3IKO	Structural Protein, Protein Transport	date	Aug 06, 2009
title	Crystal Structure Of The Heterotrimeric Sec13-Nup145c-Nup84 Nucleoporin Complex
authors	V.Nagy, K.C.Hsia, E.W.Debler, A.Davenport, G.Blobel, A.Hoelz
compound		source
Molecule: Protein Transport Protein Sec13 Chain: A, D, G Fragment: Unp Residues 1-297 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Sec13, Anu3, Ylr208w, L8167.4 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-Codonplus (De3)-Ril Expression_system_vector_type: Pet
Molecule: Nucleoporin Nup145c Chain: B, E, H Fragment: Unp Residues 731-1158 Synonym: Nucleoporin Nup145c, C-Nup145 Ec: 3.4.21.- Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Nup145, Rat10, Ygl092w Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-Codonplus (De3)-Ril Expression_system_vector_type: Pet
Molecule: Nucleoporin Nup84 Chain: C, F, I Fragment: Unp Residues 1-460 Synonym: Nuclear Pore Protein Nup84 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932 Gene: Nup84, Ydl116w Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-Codonplus (De3)-Ril Expression_system_vector_type: Pet
symmetry	Space Group: P 21 21 21	R_factor 0.234 R_Free 0.273
crystal cell	length a length b length c angle alpha angle beta angle gamma 101.397 194.050 327.806 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.20 Å
ligand		enzyme	Hydrolase E.C.3.4.21 BRENDA
Gene Ontology	Chain Function Process Component A, D, G COPII-coated vesicle budding... E, B, H F, C, I
Primary reference	Structure of a trimeric nucleoporin complex reveals alternate oligomerization states., Nagy V, Hsia KC, Debler EW, Kampmann M, Davenport AM, Blobel G, Hoelz A, Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17693-8. Epub 2009 Oct 1. PMID:19805193

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (506 Kb) [Save to disk] Biological Unit Coordinates (3iko.pdb1.gz) 174 Kb Biological Unit Coordinates (3iko.pdb2.gz) 172 Kb Biological Unit Coordinates (3iko.pdb3.gz) 168 Kb CSU: Contacts of Structural Units for 3IKO Structure Factors (1445 Kb) Retrieve 3IKO in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3IKO from S2C, [Save to disk] Re-refined 3iko structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3IKO 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 3IKO

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 3IKO, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3iko_A] [3iko_G] [3iko_H] [3iko] [3iko_C] [3iko_E] [3iko_D] [3iko_B] [3iko_I] [3iko_F] SWISS-PROT database: [P49687] [P52891] [Q04491] Belongs to the eukaryotic nuclear pore complex (e-npc) family according to TCDB. Domain organization of [NU145_YEAST] [NUP84_YEAST] [SEC13_YEAST] by SWISSPFAM Domain found in 3IKO: [WD40 ] by SMART

Other resources with information on 3IKO

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

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