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PDBsum entry 3ewe

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protein Protein-protein interface(s) links
Protein transport,structural protein PDB id
3ewe
Jmol
Contents
Protein chains
255 a.a. *
395 a.a. *
* Residue conservation analysis
PDB id:
3ewe
Name: Protein transport,structural protein
Title: Crystal structure of the nup85/seh1 complex
Structure: Nucleoporin seh1. Chain: a, c. Synonym: nuclear pore protein seh1, sec13 homolog 1. Engineered: yes. Nucleoporin nup85. Chain: b, d. Fragment: unp residues 1-564. Synonym: nuclear pore protein nup85. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast,yeast. Organism_taxid: 4932. Gene: seh1, ygl100w. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: j1624, nup85, rat9, yjr042w.
Resolution:
3.50Å     R-factor:   0.328     R-free:   0.369
Authors: S.G.Brohawn,N.C.Leksa,K.R.Rajashankar,T.U.Schwartz
Key ref:
S.G.Brohawn et al. (2008). Structural evidence for common ancestry of the nuclear pore complex and vesicle coats. Science, 322, 1369-1373. PubMed id: 18974315 DOI: 10.1126/science.1165886
Date:
14-Oct-08     Release date:   11-Nov-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P53011  (SEH1_YEAST) -  Nucleoporin SEH1
Seq:
Struc:
349 a.a.
255 a.a.
Protein chains
Pfam   ArchSchema ?
P46673  (NUP85_YEAST) -  Nucleoporin NUP85
Seq:
Struc:
 
Seq:
Struc:
744 a.a.
395 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     Seh1-associated complex   9 terms 
  Biological process     transport   4 terms 
  Biochemical function     protein binding     2 terms  

 

 
DOI no: 10.1126/science.1165886 Science 322:1369-1373 (2008)
PubMed id: 18974315  
 
 
Structural evidence for common ancestry of the nuclear pore complex and vesicle coats.
S.G.Brohawn, N.C.Leksa, E.D.Spear, K.R.Rajashankar, T.U.Schwartz.
 
  ABSTRACT  
 
Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Architecture of ACE1. (A) ACE1 containing proteins are shown as cylinders and sheets. Crowns are shown in blue, trunks in orange, tails in green, and other domains in gray. Modules with predicted structures are shown half-transparent. [PDB codes are 2QX5 for Nic96; 3BG1, Nup145C; 3CQC, Nup107 (Nup84 homolog); and 2PM6, Sec31] (B) Cartoons illustrating the similarity and modular nature of the ACE1 element. The N-terminal elaborations are, for Nic96, a coiled-coil domain that interacts with the Nsp1 complex; for Nup85, the Seh1-interacting insertion blade; for Nup145C, the Sec13-interacting insertion blade preceded by an autocatalytic cleavage domain and Nup145N; and, for Sec31, the Sec13-interacting insertion blade is preceded by its own N-terminal seven-bladed β propeller. Sec31 has a unique proline-rich insertion C-terminal to its trunk module followed by a conserved region predicted to be -helical.
Figure 5.
Fig. 5. Lattice model for the Nup84 complex and the structural scaffold of the NPC. The ACE1 proteins Nup85, Nup145C, Nup84, Sec31, and Nic96 are colored according to Fig. 4. (A) Schematic diagram of COPII outer coat organization. The Sec31 Sec13 cuboctahedron composed of 24 edge elements (Sec31 Sec13 heterotetramers) is shown unwrapped and laid flat in two dimensions. The Sec31 Sec31 crown-crown interactions make edge elements, whereas propeller-propeller interactions are vertex elements (31). (B) Schematic diagram of the predicted latticelike organization of the structural scaffold of the NPC. The entire scaffold (eight spokes) is illustrated unwrapped and laid flat in two dimensions. The Nup84 complex comprises the nuclear and cytoplasmic rings, whereas the Nic96-containing complex makes up the inner ring. The relative position and interactions between the seven proteins in the Nup84 complex are shown with Sec13, Seh1, Nup133, and Nup120 colored in gray. The remainder of the Nic96 complex (Nup157/170, Nup188, and Nup192) is illustrated in gray. The illustration is not meant to predict relative positions of proteins or structure of the inner ring per se but shows the latticelike organization of the structural scaffold that is similar to vesicle coating complexes.
 
  The above figures are reprinted from an Open Access publication published by the AAAs: Science (2008, 322, 1369-1373) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23262493 A.J.Noble, Q.Zhang, J.O'Donnell, H.Hariri, N.Bhattacharya, A.G.Marshall, and S.M.Stagg (2013).
A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry.
  Nat Struct Mol Biol, 20, 167-173.  
21499242 M.Kampmann, C.E.Atkinson, A.L.Mattheyses, and S.M.Simon (2011).
Mapping the orientation of nuclear pore proteins in living cells with polarized fluorescence microscopy.
  Nat Struct Mol Biol, 18, 643-649.  
21056839 C.Bröcker, S.Engelbrecht-Vandré, and C.Ungermann (2010).
Multisubunit tethering complexes and their role in membrane fusion.
  Curr Biol, 20, R943-R952.  
20550937 C.M.Doucet, J.A.Talamas, and M.W.Hetzer (2010).
Cell cycle-dependent differences in nuclear pore complex assembly in metazoa.
  Cell, 141, 1030-1041.  
20721671 C.M.Doucet, and M.W.Hetzer (2010).
Nuclear pore biogenesis into an intact nuclear envelope.
  Chromosoma, 119, 469-477.  
21149569 C.S.Asensio, D.W.Sirkis, and R.H.Edwards (2010).
RNAi screen identifies a role for adaptor protein AP-3 in sorting to the regulated secretory pathway.
  J Cell Biol, 191, 1173-1187.  
20451393 C.U.Stirnimann, E.Petsalaki, R.B.Russell, and C.W.Müller (2010).
WD40 proteins propel cellular networks.
  Trends Biochem Sci, 35, 565-574.  
  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.  
20566687 G.Theerthagiri, N.Eisenhardt, H.Schwarz, and W.Antonin (2010).
The nucleoporin Nup188 controls passage of membrane proteins across the nuclear pore complex.
  J Cell Biol, 189, 1129-1142.  
20974814 J.M.Mitchell, J.Mansfeld, J.Capitanio, U.Kutay, and R.W.Wozniak (2010).
Pom121 links two essential subcomplexes of the nuclear pore complex core to the membrane.
  J Cell Biol, 191, 505-521.  
20696705 J.R.Whittle, and T.U.Schwartz (2010).
Structure of the Sec13-Sec16 edge element, a template for assembly of the COPII vesicle coat.
  J Cell Biol, 190, 347-361.
PDB codes: 3mzk 3mzl
20534429 K.C.Hsia, and A.Hoelz (2010).
Crystal structure of alpha-COP in complex with epsilon-COP provides insight into the architecture of the COPI vesicular coat.
  Proc Natl Acad Sci U S A, 107, 11271-11276.
PDB codes: 3mv2 3mv3
20110349 L.C.Titus, T.R.Dawson, D.J.Rexer, K.J.Ryan, and S.R.Wente (2010).
Members of the RSC chromatin-remodeling complex are required for maintaining proper nuclear envelope structure and pore complex localization.
  Mol Biol Cell, 21, 1072-1087.  
  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.  
20087413 R.Santarella-Mellwig, J.Franke, A.Jaedicke, M.Gorjanacz, U.Bauer, A.Budd, I.W.Mattaj, and D.P.Devos (2010).
The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins.
  PLoS Biol, 8, e1000281.  
20739998 S.C.Harrison, and T.Kirchhausen (2010).
Structural biology: Conservation in vesicle coats.
  Nature, 466, 1048-1049.  
20505070 S.L.Schmid, and M.G.Farquhar (2010).
The Palade symposium: celebrating cell biology at its best.
  Mol Biol Cell, 21, 2367-2370.  
20132544 T.Cavalier-Smith (2010).
Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution.
  Biol Direct, 5, 7.  
19625448 A.Rotem, R.Gruber, H.Shorer, L.Shaulov, E.Klein, and A.Harel (2009).
Importin beta regulates the seeding of chromatin with initiation sites for nuclear pore assembly.
  Mol Biol Cell, 20, 4031-4042.  
19641022 C.K.Lau, V.A.Delmar, R.C.Chan, Q.Phung, C.Bernis, B.Fichtman, B.A.Rasala, and D.J.Forbes (2009).
Transportin regulates major mitotic assembly events: from spindle to nuclear pore assembly.
  Mol Biol Cell, 20, 4043-4058.  
19414609 E.Onischenko, L.H.Stanton, A.S.Madrid, T.Kieselbach, and K.Weis (2009).
Role of the Ndc1 interaction network in yeast nuclear pore complex assembly and maintenance.
  J Cell Biol, 185, 475-491.  
19706512 H.S.Seo, Y.Ma, E.W.Debler, D.Wacker, S.Kutik, G.Blobel, and A.Hoelz (2009).
Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex.
  Proc Natl Acad Sci U S A, 106, 14281-14286.
PDB codes: 3f7f 3h7n
19524430 J.Fernandez-Martinez, and M.P.Rout (2009).
Nuclear pore complex biogenesis.
  Curr Opin Cell Biol, 21, 603-612.  
19674973 J.R.Whittle, and T.U.Schwartz (2009).
Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element.
  J Biol Chem, 284, 28442-28452.
PDB codes: 3i4r 3i5p 3i5q
19801417 L.J.Terry, and S.R.Wente (2009).
Flexible gates: dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic transport.
  Eukaryot Cell, 8, 1814-1827.  
19560357 M.A.Silverman, and M.R.Leroux (2009).
Intraflagellar transport and the generation of dynamic, structurally and functionally diverse cilia.
  Trends Cell Biol, 19, 306-316.  
19503077 M.Kampmann, and G.Blobel (2009).
Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex.
  Nat Struct Mol Biol, 16, 782-788.  
19576787 N.C.Leksa, S.G.Brohawn, and T.U.Schwartz (2009).
The structure of the scaffold nucleoporin Nup120 reveals a new and unexpected domain architecture.
  Structure, 17, 1082-1091.
PDB code: 3hxr
19327984 N.Elad, T.Maimon, D.Frenkiel-Krispin, R.Y.Lim, and O.Medalia (2009).
Structural analysis of the nuclear pore complex by integrated approaches.
  Curr Opin Struct Biol, 19, 226-232.  
19234477 S.Güttinger, E.Laurell, and U.Kutay (2009).
Orchestrating nuclear envelope disassembly and reassembly during mitosis.
  Nat Rev Mol Cell Biol, 10, 178-191.  
19748337 S.G.Brohawn, J.R.Partridge, J.R.Whittle, and T.U.Schwartz (2009).
The nuclear pore complex has entered the atomic age.
  Structure, 17, 1156-1168.  
  19641729 S.G.Brohawn, and T.U.Schwartz (2009).
A lattice model of the nuclear pore complex.
  Commun Integr Biol, 2, 205-207.  
19855394 S.G.Brohawn, and T.U.Schwartz (2009).
Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice.
  Nat Struct Mol Biol, 16, 1173-1177.
PDB codes: 3jro 3jrp
19805193 V.Nagy, K.C.Hsia, E.W.Debler, M.Kampmann, A.M.Davenport, G.Blobel, and A.Hoelz (2009).
Structure of a trimeric nucleoporin complex reveals alternate oligomerization states.
  Proc Natl Acad Sci U S A, 106, 17693-17698.
PDB code: 3iko
19575675 Y.Shibata, J.Hu, M.M.Kozlov, and T.A.Rapoport (2009).
Mechanisms shaping the membranes of cellular organelles.
  Annu Rev Cell Dev Biol, 25, 329-354.  
19111661 E.W.Debler, Y.Ma, H.S.Seo, K.C.Hsia, T.R.Noriega, G.Blobel, and A.Hoelz (2008).
A fence-like coat for the nuclear pore membrane.
  Mol Cell, 32, 815-826.
PDB codes: 3f3f 3f3g 3f3p
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.