1D3B	Rna Binding Protein	date	Dec 22, 1998
title	Crystal Structure Of The D3b Subcomplex Of The Human Core Sn At 2.0a Resolution
authors	C.Kambach, S.Walke, J.M.Avis, E.De La Fortelle, J.Li, K.Nagai
compound		source
Molecule: Protein (Small Nuclear Ribonucleoprotein Sm D3) Chain: A, C, E, G, I, K Fragment: Sm Motif Synonym: D3 Core Snrnp Protein Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Cellular_location: Nucleus Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Sg13009 Expression_system_cellular_location: Cytoplasm Expression_system_vector_type: Plasmid Expression_system_vector: T5 Promoter Expression_system_plasmid: Pqe30 Other_details: N-Terminal His6 Tag Cleaved Off,Truncated At 75;
Molecule: Protein (Small Nuclear Ribonucleoprotein Associat B); Chain: B, D, F, H, J, L Fragment: Sm Motif Synonym: B Core Snrnp Protein		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Cellular_location: Nucleus Other_details: Polycistronic Coexpression Vector With Sm D3 Truncated At Position 91.
symmetry	Space Group: P 21 21 21	R_factor 0.213 R_Free 0.265
crystal cell	length a length b length c angle alpha angle beta angle gamma 107.350 108.450 110.420 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	CIT, GOL	enzyme
note	1D3B is a representative structure
Gene Ontology	Chain Function Process Component A, C, K, I, G, E
Primary reference	Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs., Kambach C, Walke S, Young R, Avis JM, de la Fortelle E, Raker VA, Luhrmann R, Li J, Nagai K, Cell 1999 Feb 5;96(3):375-87. PMID:10025403

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (171 Kb) [Save to disk] Biological Unit Coordinates (1d3b.pdb1.gz) 30 Kb Biological Unit Coordinates (1d3b.pdb2.gz) 31 Kb Biological Unit Coordinates (1d3b.pdb3.gz) 31 Kb Biological Unit Coordinates (1d3b.pdb4.gz) 32 Kb Biological Unit Coordinates (1d3b.pdb5.gz) 31 Kb Biological Unit Coordinates (1d3b.pdb6.gz) 32 Kb LPC: Ligand-Protein Contacts for 1D3B CSU: Contacts of Structural Units for 1D3B Likely Quarternary Molecular Structure file(s) for 1D3B Structure Factors (681 Kb) Retrieve 1D3B in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1D3B from S2C, [Save to disk] Re-refined 1d3b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1D3B 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 1D3B

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 1D3B, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1d3ba_, region A [Jmol] [rasmolscript] [script source]     - Domain d1d3bb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1d3bc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1d3bd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1d3be_, region E [Jmol] [rasmolscript] [script source]     - Domain d1d3bf_, region F [Jmol] [rasmolscript] [script source]     - Domain d1d3bg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1d3bh_, region H [Jmol] [rasmolscript] [script source]     - Domain d1d3bi_, region I [Jmol] [rasmolscript] [script source]     - Domain d1d3bj_, region J [Jmol] [rasmolscript] [script source]     - Domain d1d3bk_, region K [Jmol] [rasmolscript] [script source]     - Domain d1d3bl_, region L [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: [1d3b_I] [1d3b_B] [1d3b_C] [1d3b] [1d3b_A] [1d3b_J] [1d3b_K] [1d3b_L] [1d3b_G] [1d3b_F] [1d3b_E] [1d3b_H] [1d3b_D] SWISS-PROT database: [P14678] [P62318] Domain organization of [RSMB_HUMAN] [SMD3_HUMAN] by SWISSPFAM Domain found in 1D3B: [Sm ] by SMART

Other resources with information on 1D3B

Community annotation for 1D3B at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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