1S72 Ribosome date Jan 28, 2004
title Refined Crystal Structure Of The Haloarcula Marismortui Larg Ribosomal Subunit At 2.4 Angstrom Resolution
authors D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz
compound source
Molecule: 23s Ribosomal Rna
Chain
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L2p
Chain: A
Synonym: Hmal2, Hl4

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L3p
Chain: B
Synonym: Hmal3, Hl1

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L4e
Chain: C
Synonym: Hmal4, Hl6

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L5p
Chain: D
Synonym: Hmal5, Hl13

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L6p
Chain: E
Synonym: Hmal6, Hl10

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L7ae
Chain: F
Synonym: Hs6

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Acidic Ribosomal Protein P0 Homolog
Chain: G
Synonym: L10e, Hmal10

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: H

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L11p
Chain: I
Synonym: Hmal11

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L13p
Chain: J
Synonym: Hmal13

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L14p
Chain: K
Synonym: Hmal14, Hl27

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15p
Chain: L
Synonym: Hmal15, Hl9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15e
Chain: M

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18p
Chain: N
Synonym: Hmal18, Hl12

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18e
Chain: O
Synonym: Hl29, L19

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L19e
Chain: P
Synonym: Hmal19, Hl24

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L21e
Chain: Q
Synonym: Hl31

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L22p
Chain: R
Synonym: Hmal22, Hl23

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L23p
Chain: S
Synonym: Hmal23, Hl25, L21

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24p
Chain: T
Synonym: Hmal24, Hl16, Hl15

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24e
Chain: U
Synonym: Hl21hl22

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L29p
Chain: V
Synonym: Hmal29, Hl33

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L30p
Chain: W
Synonym: Hmal30, Hl20, Hl16

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L31e
Chain: X
Synonym: L34, Hl30

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L32e
Chain: Y
Synonym: Hl5

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37ae
Chain: Z

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37e
Chain: 1
Synonym: L35e

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L39e
Chain: 2
Synonym: Hl39e, Hl46e

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L44e
Chain: 3
Synonym: La, Hla

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.188 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
211.660 299.670 573.770 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 1MA, CD, CL, K, MG, NA, OMG, OMU, PSU, UR3 enzyme
related structures by homologous chain: 1JJ2, 1YHQ
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


A


B


C


D


E


F
  • ribonuclease P activity


  • G


    H


    I


    J


    K


    L


    M


    N


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceThe roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit., Klein DJ, Moore PB, Steitz TA, J Mol Biol 2004 Jun 25;340(1):141-77. PMID:15184028
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2008 Kb) [Save to disk]
  • Biological Unit Coordinates (1s72.pdb1.gz) 1970 Kb
  • LPC: Ligand-Protein Contacts for 1S72
  • CSU: Contacts of Structural Units for 1S72
  • Likely Quarternary Molecular Structure file(s) for 1S72
  • Structure Factors (4946 Kb)
  • Retrieve 1S72 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S72 from S2C, [Save to disk]
  • Re-refined 1s72 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1S72 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 1S72
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1S72, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s721_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1s722_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1s723_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1s72a2, region A:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1s72a1, region A:91-237 [Jmol] [rasmolscript] [script source]
        - Domain d1s72b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1s72c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1s72d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1s72e1, region E:1-79 [Jmol] [rasmolscript] [script source]
        - Domain d1s72e2, region E:80-172 [Jmol] [rasmolscript] [script source]
        - Domain d1s72f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1s72g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1s72h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1s72i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1s72j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1s72k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1s72l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1s72m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1s72n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1s72o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1s72p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1s72q_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1s72r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1s72s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1s72t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1s72u_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1s72v_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1s72w_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1s72x_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1s72y_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1s72z_, region Z [Jmol] [rasmolscript] [script source]
  • Fold representative 1s72 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1s72_B] [1s72_R] [1s72_W] [1s72_P] [1s72_T] [1s72_H] [1s72_1] [1s72_I] [1s72_V] [1s72_2] [1s72_O] [1s72_X] [1s72_G] [1s72_M] [1s72_J] [1s72_S] [1s72_9] [1s72_U] [1s72_K] [1s72_E] [1s72] [1s72_3] [1s72_N] [1s72_Q] [1s72_0] [1s72_A] [1s72_D] [1s72_C] [1s72_Y] [1s72_L] [1s72_F] [1s72_Z]
  • SWISS-PROT database: [P60617] [P14122] [P29198] [P22450] [P60618] [P12737] [P12733] [P14123] [P14119] [P12734] [P10970] [P12732] [P14116] [P10972] [P10971] [P20276] [P14121] [P18138] [P12736] [P60619] [P32410] [P22452] [P20279] [P32411] [P12735] [P14124] [P14135] [P12743] [P15825]
  • Domain organization of [RL10_HALMA] [RL11_HALMA] [RL13_HALMA] [RL14_HALMA] [RL15E_HALMA] [RL15_HALMA] [RL18E_HALMA] [RL18_HALMA] [RL19_HALMA] [RL21_HALMA] [RL22_HALMA] [RL23_HALMA] [RL24E_HALMA] [RL24_HALMA] [RL29_HALMA] [RL2_HALMA] [RL30_HALMA] [RL31_HALMA] [RL32_HALMA] [RL37A_HALMA] [RL37_HALMA] [RL39_HALMA] [RL3_HALMA] [RL44_HALMA] [RL4_HALMA] [RL5_HALMA] [RL6_HALMA] [RL7A_HALMA] [RLA0_HALMA] by SWISSPFAM
  • Domains found in 1S72: [HhH1] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
  • Other resources with information on 1S72
  • Community annotation for 1S72 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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