOSOMAL PROTEIN L4 / / L1E


Mass: 23271.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN9
#41: Protein 50S RIBOSOMAL PROTEIN L5 /


Mass: 21061.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ0
#42: Protein 50S RIBOSOMAL PROTEIN L6 /


Mass: 19568.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#43: Protein 50S RIBOSOMAL PROTEIN L11 /


Mass: 15526.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SLP6
#44: Protein 50S RIBOSOMAL PROTEIN L7/L12 / Ribosome


Mass: 12309.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7K2
#45: Protein 50S RIBOSOMAL PROTEIN L13 /


Mass: 15927.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60488
#46: Protein 50S RIBOSOMAL PROTEIN L14 /


Mass: 13323.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP8
#47: Protein 50S RIBOSOMAL PROTEIN L15 /


Mass: 16319.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ7
#48: Protein 50S RIBOSOMAL PROTEIN L16 /


Mass: 15993.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60489
#49: Protein 50S RIBOSOMAL PROTEIN L17 /


Mass: 13750.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q9Z9H5
#50: Protein 50S RIBOSOMAL PROTEIN L18 / / TL24


Mass: 12639.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ4
#51: Protein 50S RIBOSOMAL PROTEIN L19 /


Mass: 17188.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60490
#52: Protein 50S RIBOSOMAL PROTEIN L20 /


Mass: 13779.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60491
#53: Protein 50S RIBOSOMAL PROTEIN L21 /


Mass: 11069.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60492
#54: Protein 50S RIBOSOMAL PROTEIN L22 /


Mass: 12808.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP3
#55: Protein 50S RIBOSOMAL PROTEIN L23 /


Mass: 10759.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP0
#56: Protein 50S RIBOSOMAL PROTEIN L24 /


Mass: 12085.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP9
#57: Protein 50S RIBOSOMAL PROTEIN L25 / / TL5


Mass: 23238.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHZ1

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Non-polymers , 2 types, 2 molecules

#58: Chemical ChemComp-FUA / FUSIDIC ACID / Fusidic acid


Mass: 516.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H48O6 / Comment: antibiotic, Antimicrobial*YM
#59: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Details

Sequence detailsCHAIN V: MRNA WAS COPURIFIED, THEREFORE UNKNOWN SEQUENCE CHAIN X: TRNA WAS COPURIFIED, THEREFORE ...CHAIN V: MRNA WAS COPURIFIED, THEREFORE UNKNOWN SEQUENCE CHAIN X: TRNA WAS COPURIFIED, THEREFORE UNKNOWN SEQUENCE

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Experimental details

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Experiment

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

-
Sample preparation

ComponentName: 70S-EFG-GDP-FA COMPLEX / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- VITROBOT (FEI)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Details: LOW-DOSE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Calibrated magnification: 65520 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 77 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 677
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1GROMACSmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: DEFOCUS GROUPS
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MULTIPARTICLE REFINEMENT / Resolution: 7.6 Å / Nominal pixel size: 1.26 Å / Actual pixel size: 1.26 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1799. (DEPOSITION ID: 7584).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--MDFIT REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-ID
12WRI

2wri
PDB Unreleased entry

1
22WRJ

2wrj
PDB Unreleased entry

1
RefinementHighest resolution: 7.6 Å
Refinement stepCycle: LAST / Highest resolution: 7.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24360 34199 65 0 58624

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