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- PDB-4uje: Regulation of the mammalian elongation cycle by 40S subunit rolli... -

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Basic information

Entry
Database: PDB / ID: 4uje
TitleRegulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement
Components
  • (40S RIBOSOMAL PROTEIN ...) x 31
  • (60S RIBOSOMAL PROTEIN ...) x 42
  • 18S Ribosomal RNA
  • 28S Ribosomal RNA
  • 5.8S Ribosomal RNA
  • 5S Ribosomal RNA
  • GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
  • Messenger RNA
  • TRNA-LYS
  • TRNA-PHE
  • UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
  • UBIQUITIN-60S RIBOSOMAL PROTEIN L40
KeywordsRIBOSOME / TRANSLATION / MAMMALIAN 80S RIBOSOME / ELONGATION CYCLE / POST-TRANSLOCATIONAL STATE / TRNA SELECTION
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
ORYCTOLAGUS CUNICULUS (rabbit)
BOS TAURUS (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsBudkevich, T.V. / Giesebrecht, J. / Behrmann, E. / Loerke, J. / Ramrath, D.J.F. / Mielke, T. / Ismer, J. / Hildebrand, P. / Tung, C.-S. / Nierhaus, K.H. ...Budkevich, T.V. / Giesebrecht, J. / Behrmann, E. / Loerke, J. / Ramrath, D.J.F. / Mielke, T. / Ismer, J. / Hildebrand, P. / Tung, C.-S. / Nierhaus, K.H. / Sanbonmatsu, K.Y. / Spahn, C.M.T.
CitationJournal: Cell / Year: 2014
Title: Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement.
Authors: Tatyana V Budkevich / Jan Giesebrecht / Elmar Behrmann / Justus Loerke / David J F Ramrath / Thorsten Mielke / Jochen Ismer / Peter W Hildebrand / Chang-Shung Tung / Knud H Nierhaus / ...Authors: Tatyana V Budkevich / Jan Giesebrecht / Elmar Behrmann / Justus Loerke / David J F Ramrath / Thorsten Mielke / Jochen Ismer / Peter W Hildebrand / Chang-Shung Tung / Knud H Nierhaus / Karissa Y Sanbonmatsu / Christian M T Spahn /
Abstract: The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution ...The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅Val-tRNA⋅GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ribosomes, a rotation of the small subunit around its long axis and orthogonal to the well-known intersubunit rotation distinguishes the posttranslocational state from the classical pretranslocational state ribosome. We term this motion "subunit rolling." Correspondingly, a mammalian decoding complex visualized in substates before and after codon recognition reveals structural distinctions from the bacterial system. These findings suggest how codon recognition leads to GTPase activation in the mammalian system and demonstrate that in mammalia subunit rolling occurs during tRNA selection.
History
DepositionApr 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4CXB, 4CXC, 4CXD, 4CXE / Details: supersedes the associated split entries
Revision 1.1Jun 8, 2016Group: Other / Source and taxonomy
Revision 1.2Jul 5, 2017Group: Data collection / Structure summary / Category: diffrn_radiation_wavelength / entity / Item: _entity.pdbx_description
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / em_3d_fitting ...atom_site / em_3d_fitting / em_software / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_3d_fitting.target_criteria / _em_software.image_processing_id / _pdbx_validate_close_contact.auth_atom_id_1
Revision 3.0Jun 26, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_seq_map_depositor_info / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Dec 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 3.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

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Assembly

Deposited unit
AV: TRNA-LYS
AW: TRNA-PHE
AX: Messenger RNA
B1: 18S Ribosomal RNA
BA: 40S RIBOSOMAL PROTEIN SA
BB: 40S RIBOSOMAL PROTEIN S3A
BC: 40S RIBOSOMAL PROTEIN S2
BD: 40S RIBOSOMAL PROTEIN S3
BE: 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1
BF: 40S RIBOSOMAL PROTEIN S5
BG: 40S RIBOSOMAL PROTEIN S6
BH: 40S RIBOSOMAL PROTEIN S7
BI: 40S RIBOSOMAL PROTEIN S8
BJ: 40S RIBOSOMAL PROTEIN S9
BK: 40S RIBOSOMAL PROTEIN S10
BL: 40S RIBOSOMAL PROTEIN S11
BM: 40S RIBOSOMAL PROTEIN S12
BN: 40S RIBOSOMAL PROTEIN S13
BO: 40S RIBOSOMAL PROTEIN S14
BP: 40S RIBOSOMAL PROTEIN S15
BQ: 40S RIBOSOMAL PROTEIN S16
BR: 40S RIBOSOMAL PROTEIN S17
BS: 40S RIBOSOMAL PROTEIN S18
BT: 40S RIBOSOMAL PROTEIN S19
BU: 40S RIBOSOMAL PROTEIN S20
BV: 40S RIBOSOMAL PROTEIN S21
BW: 40S RIBOSOMAL PROTEIN S15A
BX: 40S RIBOSOMAL PROTEIN S23
BY: 40S RIBOSOMAL PROTEIN S24
BZ: 40S RIBOSOMAL PROTEIN S25
Ba: 40S RIBOSOMAL PROTEIN S26
Bb: 40S RIBOSOMAL PROTEIN S27
Bc: 40S RIBOSOMAL PROTEIN S28
Bd: 40S RIBOSOMAL PROTEIN S29
Be: 40S RIBOSOMAL PROTEIN S30
Bf: UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
Bg: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
CA: 60S RIBOSOMAL PROTEIN L8
CB: 60S RIBOSOMAL PROTEIN L3
CC: 60S RIBOSOMAL PROTEIN L4
CD: 60S RIBOSOMAL PROTEIN L5
CE: 60S RIBOSOMAL PROTEIN L6
CF: 60S RIBOSOMAL PROTEIN L7
CG: 60S RIBOSOMAL PROTEIN L7A
CH: 60S RIBOSOMAL PROTEIN L9
CI: 60S RIBOSOMAL PROTEIN L10
CJ: 60S RIBOSOMAL PROTEIN L11
CL: 60S RIBOSOMAL PROTEIN L13
CM: 60S RIBOSOMAL PROTEIN L14
CN: 60S RIBOSOMAL PROTEIN L15
CO: 60S RIBOSOMAL PROTEIN L13A
CP: 60S RIBOSOMAL PROTEIN L17
CQ: 60S RIBOSOMAL PROTEIN L18
CR: 60S RIBOSOMAL PROTEIN L19
CS: 60S RIBOSOMAL PROTEIN L18A
CT: 60S RIBOSOMAL PROTEIN L21
CU: 60S RIBOSOMAL PROTEIN L22
CV: 60S RIBOSOMAL PROTEIN L23
CW: 60S RIBOSOMAL PROTEIN L24
CX: 60S RIBOSOMAL PROTEIN L23A
CY: 60S RIBOSOMAL PROTEIN L26
CZ: 60S RIBOSOMAL PROTEIN L27
Ca: 60S RIBOSOMAL PROTEIN L27A
Cb: 60S RIBOSOMAL PROTEIN L29
Cc: 60S RIBOSOMAL PROTEIN L30
Cd: 60S RIBOSOMAL PROTEIN L31
Ce: 60S RIBOSOMAL PROTEIN L32
Cf: 60S RIBOSOMAL PROTEIN L35A
Cg: 60S RIBOSOMAL PROTEIN L34
Ch: 60S RIBOSOMAL PROTEIN L35
Ci: 60S RIBOSOMAL PROTEIN L36
Cj: 60S RIBOSOMAL PROTEIN L37
Ck: 60S RIBOSOMAL PROTEIN L38
Cl: 60S RIBOSOMAL PROTEIN L39
Cm: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
Cn: 60S RIBOSOMAL PROTEIN L41
Co: 60S RIBOSOMAL PROTEIN L36A
Cp: 60S RIBOSOMAL PROTEIN L37A
Ct: 60S RIBOSOMAL PROTEIN L28
Cu: 60S RIBOSOMAL PROTEIN L10A
A2: 28S Ribosomal RNA
A3: 5.8S Ribosomal RNA
A4: 5S Ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)3,858,79683
Polymers3,858,79683
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 , 7 types, 7 molecules AVAWAXB1A2A3A4

#1: RNA chain TRNA-LYS


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: FOR MODELING E.COLI TRNAPHE (CHAIN C, PDB ID CODE 3I8G) WAS USED.
Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#2: RNA chain TRNA-PHE


Mass: 24599.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: FOR MODELING E.COLI TRNAPHE (CHAIN D, PDB ID CODE 3I8G) WAS USED.
Source: (natural) BOS TAURUS (domestic cattle) / Organ: LIVER
#3: RNA chain Messenger RNA


Mass: 8527.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOR MODELING MRNA (CHAIN 1, PDB ID CODE 3I8G) WAS USED.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
#4: RNA chain 18S Ribosomal RNA


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#81: RNA chain 28S Ribosomal RNA


Mass: 1625917.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#82: RNA chain 5.8S Ribosomal RNA


Mass: 62616.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#83: RNA chain 5S Ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

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40S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBe

#5: Protein 40S RIBOSOMAL PROTEIN SA / 40S RIBOSOMAL PROTEIN US2 / 37 KDA LAMININ RECEPTOR PRECURSOR / 37LRP / 37/67 KDA LAMININ RECEPTOR ...40S RIBOSOMAL PROTEIN US2 / 37 KDA LAMININ RECEPTOR PRECURSOR / 37LRP / 37/67 KDA LAMININ RECEPTOR / LRP/LR / 67 KDA LAMININ RECEPTOR / 67LR / COLON CARCINOMA LAMININ-BINDING PROTEIN / LAMININ RECEPTOR 1 / LAMR / LAMININ-BINDING PROTEIN PRECURSOR P40 / LBP/P40 / MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN MGR1-AG / NEM/1CHD4


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#6: Protein 40S RIBOSOMAL PROTEIN S3A / 40S RIBOSOMAL PROTEIN ES1 / V-FOS TRANSFORMATION EFFECTOR PROTEIN / FTE-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#7: Protein 40S RIBOSOMAL PROTEIN S2 / 40S RIBOSOMAL PROTEIN US5 / PROTEIN LLREP3


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#8: Protein 40S RIBOSOMAL PROTEIN S3 / 40S RIBOSOMAL PROTEIN US3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#9: Protein 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1 / 40S RIBOSOMAL PROTEIN ES4


Mass: 29512.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#10: Protein 40S RIBOSOMAL PROTEIN S5 / 40S RIBOSOMAL PROTEIN US7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#11: Protein 40S RIBOSOMAL PROTEIN S6 / 40S RIBOSOMAL PROTEIN ES6 / PHOSPHOPROTEIN NP33


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#12: Protein 40S RIBOSOMAL PROTEIN S7 / 40S RIBOSOMAL PROTEIN ES7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#13: Protein 40S RIBOSOMAL PROTEIN S8 / 40S RIBOSOMAL PROTEIN ES8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#14: Protein 40S RIBOSOMAL PROTEIN S9 / 40S RIBOSOMAL PROTEIN US4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#15: Protein 40S RIBOSOMAL PROTEIN S10 / 40S RIBOSOMAL PROTEIN ES10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#16: Protein 40S RIBOSOMAL PROTEIN S11 / 40S RIBOSOMAL PROTEIN US17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#17: Protein 40S RIBOSOMAL PROTEIN S12 / 40S RIBOSOMAL PROTEIN ES12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#18: Protein 40S RIBOSOMAL PROTEIN S13 / 40S RIBOSOMAL PROTEIN US15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#19: Protein 40S RIBOSOMAL PROTEIN S14 / 40S RIBOSOMAL PROTEIN US11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#20: Protein 40S RIBOSOMAL PROTEIN S15 / 40S RIBOSOMAL PROTEIN US19 / RIG PROTEIN


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#21: Protein 40S RIBOSOMAL PROTEIN S16 / 40S RIBOSOMAL PROTEIN US9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#22: Protein 40S RIBOSOMAL PROTEIN S17 / 40S RIBOSOMAL PROTEIN ES17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#23: Protein 40S RIBOSOMAL PROTEIN S18 / 40S RIBOSOMAL PROTEIN US13 / KE-3 / KE3


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#24: Protein 40S RIBOSOMAL PROTEIN S19 / 40S RIBOSOMAL PROTEIN ES19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#25: Protein 40S RIBOSOMAL PROTEIN S20 / 40S RIBOSOMAL PROTEIN US10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#26: Protein 40S RIBOSOMAL PROTEIN S21 / 40S RIBOSOMAL PROTEIN ES21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#27: Protein 40S RIBOSOMAL PROTEIN S15A / 40S RIBOSOMAL PROTEIN US8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#28: Protein 40S RIBOSOMAL PROTEIN S23 / 40S RIBOSOMAL PROTEIN US12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#29: Protein 40S RIBOSOMAL PROTEIN S24 / 40S RIBOSOMAL PROTEIN ES24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#30: Protein 40S RIBOSOMAL PROTEIN S25 / 40S RIBOSOMAL PROTEIN ES25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#31: Protein 40S RIBOSOMAL PROTEIN S26 / 40S RIBOSOMAL PROTEIN ES26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#32: Protein 40S RIBOSOMAL PROTEIN S27 / 40S RIBOSOMAL PROTEIN ES27 / METALLOPAN-STIMULIN 1 / MPS-1


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#33: Protein 40S RIBOSOMAL PROTEIN S28 / 40S RIBOSOMAL PROTEIN ES28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#34: Protein 40S RIBOSOMAL PROTEIN S29 / 40S RIBOSOMAL PROTEIN US14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#35: Protein 40S RIBOSOMAL PROTEIN S30 / 40S RIBOSOMAL PROTEIN ES30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

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Protein , 3 types, 3 molecules BfBgCm

#36: Protein UBIQUITIN-40S RIBOSOMAL PROTEIN S27A / 40S RIBOSOMAL PROTEIN ES31 / UBIQUITIN CARBOXYL EXTENSION PROTEIN 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#37: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 / CELL PROLIFERATION-INDUCING GENE 21 PROTEIN / GUANINE NUCLEO TIDE-BINDING PROTEIN SUBUNIT BETA-LIKE ...CELL PROLIFERATION-INDUCING GENE 21 PROTEIN / GUANINE NUCLEO TIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN 12.3 / HUMAN LUNG CA NCER ONCOGENE 7 PROTEIN / HLC-7 / RECEPTOR FOR ACTIVATED C KINASE / R ECEPTOR OF ACTIVATED PROTEIN KINASE C 1 / RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#75: Protein UBIQUITIN-60S RIBOSOMAL PROTEIN L40 / 60S RIBOSOMAL PROTEIN EL40 / EP52 / UBIQUITIN A-52 RESIDUE RIBOSOMAL PROTEIN FUSION PRODUCT 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

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60S RIBOSOMAL PROTEIN ... , 42 types, 42 molecules CACBCCCDCECFCGCHCICJCLCMCNCOCPCQCRCSCTCUCVCWCXCYCZCaCbCcCdCe...

#38: Protein 60S RIBOSOMAL PROTEIN L8 / 60S RIBOSOMAL PROTEIN UL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#39: Protein 60S RIBOSOMAL PROTEIN L3 / 60S RIBOSOMAL PROTEIN UL3 / HIV-1 TAR RNA-BINDING PROTEIN B / TARBP-B


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#40: Protein 60S RIBOSOMAL PROTEIN L4 / 60S RIBOSOMAL PROTEIN UL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#41: Protein 60S RIBOSOMAL PROTEIN L5 / 60S RIBOSOMAL PROTEIN UL18


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#42: Protein 60S RIBOSOMAL PROTEIN L6 / 60S RIBOSOMAL PROTEIN EL6 / NEOPLASM-RELATED PROTEIN C140 / TAX-RESPONSIVE ENHANCER ELEM ENT- ...60S RIBOSOMAL PROTEIN EL6 / NEOPLASM-RELATED PROTEIN C140 / TAX-RESPONSIVE ENHANCER ELEM ENT-BINDING PROTEIN 107 / TAXREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#43: Protein 60S RIBOSOMAL PROTEIN L7 / 60S RIBOSOMAL PROTEIN UL30


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#44: Protein 60S RIBOSOMAL PROTEIN L7A / 60S RIBOSOMAL PROTEIN EL8 / PLA-X POLYPEPTIDE / SURFEIT LOCUS PROTEIN 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#45: Protein 60S RIBOSOMAL PROTEIN L9 / 60S RIBOSOMAL PROTEIN UL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#46: Protein 60S RIBOSOMAL PROTEIN L10 / 60S RIBOSOMAL PROTEIN UL16 / LAMININ RECEPTOR HOMOLOG / PROTEIN QM / TUMOR SUPPRESSOR QM


Mass: 24657.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#47: Protein 60S RIBOSOMAL PROTEIN L11 / 60S RIBOSOMAL PROTEIN UL5 / CLL-ASSOCIATED ANTIGEN KW-12


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#48: Protein 60S RIBOSOMAL PROTEIN L13 / 60S RIBOSOMAL PROTEIN EL13 / BREAST BASIC CONSERVED PROTEIN 1


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#49: Protein 60S RIBOSOMAL PROTEIN L14 / 60S RIBOSOMAL PROTEIN EL14 / CAG-ISL 7


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#50: Protein 60S RIBOSOMAL PROTEIN L15 / 60S RIBOSOMAL PROTEIN EL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#51: Protein 60S RIBOSOMAL PROTEIN L13A / 60S RIBOSOMAL PROTEIN UL13 / 23 KDA HIGHLY BASIC PROTEIN


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#52: Protein 60S RIBOSOMAL PROTEIN L17 / 60S RIBOSOMAL PROTEIN UL22 / 60S RIBOSOMAL PROTEIN L23 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#53: Protein 60S RIBOSOMAL PROTEIN L18 / 60S RIBOSOMAL PROTEIN EL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#54: Protein 60S RIBOSOMAL PROTEIN L19 / 60S RIBOSOMAL PROTEIN EL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#55: Protein 60S RIBOSOMAL PROTEIN L18A / 60S RIBOSOMAL PROTEIN EL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#56: Protein 60S RIBOSOMAL PROTEIN L21 / 60S RIBOSOMAL PROTEIN EL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#57: Protein 60S RIBOSOMAL PROTEIN L22 / 60S RIBOSOMAL PROTEIN EL22 / EBER-ASSOCIATED PROTEIN / EAP / EPSTEIN-BARR VIRUS SMALL RNA- ...60S RIBOSOMAL PROTEIN EL22 / EBER-ASSOCIATED PROTEIN / EAP / EPSTEIN-BARR VIRUS SMALL RNA- ASSOCIATED PROTEIN / HEPARIN-BINDING PROTEIN HBP15


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#58: Protein 60S RIBOSOMAL PROTEIN L23 / 60S RIBOSOMAL PROTEIN UL14 / 60S RIBOSOMAL PROTEIN L17


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#59: Protein 60S RIBOSOMAL PROTEIN L24 / 60S RIBOSOMAL PROTEIN EL24 / 60S RIBOSOMAL PROTEIN L30


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#60: Protein 60S RIBOSOMAL PROTEIN L23A / 60S RIBOSOMAL PROTEIN UL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#61: Protein 60S RIBOSOMAL PROTEIN L26 / 60S RIBOSOMAL PROTEIN UL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#62: Protein 60S RIBOSOMAL PROTEIN L27 / 60S RIBOSOMAL PROTEIN EL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#63: Protein 60S RIBOSOMAL PROTEIN L27A / 60S RIBOSOMAL PROTEIN UL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#64: Protein 60S RIBOSOMAL PROTEIN L29 / 60S RIBOSOMAL PROTEIN EL29 / CELL SURFACE HEPARIN-BINDING PROTEIN HIP


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#65: Protein 60S RIBOSOMAL PROTEIN L30 / 60S RIBOSOMAL PROTEIN EL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#66: Protein 60S RIBOSOMAL PROTEIN L31 / 60S RIBOSOMAL PROTEIN EL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#67: Protein 60S RIBOSOMAL PROTEIN L32 / 60S RIBOSOMAL PROTEIN EL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#68: Protein 60S RIBOSOMAL PROTEIN L35A / 60S RIBOSOMAL PROTEIN EL33 / CELL GROWTH-INHIBITING GENE 33 PROTEIN


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#69: Protein 60S RIBOSOMAL PROTEIN L34 / 60S RIBOSOMAL PROTEIN EL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#70: Protein 60S RIBOSOMAL PROTEIN L35 / 60S RIBOSOMAL PROTEIN UL29


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#71: Protein 60S RIBOSOMAL PROTEIN L36 / 60S RIBOSOMAL PROTEIN EL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#72: Protein 60S RIBOSOMAL PROTEIN L37 / 60S RIBOSOMAL PROTEIN EL37 / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#73: Protein 60S RIBOSOMAL PROTEIN L38 / 60S RIBOSOMAL PROTEIN EL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#74: Protein 60S RIBOSOMAL PROTEIN L39 / 60S RIBOSOMAL PROTEIN EL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#76: Protein/peptide 60S RIBOSOMAL PROTEIN L41 / 60S RIBOSOMAL PROTEIN EL41 / HG12


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#77: Protein 60S RIBOSOMAL PROTEIN L36A / 60S RIBOSOMAL PROTEIN EL44 / 60S RIBOSOMAL PROTEIN L44 / CELL GROWTH-INHIBITING GENE 15 PROTEIN / ...60S RIBOSOMAL PROTEIN EL44 / 60S RIBOSOMAL PROTEIN L44 / CELL GROWTH-INHIBITING GENE 15 PROTEIN / CELL MIGRATION-INDUCING GENE 6 PROTEIN


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#78: Protein 60S RIBOSOMAL PROTEIN L37A / 60S RIBOSOMAL PROTEIN EL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#79: Protein 60S RIBOSOMAL PROTEIN L28 / 60S RIBOSOMAL PROTEIN EL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#80: Protein 60S RIBOSOMAL PROTEIN L10A / 60S RIBOSOMAL PROTEIN UL1 / CSA-19 / NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED ...60S RIBOSOMAL PROTEIN UL1 / CSA-19 / NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 6 / NEDD-6


Mass: 23174.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

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Details

Has protein modificationY

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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: POST-TRANSLOCATIONAL RABBIT 80S RIBOSOME WITH TWO TRNAS AND MRNA BOUND
Type: RIBOSOME
Buffer solutionName: 20MM HEPES-KOH, 5MM MGCL2, 100 MM NH4CL, 6 MM BETA-MERCAPTOETHANOL 0.8 MM SPERMIDINE, 0.6 MM SPERMINE
pH: 7.5
Details: 20MM HEPES-KOH, 5MM MGCL2, 100 MM NH4CL, 6 MM BETA-MERCAPTOETHANOL 0.8 MM SPERMIDINE, 0.6 MM SPERMINE
SpecimenConc.: 1.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 80, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jun 2, 2008 / Details: MINIMAL DOSE SYSTEM
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 65520 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 826
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1SPARX3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: DEFOCUS GROUP
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MULTI-REFERENCE TEMPLATE MATCHING / Resolution: 6.9 Å / Num. of particles: 236113 / Nominal pixel size: 1.26 Å / Actual pixel size: 1.26 Å
Magnification calibration: CROSS- -CORRELATION WITH KNOWN STRUCTURE
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2620. (DEPOSITION ID: 12402).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--MDFIT
RefinementHighest resolution: 6.9 Å
Refinement stepCycle: LAST / Highest resolution: 6.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3805 0 0 3805

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