3I20	Ribosome	date	Jun 28, 2009
title	Crystal Structure Of The E. Coli 70s Ribosome In An Intermediate State Of Ratcheting
authors	W.Zhang, J.A.Dunkle, J.H.D.Cate
compound		source
Molecule: 50s Ribosomal Protein L2 Chain: C		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L3 Chain: D		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L4 Chain: E		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L5 Chain: F		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L6 Chain: G		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L9 Chain: H		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L11 Chain: I		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L13 Chain: J		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L14 Chain: K		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L15 Chain: L		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L16 Chain: M		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L17 Chain: N		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L18 Chain: O		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L19 Chain: P		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L20 Chain: Q		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L21 Chain: R		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L22 Chain: S		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L23 Chain: T		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L24 Chain: U		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L25 Chain: V		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L27 Chain: W		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L28 Chain: X		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L29 Chain: Y		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L30 Chain: Z		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L32 Chain		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L33 Chain: 1		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L34 Chain: 2		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L35 Chain: 3 Synonym: Ribosomal Protein A		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 50s Ribosomal Protein L36 Chain: 4 Synonym: Ribosomal Protein B		Organism_scientific: Escherichia Coli K-12 Organism_taxid: 83333
Molecule: 23s Rrna Chain: A		Organism_scientific: Escherichia Coli Organism_taxid: 562
Molecule: 5s Rrna Chain: B		Organism_scientific: Escherichia Coli Organism_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.227 R_Free 0.268
crystal cell	length a length b length c angle alpha angle beta angle gamma 210.952 433.082 624.495 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.71 Å
ligand	MG, ZN	enzyme
Gene Ontology	Chain Function Process Component 0 structural constituent of ri... translation intracellular ribosome large ribosomal subunit ribonucleoprotein complex 1 tRNA binding RNA binding structural constituent of ri... translation intracellular ribosome ribonucleoprotein complex 3 structural constituent of ri... translation intracellular ribosome cytosolic large ribosomal su... ribonucleoprotein complex C RNA binding structural constituent of ri... protein binding zinc ion binding transferase activity rRNA binding translation intracellular ribosome large ribosomal subunit ribonucleoprotein complex E RNA binding structural constituent of ri... rRNA binding translation repressor activi... transcription, DNA-dependent... DNA-dependent transcription,... regulation of transcription,... translation regulation of translation negative regulation of trans... response to antibiotic ribosome ribonucleoprotein complex F, M, W tRNA binding RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex G RNA binding structural constituent of ri... rRNA binding translation response to antibiotic intracellular ribosome ribonucleoprotein complex I RNA binding structural constituent of ri... protein binding rRNA binding translation translational termination stringent response ribosome cytosolic large ribosomal su... ribonucleoprotein complex J structural constituent of ri... zinc ion binding translation ribosome ribonucleoprotein complex K RNA binding structural constituent of ri... protein binding rRNA binding LSU rRNA binding translation ribosome large ribosomal subunit cytosolic large ribosomal su... ribonucleoprotein complex L RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome large ribosomal subunit ribonucleoprotein complex N, 2, X, 4 structural constituent of ri... translation intracellular ribosome ribonucleoprotein complex Q translation repressor activi... RNA binding structural constituent of ri... rRNA binding ribosomal large subunit asse... translation intracellular ribosome cytosolic large ribosomal su... ribonucleoprotein complex S RNA binding structural constituent of ri... rRNA binding translation response to antibiotic intracellular ribosome large ribosomal subunit ribonucleoprotein complex T nucleotide binding RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex V RNA binding structural constituent of ri... 5S rRNA binding rRNA binding translation intracellular ribosome ribonucleoprotein complex Y, O, P, H, D, R, U RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex Z structural constituent of ri... translation ribosome large ribosomal subunit ribonucleoprotein complex
Primary reference	Structures of the ribosome in intermediate states of ratcheting., Zhang W, Dunkle JA, Cate JH, Science. 2009 Aug 21;325(5943):1014-7. PMID:19696352

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3807 Kb) [Save to disk] Biological Unit Coordinates (3i20.pdb1.gz) 3771 Kb LPC: Ligand-Protein Contacts for 3I20 CSU: Contacts of Structural Units for 3I20 Structure Factors (4129 Kb) Retrieve 3I20 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3I20 from S2C, [Save to disk]

View 3I20 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3I20

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 3I20, from MSDmotif at EBI Fold representative 3i20 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3i20_0] [3i20_1] [3i20_2] [3i20_3] [3i20_4] [3i20_A] [3i20_B] [3i20_C] [3i20_D] [3i20_E] [3i20_F] [3i20_G] [3i20_H] [3i20_I] [3i20_J] [3i20_K] [3i20_L] [3i20_M] [3i20_N] [3i20_O] [3i20_P] [3i20_Q] [3i20_R] [3i20_S] [3i20_T] [3i20_U] [3i20_V] [3i20_W] [3i20_X] [3i20_Y] [3i20_Z] SWISS-PROT database: [P0A7J7] [P0AA10] [P0ADY3] [P02413] [P0ADY7] [P0AG44] [P0C018] [P0A7K6] [P0A7L3] [P0AG48] [P61175] [P0ADZ0] [P60624] [P68919] [P0A7L8] [P0A7M2] [P0A7M6] [P60422] [P0AG51] [P0A7N4] [P0A7N9] [P0A7P5] [P0A7Q1] [P0A7Q6] [P60438] [P60723] [P62399] [P0AG55] [P0A7R1] Domain organization of [RL11_ECOLI] [RL13_ECOLI] [RL14_ECOLI] [RL15_ECOLI] [RL16_ECOLI] [RL17_ECOLI] [RL18_ECOLI] [RL19_ECOLI] [RL20_ECOLI] [RL21_ECOLI] [RL22_ECOLI] [RL23_ECOLI] [RL24_ECOLI] [RL25_ECOLI] [RL27_ECOLI] [RL28_ECOLI] [RL29_ECOLI] [RL2_ECOLI] [RL30_ECOLI] [RL32_ECOLI] [RL33_ECOLI] [RL34_ECOLI] [RL35_ECOLI] [RL36_ECOLI] [RL3_ECOLI] [RL4_ECOLI] [RL5_ECOLI] [RL6_ECOLI] [RL9_ECOLI] by SWISSPFAM Domains found in 3I20: [KOW] [RL11 ] by SMART Alignments of the sequence of 3I20 with the sequences similar proteins can be viewed for 3I20's classification [RL11_ECOLI] [RL13_ECOLI] [RL14_ECOLI] [RL15_ECOLI] [RL16_ECOLI] [RL17_ECOLI] [RL18_ECOLI] [RL19_ECOLI] [RL20_ECOLI] [RL21_ECOLI] [RL22_ECOLI] [RL23_ECOLI] [RL24_ECOLI] [RL25_ECOLI] [RL27_ECOLI] [RL28_ECOLI] [RL29_ECOLI] [RL2_ECOLI] [RL30_ECOLI] [RL32_ECOLI] [RL33_ECOLI] [RL34_ECOLI] [RL35_ECOLI] [RL36_ECOLI] [RL3_ECOLI] [RL4_ECOLI] [RL5_ECOLI] [RL6_ECOLI] [RL9_ECOLI] 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 [RL11_ECOLI] [RL13_ECOLI] [RL14_ECOLI] [RL15_ECOLI] [RL16_ECOLI] [RL17_ECOLI] [RL18_ECOLI] [RL19_ECOLI] [RL20_ECOLI] [RL21_ECOLI] [RL22_ECOLI] [RL23_ECOLI] [RL24_ECOLI] [RL25_ECOLI] [RL27_ECOLI] [RL28_ECOLI] [RL29_ECOLI] [RL2_ECOLI] [RL30_ECOLI] [RL32_ECOLI] [RL33_ECOLI] [RL34_ECOLI] [RL35_ECOLI] [RL36_ECOLI] [RL3_ECOLI] [RL4_ECOLI] [RL5_ECOLI] [RL6_ECOLI] [RL9_ECOLI] at ProtoMap. Click on the Cluster number.

Other resources with information on 3I20

Community annotation for 3I20 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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