3J00 Ribosome Ribosomal Protein date Feb 08, 2011
title Structure Of The Ribosome-Secye Complex In The Membrane Envi
authors J.Frauenfeld, J.Gumbart, E.O.Van Der Sluis, S.Funes, M.Gartmann, B.Beatrix, T.Mielke, O.Berninghausen, T.Becker, K.Schulten, R.Be
compound source
Molecule: 16s Ribosomal Rna
Chain: A
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Mrna
Chain: X

Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ftsq Nascent Chain
Chain: V

Organism_scientific: Escherichia Coli Dh1
Organism_common: Ftsq Nascent Chain
Organism_taxid: 536056

Molecule: Cell Division Protein Ftsq
Chain: Z
Synonym: Cell Division Protein; Ingrowth Of Wall At Septum

Organism_scientific: Escherichia Coli O157:H7
Organism_taxid: 83334

Molecule: Apolipoprotein A-I
Chain: 0, 1
Synonym: Apo-Ai, Apoa-I, Apolipoprotein A1, Apolipoprotein 242);
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Nanodiscs Derived From Human Apo-A1

Molecule: 30s Ribosomal Protein S2
Chain: B

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S3
Chain: C

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S4
Chain: D

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S5
Chain: E

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: 30s Ribosomal Protein S6, Fully Modified Isoform, Ribosomal Protein S6, Non-Modified Isoform;

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S7
Chain: G

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S8
Chain: H

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S9
Chain: I

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S10
Chain: J

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S11
Chain: K

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S12
Chain: L

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S13
Chain: M

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S14
Chain: N

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S12
Chain: O

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S16
Chain: P

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S17
Chain: Q

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S18
Chain: R

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S19
Chain: S

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S20
Chain: T

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12

Molecule: 30s Ribosomal Protein S21
Chain: U

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Strain: K12
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
0.000 0.000 0.000 90.00 90.00 90.00
method Electron Microscopyresolution 7.10 Å
ligand PEV, PGV enzyme
Gene
Ontology
ChainFunctionProcessComponent
1, 0


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


Primary referenceCryo-EM structure of the ribosome-SecYE complex in the membrane environment., Frauenfeld J, Gumbart J, Sluis EO, Funes S, Gartmann M, Beatrix B, Mielke T, Berninghausen O, Becker T, Schulten K, Beckmann R, Nat Struct Mol Biol. 2011 May;18(5):614-21. Epub 2011 Apr 17. PMID:21499241
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1160 Kb) [Save to disk]
  • Biological Unit Coordinates (3j00.pdb1.gz) 1112 Kb
  • LPC: Ligand-Protein Contacts for 3J00
  • CSU: Contacts of Structural Units for 3J00
  • Retrieve 3J00 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J00 from S2C, [Save to disk]
  • View 3J00 in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3J00
  • 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
  • 3D motif for 3J00, from MSDmotif at EBI
  • Fold representative 3j00 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j00_M] [3j00_L] [3j00_X] [3j00_K] [3j00_S] [3j00_H] [3j00_A] [3j00_F] [3j00_N] [3j00_R] [3j00_T] [3j00_D] [3j00_G] [3j00_1] [3j00_Q] [3j00_Z] [3j00_B] [3j00_U] [3j00_P] [3j00_I] [3j00_O] [3j00_E] [3j00_J] [3j00_V] [3j00_0] [3j00] [3j00_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3J00 with the sequences similar proteins can be viewed for 3J00's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3J00
  • Community annotation for 3J00 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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