3CMA Ribosome date Mar 21, 2008
title The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The Large Subunit Of Haloarcula Marismortui
authors M.Simonovic, T.A.Steitz
compound source
Molecule: 50s Ribosomal Protein L2p
Chain: A
Synonym: Hmal2, Hl4
Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L4p
Chain: C
Synonym: Hmal4, Hl6

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: G
Synonym: Ribosomal Protein L10, Acidic Ribosomal Protein P0 L10e, Hmal10;

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: H
Synonym: Hmal11

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L11p
Chain: I
Synonym: Hmal13

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L13p
Chain: J
Synonym: Hmal14, Hl27

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L14p
Chain: K
Synonym: Hmal15, Hl9

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15p
Chain: L
Synonym: 50s Ribosomal Protein Lc12

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15e
Chain: M
Synonym: Hmal18, Hl12

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18p
Chain: N
Synonym: Hl29, L19

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18e
Chain: O

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37ae
Chain: Z

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 23s Ribosomal Rna
Chain

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238

Molecule: Rna (5'-R(Cpcpa)-3')
Chain: 5
Engineered: Yes

Synthetic: Yes

Molecule: Rna (5'-R(Cpcp(8an))-3')
Chain: 6
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.194 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
211.316 297.905 573.138 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 1MA, 8AN, ACA, CD, CL, K, MG, NA, OMG, OMU, PHE, PSU, SR, UR3 enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


A


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Y


Z


Primary referencePeptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA., Simonovic M, Steitz TA, RNA. 2008 Nov;14(11):2372-8. Epub 2008 Sep 25. PMID:18818369
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1993 Kb) [Save to disk]
  • Biological Unit Coordinates (3cma.pdb1.gz) 1970 Kb
  • LPC: Ligand-Protein Contacts for 3CMA
  • CSU: Contacts of Structural Units for 3CMA
  • Likely Quarternary Molecular Structure file(s) for 3CMA
  • Structure Factors (3581 Kb)
  • Retrieve 3CMA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CMA from S2C, [Save to disk]
  • Re-refined 3cma structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CMA 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 3CMA
  • 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 3CMA, from MSDmotif at EBI
  • Fold representative 3cma from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cma_L] [3cma_X] [3cma_F] [3cma_2] [3cma_O] [3cma_0] [3cma_S] [3cma_C] [3cma_G] [3cma_9] [3cma_R] [3cma_B] [3cma_K] [3cma_6] [3cma_U] [3cma_J] [3cma_1] [3cma_I] [3cma_T] [3cma_M] [3cma_W] [3cma_H] [3cma_E] [3cma_N] [3cma_5] [3cma_Z] [3cma_Q] [3cma_D] [3cma_V] [3cma_3] [3cma_P] [3cma] [3cma_Y] [3cma_A]
  • 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 3CMA: [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 3CMA
  • Community annotation for 3CMA 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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