1ML5 Ribosome date Aug 30, 2002
title Structure Of The E. Coli Ribosomal Termination Complex With Factor 2
authors B.P.Klaholz, T.Pape, A.V.Zavialov, A.G.Myasnikov, E.V.Orlova, B.Vestergaard, M.Ehrenberg, M.Van Heel
compound source
Molecule: 30s 16s Ribosomal Rna
Chain: A
 Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: T-Rna(Phe)
Chain: B
Other_details: Trna P-Site
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: A- And P-Site Messenger Rna Codons
Chain: C
Other_details: 6 Nt Long Mrna Fragment
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s 23s Ribosomal Rna
Chain: a
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s 5s Ribosomal Rna
Chain: b
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Peptide Chain Release Factor 2
Chain: Z
Synonym: Rf-2; Translation Releasing Factor Rf-2
Engineered: Yes
Other_details: Em Reconstruction Of The Backbone Trace Of T Ribosome;
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Prfbsupk
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a

Molecule: 30s Ribosomal Protein S2
Chain: E
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S3
Chain: F
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S4
Chain: G
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S5
Chain: H
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S6
Chain: I
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S7
Chain: J
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S8
Chain: K
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S9
Chain: L
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S10
Chain: M
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S11
Chain: N
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S12
Chain: O
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S13
Chain: P
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S14
Chain: Q
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S15
Chain: R
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S16
Chain: S
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S17
Chain: T
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S18
Chain: U
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S19
Chain: V
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S20
Chain: W
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein Thx
Chain: X
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L1
Chain: c
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L2
Chain: d
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L3
Chain: e
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L4
Chain: f
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L5
Chain: g
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L6
Chain: h
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L11
Chain: l
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L13
Chain: m
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L14
Chain: n
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L15
Chain: o
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L16
Chain: p
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L18
Chain: q
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L19
Chain: r
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L22
Chain: s
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L23
Chain: t
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L24
Chain: u
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L25
Chain: v
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L29
Chain: w
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L30
Chain: x
Organism_scientific: Escherichia Coli
Organism_taxid: 562
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 14.00 Å
ligand 1MA, 2MG, 5MC, 5MU, 7MG, H2U, M2G, OMC, OMG, PSU, YG enzyme
Gene
Ontology
ChainFunctionProcessComponent
E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Z


c


d


e


f


g


h


l


m


n


o


p


q


r


s


t


u


v


w


x


Primary referenceStructure of the Escherichia coli ribosomal termination complex with release factor 2., Klaholz BP, Pape T, Zavialov AV, Myasnikov AG, Orlova EV, Vestergaard B, Ehrenberg M, van Heel M, Nature 2003 Jan 2;421(6918):90-4. PMID:12511961
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (222 Kb) [Save to disk]
  • Biological Unit Coordinates (1ml5.pdb1.gz) 212 Kb
  • LPC: Ligand-Protein Contacts for 1ML5
  • CSU: Contacts of Structural Units for 1ML5
  • Likely Quarternary Molecular Structure file(s) for 1ML5
  • Retrieve 1ML5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ML5 from S2C, [Save to disk]
    • View 1ML5 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 1ML5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1ML5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ml5a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ml5b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ml5c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ml5e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1ml5f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1ml5g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1ml5h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1ml5i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1ml5j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1ml5k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1ml5l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1ml5m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1ml5n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1ml5o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1ml5p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1ml5q_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1ml5r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1ml5s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1ml5t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1ml5u_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1ml5v_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1ml5w_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1ml5x_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1ml5z_, region Z [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ml5_f] [1ml5_Z] [1ml5_C] [1ml5_a] [1ml5_U] [1ml5_b] [1ml5_V] [1ml5] [1ml5_T] [1ml5_t] [1ml5_J] [1ml5_d] [1ml5_R] [1ml5_O] [1ml5_L] [1ml5_r] [1ml5_m] [1ml5_o] [1ml5_W] [1ml5_u] [1ml5_e] [1ml5_p] [1ml5_x] [1ml5_G] [1ml5_c] [1ml5_Q] [1ml5_X] [1ml5_B] [1ml5_v] [1ml5_F] [1ml5_n] [1ml5_S] [1ml5_g] [1ml5_E] [1ml5_q] [1ml5_A] [1ml5_H] [1ml5_M] [1ml5_N] [1ml5_l] [1ml5_h] [1ml5_K] [1ml5_w] [1ml5_s] [1ml5_I] [1ml5_P]
  • SWISS-PROT database: [P07012] [Q72GV9] [P68919] [Q5SHQ6]
  • Domain organization of [RF2_ECOLI] [RL1_THET2] [RL25_ECOLI] [RL30_THET8] by SWISSPFAM
  • Domains found in 1ML5: [KH] [KOW] [PCRF] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4] [TRASH ] by SMART
    • Other resources with information on 1ML5
  • Community annotation for 1ML5 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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