4D61 Ribosome date Nov 07, 2014
title Cryo-Em Structures Of Ribosomal 80s Complexes With Terminati And Cricket Paralysis Virus Ires Reveal The Ires In The Tra State
authors M.Muhs, T.Hilal, T.Mielke, M.A.Skabkin, K.Y.Sanbonmatsu, T.V.Pest C.M.T.Spahn
compound source
Molecule: 18s Rrna
Chain: 1
Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein Sa
Chain: A
Synonym: 40s Ribosomal Protein Us2,37 Kda Laminin Receptor 37lrp, 3767 Kda Laminin Receptor, Lrplr, 67 Kda Laminin R 67lr, Colon Carcinoma Laminin-Binding Protein, Laminin Rece Lamr, Laminin-Binding Protein Precursor P40, Lbpp40, Multi Resistance-Associated Protein Mgr1-Ag, Nem1chd4;

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S3a
Chain: B
Synonym: 40s Ribosomal Protein Es1, V-Fos Transformation Ef Protein, Fte-1;

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S2
Chain: C
Synonym: 40s Ribosomal Protein Us5, Protein Llrep3

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S3
Chain: D
Synonym: 40s Ribosomal Protein Us3

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S4, Y Isoform 1
Chain: E
Synonym: 40s Ribosomal Protein Es4

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S5
Chain: F
Synonym: 40s Ribosomal Protein Us7

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S6
Chain: G
Synonym: 40s Ribosomal Protein Es6, Phosphoprotein Np33

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S7
Chain: H
Synonym: 40s Ribosomal Protein Es7

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S8
Chain: I
Synonym: 40s Ribosomal Protein Es8

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S9
Chain: J
Synonym: 40s Ribosomal Protein Us4

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S10
Chain: K
Synonym: 40s Ribosomal Protein Es10

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S11
Chain: L
Synonym: 40s Ribosomal Protein Us17

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S12
Chain: M
Synonym: 40s Ribosomal Protein Es12

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S13
Chain: N
Synonym: 40s Ribosomal Protein Us15

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S14
Chain: O
Synonym: 40s Ribosomal Protein Us11

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S15
Chain: P
Synonym: 40s Ribosomal Protein Us19, Rig Protein

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S16
Chain: Q
Synonym: 40s Ribosomal Protein Us9

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S17
Chain: R
Synonym: 40s Ribosomal Protein Es17

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S18
Chain: S
Synonym: 40s Ribosomal Protein Us13, Ke-3, Ke3

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S19
Chain: T
Synonym: 40s Ribosomal Protein Es19

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S20
Chain: U
Synonym: 40s Ribosomal Protein Us10

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S21
Chain: V
Synonym: 40s Ribosomal Protein Es21

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S15a
Chain: W
Synonym: 40s Ribosomal Protein Us8

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S23
Chain: X
Synonym: 40s Ribosomal Protein Us12

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S24
Chain: Y
Synonym: 40s Ribosomal Protein Es24

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S25
Chain: Z
Synonym: 40s Ribosomal Protein Es25

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S26
Chain: a
Synonym: 40s Ribosomal Protein Es26

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S27
Chain: b
Synonym: 40s Ribosomal Protein Es27, Metallopan-Stimulin 1,

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S28
Chain: c
Synonym: 40s Ribosomal Protein Es28

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S29
Chain: d
Synonym: 40s Ribosomal Protein Us14

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: 40s Ribosomal Protein S30
Chain: e
Synonym: 40s Ribosomal Protein Es30

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: Ubiquitin-40s Ribosomal Protein S27a
Chain: f
Synonym: 40s Ribosomal Protein Es31, Ubiquitin Carboxyl Ext Protein 80;

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: Guanine Nucleotide-Binding Protein Subunit Beta-2
Chain: g
Synonym: Cell Proliferation-Inducing Gene 21 Protein, Guani Tide-Binding Protein Subunit Beta-Like Protein 12.3, Human Ncer Oncogene 7 Protein, Hlc-7, Receptor For Activated C Ki Eceptor Of Activated Protein Kinase C 1, Rack1;

Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986

Molecule: Eukaryotic Peptide Chain Release Factor Subunit 1
Chain: h
Synonym: Eukaryotic Release Factor 1, Erf1, Protein Cl1, Tb
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Eukaryotic Peptide Chain Release Factor Gtp-Bindi Erf3a;
Chain: I
Fragment: G-Domain, Unp Residues 210-635
Synonym: Eukaryotic Peptide Chain Release Factor Subunit 3a G1 To S Phase Transition Protein 1 Homolog;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Cricket Paralysis Virus Ires Rna
Chain: j
Engineered: Yes

Synthetic: Yes
Organism_scientific: Cricket Paralysis Virus
Organism_taxid: 12136
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 9.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


L


M


N


O
  • translation regulator activi...


  • P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    a


    b


    c


    d


    e


    f


    h


    i


    Primary referenceCryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES., Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CM, Mol Cell. 2015 Feb 5;57(3):422-432. doi: 10.1016/j.molcel.2014.12.016. Epub 2015 , Jan 15. PMID:25601755
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1500 Kb) [Save to disk]
  • Biological Unit Coordinates (4d61.pdb1.gz) 1486 Kb
  • CSU: Contacts of Structural Units for 4D61
  • Retrieve 4D61 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D61 from S2C, [Save to disk]
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  • Visual 3D analysis of 4D61
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  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4D61, from MSDmotif at EBI
  • Fold representative 4d61 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d61_A] [4d61_i] [4d61_T] [4d61_C] [4d61_M] [4d61_D] [4d61_J] [4d61_O] [4d61_I] [4d61_W] [4d61_S] [4d61_g] [4d61_f] [4d61_F] [4d61_e] [4d61] [4d61_h] [4d61_j] [4d61_b] [4d61_X] [4d61_c] [4d61_d] [4d61_1] [4d61_H] [4d61_E] [4d61_Y] [4d61_R] [4d61_Q] [4d61_P] [4d61_N] [4d61_V] [4d61_U] [4d61_G] [4d61_Z] [4d61_a] [4d61_K] [4d61_L] [4d61_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4D61: [KH] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4] [UBQ] [WD40] [eRF1_1 ] by SMART
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