5JPQ Ribosome date May 04, 2016
title Cryo-Em Structure Of The 90s Pre-Ribosome
authors M.Turk, J.Cheng, O.Berninghausen, M.Kornprobst, D.Flemming, I.C.K M.Kos, M.Thoms, E.Hurt, R.Beckmann
compound source
Molecule: Wd40 Domain Proteins
Chain: A, B, C, D, E, F, J, K, L, N, P, l, n
Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Utp10
Chain: G

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Utp-A Oligomerization Domain
Chain: H

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: U3 Small Nucleolar Rna-Associated Protein 21
Chain: I
Synonym: U3 Snorna-Associated Protein 21,U Three Protein 21

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292

Molecule: Wd40 Domain Proteins
Chain: M, O, m

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Utp6
Chain: Q

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Utp-B Oligomerisation Domain
Chain: R

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Pre Mrna Splicing Protein
Chain: S, T

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Snu13
Chain: U, V

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Nop1
Chain: W, X

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Rrp9
Chain: Y

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Rcl1
Chain: Z

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Bms1
Chain: a

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Imp3
Chain: b

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Putative U3 Small Nucleolar Ribonucleoprotein
Chain: c

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Utp24
Chain: d

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 285209

Molecule: Emg1
Chain: e, f

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Krr1 Small Subunit Processome Component
Chain: g, h
Synonym: Krr-R Motif-Containing Protein 1

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 759272

Molecule: Kre33
Chain: I, j

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Utp30
Chain: k

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Es1
Chain: o

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Es4
Chain: p

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Us7
Chain: q

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Es6
Chain: r

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Es7
Chain: s

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Es8
Chain: t

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Us4
Chain: u

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Us15
Chain: v

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Us11
Chain: w

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Us9
Chain: x

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Us17
Chain: y

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Us8
Chain: z

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Es24
Chain

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: Es28
Chain: 1

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: 18s Ribosomal Rna
Chain: 2

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285

Molecule: U3 Rna
Chain: 3

Organism_scientific: Chaetomium Thermophilum
Organism_taxid: 209285
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 7.30 Å
Gene
Ontology
ChainFunctionProcessComponent
0


1

  • cytosolic small ribosomal su...
  • A


    B


    D


    E, F


    H, G


    I

  • small-subunit processome
  • J


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z
  • enzyme activator activity


  • a


    c


    e, f


    g, h


    j, i


    o


    p


    q

  • cytosolic small ribosomal su...
  • r


    s


    t


    u

  • cytosolic small ribosomal su...
  • v

  • cytosolic small ribosomal su...
  • w


    x


    y


    z

  • cytosolic small ribosomal su...
  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1950 Kb) [Save to disk]
  • Biological Unit Coordinates (5jpq.pdb1.gz) 1835 Kb
  • CSU: Contacts of Structural Units for 5JPQ
  • Retrieve 5JPQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JPQ from S2C, [Save to disk]
  • View 5JPQ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5JPQ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5jpq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jpq_l] [5jpq_2] [5jpq_o] [5jpq_3] [5jpq_b] [5jpq_H] [5jpq_c] [5jpq_r] [5jpq_q] [5jpq_M] [5jpq_v] [5jpq_p] [5jpq_K] [5jpq_O] [5jpq_u] [5jpq_X] [5jpq_s] [5jpq_z] [5jpq_D] [5jpq_B] [5jpq_P] [5jpq_f] [5jpq_y] [5jpq_V] [5jpq_C] [5jpq_m] [5jpq_A] [5jpq_U] [5jpq_N] [5jpq_h] [5jpq_J] [5jpq_t] [5jpq_x] [5jpq] [5jpq_e] [5jpq_n] [5jpq_a] [5jpq_0] [5jpq_Z] [5jpq_j] [5jpq_F] [5jpq_E] [5jpq_g] [5jpq_k] [5jpq_L] [5jpq_I] [5jpq_W] [5jpq_w] [5jpq_1] [5jpq_T] [5jpq_Q] [5jpq_S] [5jpq_R] [5jpq_Y] [5jpq_G] [5jpq_i] [5jpq_d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JPQ: [AARP2CN] [BP28CT] [Brix] [DUF663] [Fibrillarin] [KH] [NOSIC] [PINc] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4] [WD40 ] by SMART
  • Other resources with information on 5JPQ
  • Community annotation for 5JPQ at PDBWiki (http://pdbwiki.org)

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