2ZM6	Ribosome	date	Apr 11, 2008
title	Crystal Structure Of The Thermus Thermophilus 30s Ribosomal Subunit
authors	T.Kaminishi, H.Wang, M.Kawazoe, R.Ishii, F.Schluenzen, K.Hanawa- Suetsugu, D.N.Wilson, M.Nomura, C.Takemoto, M.Shirouzu, P.Fucini S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: 16s Ribosomal Rna Chain: A		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S2 Chain: B		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S3 Chain: C		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S4 Chain: D		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S5 Chain: E		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S6 Chain: F Synonym: Ts9		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S7 Chain: G		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S8 Chain: H		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S9 Chain: I		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S10 Chain: J		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S11 Chain: K		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S12 Chain: L		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S13 Chain: M		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S14 Type Z Chain: N		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S15 Chain: O		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S16 Chain: P		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S17 Chain: Q		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S18 Chain: R		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S19 Chain: S		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein S20 Chain: T		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 30s Ribosomal Protein Thx Chain: V Synonym: S31		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
symmetry	Space Group: P 41 21 2	R_factor 0.292 R_Free 0.323
crystal cell	length a length b length c angle alpha angle beta angle gamma 411.500 411.500 172.580 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.30 Å
ligand	ZN	enzyme
Gene Ontology	Chain Function Process Component C RNA binding mRNA binding structural constituent of ri... rRNA binding translation intracellular ribosome small ribosomal subunit ribonucleoprotein complex D RNA binding structural constituent of ri... rRNA binding metal ion binding translation intracellular ribosome small ribosomal subunit ribonucleoprotein complex E, B RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome small ribosomal subunit ribonucleoprotein complex F RNA binding structural constituent of ri... rRNA binding translation ribosome ribonucleoprotein complex J, I tRNA binding RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex L, G tRNA binding RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome small ribosomal subunit ribonucleoprotein complex M tRNA binding nucleic acid binding RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex N RNA binding structural constituent of ri... zinc ion binding rRNA binding metal ion binding translation intracellular ribosome ribonucleoprotein complex P structural constituent of ri... translation intracellular ribosome ribonucleoprotein complex S RNA binding structural constituent of ri... rRNA binding translation ribosome small ribosomal subunit ribonucleoprotein complex T, K, Q, O, H, R RNA binding structural constituent of ri... rRNA binding translation intracellular ribosome ribonucleoprotein complex V RNA binding rRNA binding ribosome ribonucleoprotein complex

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (935 Kb) [Save to disk] Biological Unit Coordinates (2zm6.pdb1.gz) 922 Kb LPC: Ligand-Protein Contacts for 2ZM6 CSU: Contacts of Structural Units for 2ZM6 Likely Quarternary Molecular Structure file(s) for 2ZM6 Structure Factors (2129 Kb) Retrieve 2ZM6 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2ZM6 from S2C, [Save to disk] Re-refined 2zm6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2ZM6 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 2ZM6

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2ZM6, from MSDmotif at EBI Fold representative 2zm6 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2zm6_A] [2zm6_B] [2zm6_C] [2zm6_D] [2zm6_E] [2zm6_F] [2zm6_G] [2zm6_H] [2zm6_I] [2zm6_J] [2zm6_K] [2zm6_L] [2zm6_M] [2zm6_N] [2zm6_O] [2zm6_P] [2zm6_Q] [2zm6_R] [2zm6_S] [2zm6_T] [2zm6_V] SWISS-PROT database: [Q5SHN7] [P80376] [Q5SHN3] [P80377] [Q5SHQ1] [Q5SJ76] [Q5SJH3] [Q5SHP7] [Q5SLQ0] [Q5SHP2] [P80380] [P80371] [P80372] [P80373] [Q5SHQ5] [Q5SLP8] [P17291] [Q5SHQ2] [P80374] [Q5SIH3] Domain organization of [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THET8] [RS18_THET8] [RS19_THET8] [RS20_THET8] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET8] [RSHX_THET8] by SWISSPFAM Domains found in 2ZM6: [KH] [S4 ] by SMART Alignments of the sequence of 2ZM6 with the sequences similar proteins can be viewed for 2ZM6's classification [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THET8] [RS18_THET8] [RS19_THET8] [RS20_THET8] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET8] [RSHX_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 [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THET8] [RS18_THET8] [RS19_THET8] [RS20_THET8] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET8] [RSHX_THET8] at ProtoMap. Click on the Cluster number.

Other resources with information on 2ZM6

Community annotation for 2ZM6 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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