[English] 日本語
Yorodumi
- PDB-4v5z: Structure of a mammalian 80S ribosome obtained by docking homolog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v5z
TitleStructure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map
Components
  • (40S Ribosomal protein ...) x 16
  • (60S Ribosomal protein ...) x 33
  • (RNA Expansion segment ...) x 28
  • (RNA helix) x 2
  • 18S Ribosomal RNA
  • 28S Ribosomal RNA
  • 5.8S Ribosomal RNA
  • 5S Ribosomal RNA
  • 60S acidic ribosomal protein P0
  • E site t-RNA
  • RNA helices
KeywordsRIBOSOMAL PROTEIN/RNA / protein-RNA complex / 40S ribosomal subunit / RIBOSOMAL PROTEIN-RNA COMPLEX
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesCanis familiaris (dog)
canis familiaris (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsChandramouli, P. / Akey, C.W.
CitationJournal: Structure / Year: 2008
Title: Structure of the mammalian 80S ribosome at 8.7 A resolution.
Authors: Preethi Chandramouli / Maya Topf / Jean-François Ménétret / Narayanan Eswar / Jamie J Cannone / Robin R Gutell / Andrej Sali / Christopher W Akey /
Abstract: In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was ...In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.
History
DepositionMar 27, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2ZKQ, 2ZKR
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 25, 2015Group: Other
Revision 1.3Mar 20, 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 / em_image_scans / em_software / pdbx_initial_refinement_model / struct_ref_seq
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 / _em_software.name / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1480
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: 18S Ribosomal RNA
AB: RNA Expansion segment ES3
AC: RNA Expansion segment ES4
AD: RNA Expansion segment ES6 part I
AE: RNA Expansion segment ES6 part II
AF: RNA Expansion segment ES9
AG: RNA helix
AH: RNA helix
Aa: 40S Ribosomal protein RACK1
Ab: 40S Ribosomal protein SA
Ac: 40S Ribosomal protein S3e
Ad: 40S Ribosomal protein S9e
Ae: 40S Ribosomal protein S2e
Ag: 40S Ribosomal protein S5e
Ah: 40S Ribosomal protein S15ae
Ai: 40S Ribosomal protein S16e
Aj: 40S Ribosomal protein S20e
Ak: 40S Ribosomal protein S14e
Al: 40S Ribosomal protein S23e
Am: 40S Ribosomal protein S18e
An: 40S Ribosomal protein S29e
Ao: 40S Ribosomal protein S13e
Aq: 40S Ribosomal protein S11e
As: 40S Ribosomal protein S15e
B1: 5.8S Ribosomal RNA
B0: 28S Ribosomal RNA
BA: RNA Expansion segment ES3
BB: RNA Expansion segment ES4
BC: RNA Expansion segment ES5
BD: RNA Expansion segment ES7 part I
BE: RNA Expansion segment ES7 part II
BF: RNA Expansion segment ES7 part III
BG: RNA Expansion segment ES9
BH: RNA Expansion segment ES12
BI: RNA Expansion segment ES15 part I
BJ: RNA Expansion segment ES15 part II
BK: RNA Expansion segment ES19
BL: RNA Expansion segment ES20
BM: RNA Expansion segment ES24
BN: RNA Expansion segment ES27
BO: RNA Expansion segment ES30
BP: RNA Expansion segment ES31 part I
BQ: RNA Expansion segment ES31 part II
BR: RNA Expansion segment ES39 part I
BS: RNA Expansion segment ES39 part II
BT: RNA Expansion segment ES39 part III
BU: RNA Expansion segment ES41
BV: RNA Expansion segment ES9 part2
BW: RNA Expansion segment ES10
BX: RNA helices
BY: 5S Ribosomal RNA
BZ: E site t-RNA
Ba: 60S Ribosomal protein L8
Bb: 60S Ribosomal protein L3
Bc: 60S Ribosomal protein L4
Bd: 60S Ribosomal protein L11
Be: 60S Ribosomal protein L9
Bf: 60S Ribosomal protein L7a
Bg: 60S acidic ribosomal protein P0
Bh: 60S Ribosomal protein L10
Bi: 60S Ribosomal protein L12
Bj: 60S ribosomal protein L13a
Bk: 60S Ribosomal protein L23
Bl: 60S Ribosomal protein L27a
Bm: 60S Ribosomal protein L15e
Bn: 60S Ribosomal protein L5
Bo: 60S Ribosomal protein L18
Bp: 60S Ribosomal protein L19
B7: 60S Ribosomal protein L19
Bq: 60S Ribosomal protein L21
Br: 60S Ribosomal protein L17
Bs: 60S Ribosomal protein L23a
Bt: 60S Ribosomal protein L26
Bu: 60S Ribosomal protein L24
Bv: 60S Ribosomal protein L35
B8: 60S Ribosomal protein L35
Bw: 60S Ribosomal protein L7
Bx: 60S Ribosomal protein L31
By: 60S Ribosomal protein L32
B9: 60S Ribosomal protein L32
Bz: 60S Ribosomal protein L37a
B2: 60S Ribosomal protein L37e
B3: 60S Ribosomal protein L39e
B4: 60S Ribosomal protein L44e
B5: 60S Ribosomal protein L10a
B6: 60S Ribosomal protein L30e


Theoretical massNumber of molelcules
Total (without water)2,902,27586
Polymers2,902,27586
Non-polymers00
Water00
1


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

-
Components

-
RNA chain , 8 types, 8 molecules AAAGAHB1B0BXBYBZ

#1: RNA chain 18S Ribosomal RNA / Coordinate model: P atoms only


Mass: 504281.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Ribosome-channel complexes isolated from ER membranes were used to create a 3D map which was used to model the 40S subunit in the 80S ribosome.
Source: (natural) Canis familiaris (dog)
#7: RNA chain RNA helix / Coordinate model: P atoms only


Mass: 4539.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#8: RNA chain RNA helix / Coordinate model: P atoms only


Mass: 13335.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#25: RNA chain 5.8S Ribosomal RNA / Coordinate model: P atoms only


Mass: 39561.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) canis familiaris (dog)
#26: RNA chain 28S Ribosomal RNA / Coordinate model: P atoms only


Mass: 940211.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Ribosome-channel complexes isolated from ER membranes were used to create a 3D map which was used to model the 60S subunit in the 80S ribosome.
Source: (natural) canis familiaris (dog)
#50: RNA chain RNA helices / Coordinate model: P atoms only


Mass: 36425.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#51: RNA chain 5S Ribosomal RNA / Coordinate model: P atoms only


Mass: 37084.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#52: RNA chain E site t-RNA / Coordinate model: P atoms only


Mass: 23175.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)

+
RNA Expansion segment ... , 28 types, 28 molecules ABACADAEAFBABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBW

#2: RNA chain RNA Expansion segment ES3 / Coordinate model: P atoms only


Mass: 11182.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#3: RNA chain RNA Expansion segment ES4 / Coordinate model: P atoms only


Mass: 10202.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#4: RNA chain RNA Expansion segment ES6 part I / Coordinate model: P atoms only


Mass: 13476.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#5: RNA chain RNA Expansion segment ES6 part II / Coordinate model: P atoms only


Mass: 10256.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#6: RNA chain RNA Expansion segment ES9 / Coordinate model: P atoms only


Mass: 9915.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#27: RNA chain RNA Expansion segment ES3 / Coordinate model: P atoms only


Mass: 6687.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Expansion segment in 5.8S / Source: (natural) Canis familiaris (dog)
#28: RNA chain RNA Expansion segment ES4 / Coordinate model: P atoms only


Mass: 8617.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Expansion segment at the 3' end of 5.8S and 5' end of 28S
Source: (natural) Canis familiaris (dog)
#29: RNA chain RNA Expansion segment ES5 / Coordinate model: P atoms only


Mass: 5503.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#30: RNA chain RNA Expansion segment ES7 part I / Coordinate model: P atoms only


Mass: 5143.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#31: RNA chain RNA Expansion segment ES7 part II / Coordinate model: P atoms only


Mass: 17440.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#32: RNA chain RNA Expansion segment ES7 part III / Coordinate model: P atoms only


Mass: 38843.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#33: RNA chain RNA Expansion segment ES9 / Coordinate model: P atoms only


Mass: 15519.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#34: RNA chain RNA Expansion segment ES12 / Coordinate model: P atoms only


Mass: 8091.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#35: RNA chain RNA Expansion segment ES15 part I / Coordinate model: P atoms only


Mass: 23293.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#36: RNA chain RNA Expansion segment ES15 part II / Coordinate model: P atoms only


Mass: 9635.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#37: RNA chain RNA Expansion segment ES19 / Coordinate model: P atoms only


Mass: 8302.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#38: RNA chain RNA Expansion segment ES20 / Coordinate model: P atoms only


Mass: 6468.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#39: RNA chain RNA Expansion segment ES24 / Coordinate model: P atoms only


Mass: 6067.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#40: RNA chain RNA Expansion segment ES27 / Coordinate model: P atoms only


Mass: 25060.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#41: RNA chain RNA Expansion segment ES30 / Coordinate model: P atoms only


Mass: 6413.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#42: RNA chain RNA Expansion segment ES31 part I / Coordinate model: P atoms only


Mass: 4861.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#43: RNA chain RNA Expansion segment ES31 part II / Coordinate model: P atoms only


Mass: 9671.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#44: RNA chain RNA Expansion segment ES39 part I / Coordinate model: P atoms only


Mass: 9620.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#45: RNA chain RNA Expansion segment ES39 part II / Coordinate model: P atoms only


Mass: 12222.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#46: RNA chain RNA Expansion segment ES39 part III / Coordinate model: P atoms only


Mass: 9635.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#47: RNA chain RNA Expansion segment ES41 / Coordinate model: P atoms only


Mass: 5025.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#48: RNA chain RNA Expansion segment ES9 part2 / Coordinate model: P atoms only


Mass: 7064.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#49: RNA chain RNA Expansion segment ES10 / Coordinate model: P atoms only


Mass: 5128.112 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)

-
40S Ribosomal protein ... , 16 types, 16 molecules AaAbAcAdAeAgAhAiAjAkAlAmAnAoAqAs

#9: Protein 40S Ribosomal protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#10: Protein 40S Ribosomal protein SA


Mass: 32913.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#11: Protein 40S Ribosomal protein S3e


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#12: Protein 40S Ribosomal protein S9e


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#13: Protein 40S Ribosomal protein S2e


Mass: 19397.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#14: Protein 40S Ribosomal protein S5e


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#15: Protein 40S Ribosomal protein S15ae


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#16: Protein 40S Ribosomal protein S16e


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#17: Protein 40S Ribosomal protein S20e


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#18: Protein 40S Ribosomal protein S14e


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#19: Protein 40S Ribosomal protein S23e


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#20: Protein 40S Ribosomal protein S18e


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#21: Protein 40S Ribosomal protein S29e


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#22: Protein 40S Ribosomal protein S13e


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#23: Protein 40S Ribosomal protein S11e


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#24: Protein 40S Ribosomal protein S15e


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)

+
60S Ribosomal protein ... , 33 types, 33 molecules BaBbBcBdBeBfBhBiBjBkBlBmBnBoBpB7BqBrBsBtBuBvB8BwBxByB9BzB2B3...

#53: Protein 60S Ribosomal protein L8


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#54: Protein 60S Ribosomal protein L3


Mass: 46125.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#55: Protein 60S Ribosomal protein L4


Mass: 47627.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#56: Protein 60S Ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#57: Protein 60S Ribosomal protein L9


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#58: Protein 60S Ribosomal protein L7a


Mass: 30042.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#60: Protein 60S Ribosomal protein L10


Mass: 24628.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#61: Protein 60S Ribosomal protein L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#62: Protein 60S ribosomal protein L13a


Mass: 23595.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#63: Protein 60S Ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#64: Protein 60S Ribosomal protein L27a


Mass: 16634.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#65: Protein 60S Ribosomal protein L15e


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#66: Protein 60S Ribosomal protein L5


Mass: 34512.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#67: Protein 60S Ribosomal protein L18


Mass: 21698.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#68: Protein 60S Ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#69: Protein/peptide 60S Ribosomal protein L19


Mass: 1865.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C-terminal extension / Source: (natural) Canis familiaris (dog)
#70: Protein 60S Ribosomal protein L21


Mass: 18607.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#71: Protein 60S Ribosomal protein L17


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#72: Protein 60S Ribosomal protein L23a


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#73: Protein 60S Ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#74: Protein 60S Ribosomal protein L24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#75: Protein 60S Ribosomal protein L35


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#76: Protein/peptide 60S Ribosomal protein L35


Mass: 1115.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C-terminal extension / Source: (natural) Canis familiaris (dog)
#77: Protein 60S Ribosomal protein L7


Mass: 31492.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#78: Protein 60S Ribosomal protein L31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#79: Protein 60S Ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#80: Protein 60S Ribosomal protein L32


Mass: 6588.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C-terminal extension / Source: (natural) Canis familiaris (dog)
#81: Protein 60S Ribosomal protein L37a


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#82: Protein 60S Ribosomal protein L37e


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#83: Protein 60S Ribosomal protein L39e


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#84: Protein 60S Ribosomal protein L44e


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#85: Protein 60S Ribosomal protein L10a


Mass: 23376.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)
#86: Protein 60S Ribosomal protein L30e


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)

-
Protein , 1 types, 1 molecules Bg

#59: Protein 60S acidic ribosomal protein P0


Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis familiaris (dog)

-
Details

Sequence detailsOPPOSING STRANDS OF RNA IN SOME EXPANSION SEGMENTS HAVE BEEN NUMBERED CONSECUTIVELY AND COULD ...OPPOSING STRANDS OF RNA IN SOME EXPANSION SEGMENTS HAVE BEEN NUMBERED CONSECUTIVELY AND COULD THEREFORE LEAD TO FORMATION OF LONG BONDS BETWEEN A 5' AND 3' STRAND IN VISUALIZATION SOFTWARE. SINCE THE COMPLETE GENOME SEQUENCE OF CANIS FAMILIARIS WAS NOT AVAILABLE AT THE TIME WHEN THE DEPOSITORS DID THIS MODELING. THEREFORE, THEY USED HUMAN RNA SEQUENCE(MAINLY FROM K03432 IN GB) BELOWS ARE REFERENCE USED FOR EACH RNA CHAIN; CHAINS A,B, AND C ARE NOT MODIFIED AND ARE FROM K03432, RESIDUES 141-358,454-882,1063-1548,AND 1580-2010 FOR CHAN A RESIDUES 359-376,426-442 FOR CHAIN B AND RESIDUES 667-698 FOR CHAIN C. FOR CHAIN A MODELED USING A HOMOLOGOUS T.THERMOPHILUS MOLECULE PDB ENTRY 1J5E. THIS CHIAN IS THE 18S SEQUENCE OF THE HUMAN GB K03432 BUT WITHOUT CERTAIN RNA SEGMENTS WHICH THE DEPOSITORS CALL EXPANSION SEGMENTS. THESE EXPANSION SEGMENTS ARE THE NEW INSERTS THAT THE DEPOSITOR SEE IN MAMMALIAN AS OPPOSED TO A BACTERIAL RIBOSOME. ALSO IT CONTAINS ES7 AND ES12 EXPANSION SEGMENTS. FOR CHAINS D, E AND F MODELED SECONDARY SEQUENCE DIFFERENT FROM THE ACTUAL SEQUENCE FOR CHAIN G RNA HELIX FROM T.THERMOPHILUS PDB ENTRY 1J5E, M26924 IN GB. PART OF THE VARIABLE REGION OF ES4. FOR CHAIN H RNA HELIX FROM T.THERMOPHILUS PDB ENTRY 1J5E, M26924 IN GB. MODIFIED SLIGHTLY TO FIT INTO THE BEAK REGION OF THE HEAD. MOREOVER, THE COMPLETED PROTEIN SEQUENCES OF CANIS FAMILIARIS WERE NOT AVAILABLE AT THE TIME WHEN THE DEPOSITORS DID THIS MODELING. THEY USED HOMOLOGY MODELING PROGRAM TO DETERMINE MAMMALIAN MODELS OF THE PROTEINS AND FIT THEM INTO THEIR EM MAP. THE PROTEINS ARE FROM DIFFERENT SPECIES BASED ON WHICH PROTEIN WAS DETERMINED BY MODELER AND MOD-EM PROGRAMS TO BEST FIT THE EM MODEL. THE REFERENCE USED FOR THE PROTEIN CHAINS ARE LISTED AS BELOW; CHAIN ID DATABASE REFERENCE A(LOWER) GBLP_HUMAN P63244 B(LOWER) RSSA_BOVIN P26452 C(LOWER) RS3_HUMAN P23396 D(LOWER) RS4_THET8 P80373 E(LOWER) O89072_MOUSE O89072 G(LOWER) RS5_HUMAN P46782 H(LOWER) RS15A_HUMAN P62244 I(LOWER) RS16_HUMAN P62249 J(LOWER) RS20_HUMAN P60866 K(LOWER) RS14_HUMAN P62263 L(LOWER) RS23_HUMAN P62266 M(LOWER) RS18_HUMAN P62269 N(LOWER) RS29_HUMAN P62273 O(LOWER) RS15_THETH P80378 Q(LOWER) RS11_HUMAN P62280 S(LOWER) RS15_HUMAN P62841 FOR CHAIN D(LOWER) THIS SEQUENCE IS S4P PROTEIN IN T.THERMOPHILUS. THE FIT IN THE VOLUME HOWEVER IS VERY GOOD INDICATING HIGH STRUCTURAL HOMOLOGY WITH THE MAMMALIAN S9E PROTEIN. FOR CHAIN O(LOWER) THIS SEQUENCE IS S15P PROTEIN IN T.THERMOPHILUS. THE FIT IN THE VOLUME HOWEVER IS VERY GOOD INDICATING HIGH STRUCTURAL HOMOLOGY WITH THE MAMMALIAN S13E PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent-ID
140S ribosomal subunit in the 80S ribosome-channel complexRIBOSOME0
240S ribosomal subunit1
Buffer solutionName: 30mM Hepes, 50mM KAc, 10mM Mg acetate, 1.5% digitonin / pH: 7.5
Details: 30mM Hepes, 50mM KAc, 10mM Mg acetate, 1.5% digitonin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: thin carbon film on copper 400 mesh grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: plunge freezing with a custom apparatus at 4C and RH greater than 90 percent

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Apr 1, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51000 X / Nominal defocus max: 4400 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2Insight IImodel fitting
3Mod-EMmodel fitting
4MODPIPEmodel fitting
5Omodel fitting
6RSRefmodel fitting
7RELION3D reconstruction
CTF correctionDetails: CTF correction using phase flipping and setsf in EMAN to correct the amplitudes
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: projection matching / Resolution: 8.7 Å / Num. of particles: 78800 / Nominal pixel size: 2.73 Å / Actual pixel size: 2.73 Å
Magnification calibration: Used the 4.6A spacing of vermiculite as a standard
Details: Refinements done in EMAN / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: Rigid body fitting and best visual fit using the program O for RNA. For the proteins DOPE score and other statistical techniques were used to evaluate the best fold and a local ...Target criteria: Rigid body fitting and best visual fit using the program O for RNA. For the proteins DOPE score and other statistical techniques were used to evaluate the best fold and a local exhaustive exploration of Euler angles was used to evaluate the best fit into the density.
Details: REFINEMENT PROTOCOL--Rigid body
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11J5E

1j5e

11J5E1PDBexperimental model
21VI6

1vi6

11VI62PDBexperimental model
31FJG

1fjg

11FJG3PDBexperimental model
41IGV

1igv

11IGV4PDBexperimental model
51I6U

1i6u

11I6U5PDBexperimental model
62AVY

2avy
PDB Unreleased entry

12AVY6PDBexperimental model
71G1X

1g1x

11G1X7PDBexperimental model
81RQ6

1rq6

11RQ68PDBexperimental model
91K7K

1k7k

11K7K9PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms16933 1612 0 0 18545

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more