1QVF Ribosome date Aug 27, 2003
title Structure Of A Deacylated Trna Minihelix Bound To The E Site Large Ribosomal Subunit Of Haloarcula Marismortui
authors 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: Deacylated Trna Minihelix
Chain: 3
Engineered: Yes
Synthetic: Yes

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: 50s Ribosomal Protein L10e
Chain: G
Synonym: Acidic Ribosomal Protein P0 Homolog, Hmal10
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: L10 Ribosomal Protein
Chain: H
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L13p
Chain: I
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L14p
Chain: J
Synonym: Hmal13
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15p
Chain: K
Synonym: Hmal15, Hl9
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: L15 Ribosomal Protein
Chain: L
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18p
Chain: M
Synonym: Hmal18, Hl12
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18e
Chain: N
Synonym: Hl29, L19
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L19e
Chain: O
Synonym: Hmal19, Hl24
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L21e
Chain: P
Synonym: Hl31
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L22p
Chain: Q
Synonym: Hmal22, Hl23
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L23p
Chain: R
Synonym: Hmal23, Hl25, L21
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24p
Chain: S
Synonym: Hmal24, Hl16, Hl15
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24e
Chain: T
Synonym: Hl21hl22
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L29p
Chain: U
Synonym: Hmal29, Hl33
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L30p
Chain: V
Synonym: Hmal30, Hl20, Hl16
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L31e
Chain: W
Synonym: L34, Hl30
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L32e
Chain: X
Synonym: Hl5
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: L37ae 50s Ribosomal Protein
Chain: Y
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37e
Chain: Z
Synonym: L35e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L39e
Chain: 1
Synonym: Hl39e, Hl46e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L44e
Chain: 2
Synonym: La, Hla
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.196 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
213.522 300.817 574.861 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand CD, CL, K, MG, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


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 referenceStructures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit., Schmeing TM, Moore PB, Steitz TA, RNA 2003 Nov;9(11):1345-52. PMID:14561884
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1966 Kb) [Save to disk]
  • Biological Unit Coordinates (1qvf.pdb1.gz) 1933 Kb
  • LPC: Ligand-Protein Contacts for 1QVF
  • CSU: Contacts of Structural Units for 1QVF
  • Likely Quarternary Molecular Structure file(s) for 1QVF
  • Structure Factors (2900 Kb)
  • Retrieve 1QVF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QVF from S2C, [Save to disk]
  • Re-refined 1qvf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1QVF 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 1QVF
  • 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
  • 3D motif for 1QVF, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qvf1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1qvf2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1qvfa2, region A:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1qvfa1, region A:91-237 [Jmol] [rasmolscript] [script source]
        - Domain d1qvfb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1qvfc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1qvfd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1qvfe1, region E:1-79 [Jmol] [rasmolscript] [script source]
        - Domain d1qvfe2, region E:80-172 [Jmol] [rasmolscript] [script source]
        - Domain d1qvff_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1qvfg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1qvfh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1qvfi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1qvfj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1qvfk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1qvfl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1qvfm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1qvfn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1qvfo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1qvfp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1qvfq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1qvfr_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1qvfs_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1qvft_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1qvfu_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1qvfv_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1qvfw_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1qvfx_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1qvfy_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1qvfz_, region Z [Jmol] [rasmolscript] [script source]
  • 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: [1qvf_J] [1qvf_A] [1qvf_U] [1qvf_S] [1qvf_Y] [1qvf_B] [1qvf_D] [1qvf_V] [1qvf_T] [1qvf_R] [1qvf_X] [1qvf_Z] [1qvf_N] [1qvf_0] [1qvf_K] [1qvf_W] [1qvf_O] [1qvf_G] [1qvf] [1qvf_H] [1qvf_9] [1qvf_1] [1qvf_M] [1qvf_E] [1qvf_C] [1qvf_3] [1qvf_Q] [1qvf_F] [1qvf_2] [1qvf_P] [1qvf_L] [1qvf_I]
  • SWISS-PROT database: [P60617] [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] [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 1QVF: [HhH1] [KOW] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
    • Other resources with information on 1QVF
  • Community annotation for 1QVF at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science