1M8V	Rna Binding Protein Rna	date	Jul 26, 2002
title	Structure Of Pyrococcus Abyssii Sm Protein In Complex With A Heptamer
authors	S.Thore, C.Mayer, C.Sauter, S.Weeks, D.Suck
compound		source
Molecule: 5'-R(Pupupupupupupu)-3' Chain: O, P, Q, R, S, T, U Engineered: Yes		Synthetic: Yes
Molecule: Putative Snrnp Sm-Like Protein Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N Synonym: Sm Protein Pa-Sm1 Engineered: Yes		Organism_scientific: Pyrococcus Abyssi Organism_taxid: 29292 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: De3 Expression_system_organelle: Plasmid Expression_system_vector_type: Pet24
symmetry	Space Group: P 1	R_factor 0.212 R_Free 0.282
crystal cell	length a length b length c angle alpha angle beta angle gamma 68.000 68.000 84.800 105.00 108.80 100.00
method	X-Ray Diffraction	resolution	2.60 Å
ligand	CA, U	enzyme
related structures	by homologous chain: 1I4K, 1I5L
Primary reference	Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya., Thore S, Mayer C, Sauter C, Weeks S, Suck D, J Biol Chem 2003 Jan 10;278(2):1239-47. PMID:12409299

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (194 Kb) [Save to disk] Biological Unit Coordinates (1m8v.pdb1.gz) 187 Kb LPC: Ligand-Protein Contacts for 1M8V CSU: Contacts of Structural Units for 1M8V Likely Quarternary Molecular Structure file(s) for 1M8V Structure Factors (265 Kb) Retrieve 1M8V in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1M8V from S2C, [Save to disk] Re-refined 1m8v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1M8V 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.

Visual 3D analysis of 1M8V

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 3D motif for 1M8V, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1m8va_, region A [Jmol] [rasmolscript] [script source]     - Domain d1m8vb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1m8vc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1m8vd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1m8ve_, region E [Jmol] [rasmolscript] [script source]     - Domain d1m8vf_, region F [Jmol] [rasmolscript] [script source]     - Domain d1m8vg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1m8vh_, region H [Jmol] [rasmolscript] [script source]     - Domain d1m8vi_, region I [Jmol] [rasmolscript] [script source]     - Domain d1m8vj_, region J [Jmol] [rasmolscript] [script source]     - Domain d1m8vk_, region K [Jmol] [rasmolscript] [script source]     - Domain d1m8vl_, region L [Jmol] [rasmolscript] [script source]     - Domain d1m8vm_, region M [Jmol] [rasmolscript] [script source]     - Domain d1m8vn_, region N [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1m8v_N] [1m8v_B] [1m8v_D] [1m8v_C] [1m8v_A] [1m8v_H] [1m8v_P] [1m8v_E] [1m8v_R] [1m8v] [1m8v_Q] [1m8v_K] [1m8v_G] [1m8v_O] [1m8v_U] [1m8v_M] [1m8v_T] [1m8v_L] [1m8v_F] [1m8v_S] [1m8v_I] [1m8v_J] SWISS-PROT database: [Q9V0Y8] Domain organization of [RUXX_PYRAB] by SWISSPFAM Domain found in 1M8V: [Sm ] by SMART

Other resources with information on 1M8V

Community annotation for 1M8V at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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