3F1F	Ribosome	date	Oct 27, 2008
title	Crystal Structure Of A Translation Termination Complex Forme Release Factor Rf2. This File Contains The 50s Subunit Of O Ribosome. The Entire Crystal Structure Contains Two 70s Rib Described In Remark 400.
authors	A.Korostelev, H.Asahara, L.Lancaster, M.Laurberg, A.Hirschi, H.F.
compound		source
Molecule: 23s Rrna Chain: A		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 5s Rrna Chain: B		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L2 Chain: D		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L3 Chain: E		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L4 Chain: F		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L5 Chain: G		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L6 Chain: H		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L9 Chain: I		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L11 Chain: K		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L13 Chain: N		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L14 Chain: O		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L15 Chain: P		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L16 Chain: Q		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L17 Chain: R		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L18 Chain: S		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L19 Chain: T		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L20 Chain: U		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L21 Chain: V		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L22 Chain: W		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L23 Chain: X		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L24 Chain: Y		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L25 Chain: Z Synonym: Tl5, General Stress Protein Ctc		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L27 Chain		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L28 Chain: 1		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L29 Chain: 2		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L30 Chain: 3		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L31 Chain: 4		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L32 Chain: 5		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L33 Chain: 6		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L34 Chain: 7		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
Molecule: 50s Ribosomal Protein L35 Chain: 8		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Strain: Hb27
symmetry	Space Group: P 21 21 21	R_factor 0.280 R_Free 0.316
crystal cell	length a length b length c angle alpha angle beta angle gamma 211.240 456.780 618.710 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	MG	enzyme
Gene Ontology	Chain Function Process Component 3 structural constituent of ri... translation ribosome large ribosomal subunit ribonucleoprotein complex 4 RNA binding structural constituent of ri... rRNA binding metal ion binding translation intracellular ribosome ribonucleoprotein complex 5 structural constituent of ri... translation intracellular ribosome large ribosomal subunit ribonucleoprotein complex D RNA binding structural constituent of ri... transferase activity rRNA binding translation intracellular ribosome large ribosomal subunit ribonucleoprotein complex F, K, H RNA binding structural constituent of ri... rRNA binding translation ribosome ribonucleoprotein complex G tRNA binding RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex N structural constituent of ri... translation ribosome ribonucleoprotein complex O RNA binding structural constituent of ri... rRNA binding translation ribosome large ribosomal subunit ribonucleoprotein complex Q tRNA binding RNA binding structural constituent of ri... rRNA binding translation ribosome ribonucleoprotein complex S, Y, E, V, I, U RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex T, 7, 2, 1, 0, 6, 8, R structural constituent of ri... translation intracellular ribosome ribonucleoprotein complex W, P RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome large ribosomal subunit ribonucleoprotein complex X nucleotide binding RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex Z RNA binding structural constituent of ri... 5S rRNA binding rRNA binding translation intracellular ribosome ribonucleoprotein complex
Primary reference	Crystal structure of a translation termination complex formed with release factor RF2., Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, Zhu J, Trakhanov S, Scott WG, Noller HF, Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19684-9. Epub 2008 Dec 8. PMID:19064930

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3910 Kb) [Save to disk] Biological Unit Coordinates (3f1f.pdb1.gz) 3860 Kb LPC: Ligand-Protein Contacts for 3F1F CSU: Contacts of Structural Units for 3F1F Structure Factors (9865 Kb) Retrieve 3F1F in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3F1F from S2C, [Save to disk]

View 3F1F 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 3F1F

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 3F1F, from MSDmotif at EBI Fold representative 3f1f from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3f1f_0] [3f1f_1] [3f1f_2] [3f1f_3] [3f1f_4] [3f1f_5] [3f1f_6] [3f1f_7] [3f1f_8] [3f1f_A] [3f1f_B] [3f1f_D] [3f1f_E] [3f1f_F] [3f1f_G] [3f1f_H] [3f1f_I] [3f1f_K] [3f1f_N] [3f1f_O] [3f1f_P] [3f1f_Q] [3f1f_R] [3f1f_S] [3f1f_T] [3f1f_U] [3f1f_V] [3f1f_W] [3f1f_X] [3f1f_Y] [3f1f_Z] SWISS-PROT database: [P36238] [Q72IN1] [Q72I14] [Q72I23] [Q72I11] [Q72I33] [Q72I20] [Q72JU9] [Q72L76] [Q72HR2] [Q72I09] [Q72I06] [Q72I15] [Q72IA7] [Q72HR3] [Q72G84] [Q72I12] [Q72I07] [Q72I22] [Q72JR0] [P62652] [Q72GW3] [P80340] [Q72L77] [Q72I04] [Q5SHN9] [Q72I16] [Q72I19] [Q5SLQ1] Domain organization of [RL11_THETH] [RL13_THET2] [RL14_THET2] [RL15_THET2] [RL16_THET2] [RL17_THET2] [RL18_THET2] [RL19_THET2] [RL20_THET2] [RL21_THET2] [RL22_THET2] [RL23_THET2] [RL24_THET2] [RL25_THET2] [RL27_THET2] [RL28_THET2] [RL29_THET2] [RL2_THET2] [RL30_THET2] [RL31_THET2] [RL32_THET2] [RL33_THET2] [RL34_THET8] [RL35_THET2] [RL3_THET2] [RL4_THET8] [RL5_THET2] [RL6_THET2] [RL9_THET8] by SWISSPFAM Domains found in 3F1F: [KOW] [RL11 ] by SMART Alignments of the sequence of 3F1F with the sequences similar proteins can be viewed for 3F1F's classification [RL11_THETH] [RL13_THET2] [RL14_THET2] [RL15_THET2] [RL16_THET2] [RL17_THET2] [RL18_THET2] [RL19_THET2] [RL20_THET2] [RL21_THET2] [RL22_THET2] [RL23_THET2] [RL24_THET2] [RL25_THET2] [RL27_THET2] [RL28_THET2] [RL29_THET2] [RL2_THET2] [RL30_THET2] [RL31_THET2] [RL32_THET2] [RL33_THET2] [RL34_THET8] [RL35_THET2] [RL3_THET2] [RL4_THET8] [RL5_THET2] [RL6_THET2] [RL9_THET8] 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_THETH] [RL13_THET2] [RL14_THET2] [RL15_THET2] [RL16_THET2] [RL17_THET2] [RL18_THET2] [RL19_THET2] [RL20_THET2] [RL21_THET2] [RL22_THET2] [RL23_THET2] [RL24_THET2] [RL25_THET2] [RL27_THET2] [RL28_THET2] [RL29_THET2] [RL2_THET2] [RL30_THET2] [RL31_THET2] [RL32_THET2] [RL33_THET2] [RL34_THET8] [RL35_THET2] [RL3_THET2] [RL4_THET8] [RL5_THET2] [RL6_THET2] [RL9_THET8] at ProtoMap. Click on the Cluster number.

Other resources with information on 3F1F

Community annotation for 3F1F at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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