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PDBsum entry 3iko

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protein Protein-protein interface(s) links
Structural protein, protein transport PDB id
3iko
Jmol
Contents
Protein chains
274 a.a. *
434 a.a. *
419 a.a. *
* Residue conservation analysis
PDB id:
3iko
Name: Structural protein, protein transport
Title: Crystal structure of the heterotrimeric sec13-nup145c-nup84 nucleoporin complex
Structure: Protein transport protein sec13. Chain: a, d, g. Fragment: unp residues 1-297. Engineered: yes. Nucleoporin nup145c. Chain: b, e, h. Fragment: unp residues 731-1158. Synonym: nucleoporin nup145c, c-nup145. Engineered: yes.
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: sec13, anu3, ylr208w, l8167.4. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: nup145, rat10, ygl092w. Gene: nup84, ydl116w.
Resolution:
3.20Å     R-factor:   0.234     R-free:   0.273
Authors: V.Nagy,K.-C.Hsia,E.W.Debler,A.Davenport,G.Blobel,A.Hoelz
Key ref:
V.Nagy et al. (2009). Structure of a trimeric nucleoporin complex reveals alternate oligomerization states. Proc Natl Acad Sci U S A, 106, 17693-17698. PubMed id: 19805193 DOI: 10.1073/pnas.0909373106
Date:
06-Aug-09     Release date:   13-Oct-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q04491  (SEC13_YEAST) -  Protein transport protein SEC13
Seq:
Struc:
297 a.a.
274 a.a.
Protein chains
Pfam   ArchSchema ?
P49687  (NU145_YEAST) -  Nucleoporin NUP145
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1317 a.a.
434 a.a.*
Protein chains
Pfam   ArchSchema ?
P52891  (NUP84_YEAST) -  Nucleoporin NUP84
Seq:
Struc:
 
Seq:
Struc:
726 a.a.
419 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     Seh1-associated complex   13 terms 
  Biological process     COPII-coated vesicle budding   9 terms 
  Biochemical function     structural molecule activity     3 terms  

 

 
DOI no: 10.1073/pnas.0909373106 Proc Natl Acad Sci U S A 106:17693-17698 (2009)
PubMed id: 19805193  
 
 
Structure of a trimeric nucleoporin complex reveals alternate oligomerization states.
V.Nagy, K.C.Hsia, E.W.Debler, M.Kampmann, A.M.Davenport, G.Blobel, A.Hoelz.
 
  ABSTRACT  
 
The heptameric Nup84 complex constitutes an evolutionarily conserved building block of the nuclear pore complex. Here, we present the crystal structure of the heterotrimeric Sec13 x Nup145C x Nup84 complex, the centerpiece of the heptamer, at 3.2-A resolution. Nup84 forms a U-shaped alpha-helical solenoid domain, topologically similar to two other members of the heptamer, Nup145C and Nup85. The interaction between Nup84 and Nup145C is mediated via a hydrophobic interface located in the kink regions of the two solenoids that is reinforced by additional interactions of two long Nup84 loops. The Nup84 binding site partially overlaps with the homo-dimerization interface of Nup145C, suggesting competing binding events. Fitting of the elongated Z-shaped heterotrimer into electron microscopy (EM) envelopes of the heptamer indicates that structural changes occur at the Nup145C x Nup84 interface. Docking the crystal structures of all heptamer components into the EM envelope constitutes a major advance toward the completion of the structural characterization of the Nup84 complex.
 
  Selected figure(s)  
 
Figure 1.
Structure of the S. cerevisiae Sec13·Nup145C·Nup84 NTD complex. (A) Schematic representation of the heptameric complex and the approximate localization of its seven nups (21). (B) Domain structures of Sec13, Nup145C, and Nup84. For Sec13, the six WD40 repeats (orange) are indicated. For Nup145C, the unstructured N-terminal region (gray), the domain invasion motif (DIM) (green), the αB-αC connector (C) (red), the α-helical domain (blue), and the C-terminal α-helical region (pink) are indicated. For Nup84, the N-terminal domain (NTD) and C-terminal domain (CTD) are indicated. The residue numbering is shown below and the bars above the domain structures mark the crystallized fragments of the three proteins. (C) Structure of Sec13·Nup145C·Nup84 NTD in ribbon representation, colored as in panel B. A 90°-rotated view is shown on the right. (D) Schematic representation of the Sec13·Nup145C·Nup84 NTD heterotrimer.
Figure 4.
Interaction of the Nup84 NTD with the Nup145C solenoid domain. The Sec13·Nup145C·Nup84 NTD heterotrimer is shown in ribbon representation, colored according to Fig. 1C. The kink regions of the two solenoids interact in a head-to-head fashion. The Nup84 NTD protrudes with an approximate 40° angle from the Nup145C U-shaped solenoid. The inset marks the Nup145C·Nup84 interface that is illustrated in detail on the right. For clarity, the interface shown on the right is rotated by 90°. For Nup145C, the solenoid subdomain (blue) and helix αE (green) are indicated. For Nup84, the interface helices (yellow), as well as the long αE-αF (red) and αH-αI (magenta) connectors that mediate the interaction with Nup145C are indicated.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23090414 M.Raices, and M.A.D'Angelo (2012).
Nuclear pore complex composition: a new regulator of tissue-specific and developmental functions.
  Nat Rev Mol Cell Biol, 13, 687-699.  
20512149 D.Flemming, K.Thierbach, P.Stelter, B.Böttcher, and E.Hurt (2010).
Precise mapping of subunits in multiprotein complexes by a versatile electron microscopy label.
  Nat Struct Mol Biol, 17, 775-778.  
  21326946 E.W.Debler, K.C.Hsia, V.Nagy, H.S.Seo, and A.Hoelz (2010).
Characterization of the membrane-coating Nup84 complex: Paradigm for the nuclear pore complex structure.
  Nucleus, 1, 150-157.  
20490895 H.N.Banerjee, J.Gibbs, T.Jordan, and M.Blackshear (2010).
Depletion of a single nucleoporin, Nup107, induces apoptosis in eukaryotic cells.
  Mol Cell Biochem, 343, 21-25.  
  21327078 N.C.Leksa, and T.U.Schwartz (2010).
Membrane-coating lattice scaffolds in the nuclear pore and vesicle coats: Commonalities, differences, challenges.
  Nucleus, 1, 314-318.  
20505070 S.L.Schmid, and M.G.Farquhar (2010).
The Palade symposium: celebrating cell biology at its best.
  Mol Biol Cell, 21, 2367-2370.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.