3ORB	Ribosome	date	Sep 06, 2010
title	Crystal Structure Of The E. Coli Ribosome Bound To Cem-101. Contains The 50s Subunit Of The First 70s Ribosome Bound To
authors	J.A.Dunkle, W.Zhang, J.H.D.Cate, A.S.Mankin
compound		source
Molecule: 23s Rrna Chain: A		Organism_scientific: Escherichia Coli Organism_taxid: 562
Molecule: 5s Rrna Chain: B		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L2 Chain: C		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L3 Chain: D		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L4 Chain: E		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L5 Chain: F		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L6 Chain: G		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L9 Chain: H		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L11 Chain: I		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L13 Chain: J		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L14 Chain: K		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L15 Chain: L		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L16 Chain: M		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L17 Chain: N		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L18 Chain: O		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L19 Chain: P		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L20 Chain: Q		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L21 Chain: R		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L22 Chain: S		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L23 Chain: T		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L24 Chain: U		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L25 Chain: V		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L27 Chain: W		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L28 Chain: X		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L29 Chain: Y		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L30 Chain: Z		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L32 Chain		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L33 Chain: 1		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L34 Chain: 2		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L35 Chain: 3		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
Molecule: 50s Ribosomal Protein L36 Chain: 4		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12
symmetry	Space Group: P 21 21 21	R_factor 0.187 R_Free 0.244
crystal cell	length a length b length c angle alpha angle beta angle gamma 210.759 433.272 618.863 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.30 Å
ligand	EM1, 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	Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis., Llano-Sotelo B, Dunkle J, Klepacki D, Zhang W, Fernandes P, Cate JH, Mankin AS, Antimicrob Agents Chemother. 2010 Sep 20. PMID:20855725

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3746 Kb) [Save to disk] Biological Unit Coordinates (3orb.pdb1.gz) 3712 Kb LPC: Ligand-Protein Contacts for 3ORB CSU: Contacts of Structural Units for 3ORB Structure Factors (17473 Kb) Retrieve 3ORB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3ORB from S2C, [Save to disk]

View 3ORB 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 3ORB

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3orb_0] [3orb_1] [3orb_2] [3orb_3] [3orb_4] [3orb_A] [3orb_B] [3orb_C] [3orb_D] [3orb_E] [3orb_F] [3orb_G] [3orb_H] [3orb_I] [3orb_J] [3orb_K] [3orb_L] [3orb_M] [3orb_N] [3orb_O] [3orb_P] [3orb_Q] [3orb_R] [3orb_S] [3orb_T] [3orb_U] [3orb_V] [3orb_W] [3orb_X] [3orb_Y] [3orb_Z] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3ORB with the sequences similar proteins can be viewed for 3ORB'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 3ORB

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

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