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PDBsum entry 3f3p

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protein Protein-protein interface(s) links
Structural protein PDB id
3f3p
Jmol
Contents
Protein chains
(+ 0 more) 303 a.a. *
(+ 0 more) 480 a.a. *
* Residue conservation analysis
PDB id:
3f3p
Name: Structural protein
Title: Crystal structure of the nucleoporin pair nup85-seh1, space p21212
Structure: Nucleoporin seh1. Chain: a, b, e, f, i, j. Synonym: nuclear pore protein seh1, sec13 homolog 1. Engineered: yes. Nucleoporin nup85. Chain: c, d, g, h, k, l. Fragment: unp residues 1-570. Synonym: nuclear pore protein nup85. Engineered: yes
Source: Saccharomyces cerevisiae. Organism_taxid: 4932. Gene: seh1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: nup85, rat9.
Resolution:
3.20Å     R-factor:   0.261     R-free:   0.281
Authors: E.W.Debler,H.Hseo,Y.Ma,G.Blobel,A.Hoelz
Key ref:
E.W.Debler et al. (2008). A fence-like coat for the nuclear pore membrane. Mol Cell, 32, 815-826. PubMed id: 19111661 DOI: 10.1016/j.molcel.2008.12.001
Date:
31-Oct-08     Release date:   07-Apr-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P53011  (SEH1_YEAST) -  Nucleoporin SEH1
Seq:
Struc:
349 a.a.
303 a.a.
Protein chains
Pfam   ArchSchema ?
P46673  (NUP85_YEAST) -  Nucleoporin NUP85
Seq:
Struc:
 
Seq:
Struc:
744 a.a.
480 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: 10.1016/j.molcel.2008.12.001 Mol Cell 32:815-826 (2008)
PubMed id: 19111661  
 
 
A fence-like coat for the nuclear pore membrane.
E.W.Debler, Y.Ma, H.S.Seo, K.C.Hsia, T.R.Noriega, G.Blobel, A.Hoelz.
 
  ABSTRACT  
 
We recently proposed a cylindrical coat for the nuclear pore membrane in the nuclear pore complex (NPC). This scaffold is generated by multiple copies of seven nucleoporins. Here, we report three crystal structures of the nucleoporin pair Seh1*Nup85, which is part of the coat cylinder. The Seh1*Nup85 assembly bears resemblance in its shape and dimensions to that of another nucleoporin pair, Sec13*Nup145C. Furthermore, the Seh1*Nup85 structures reveal a hinge motion that may facilitate conformational changes in the NPC during import of integral membrane proteins and/or during nucleocytoplasmic transport. We propose that Seh1*Nup85 and Sec13*Nup145C form 16 alternating, vertical rods that are horizontally linked by the three remaining nucleoporins of the coat cylinder. Shared architectural and mechanistic principles with the COPII coat indicate a common evolutionary origin and support the notion that the NPC coat represents another class of membrane coats.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Detailed Structural Analysis of Nup85 and Seh1
(A) A ribbon representation of the Nup85 structure is shown in rainbow colors along the polypeptide chain from the N to the C terminus. The N-terminal domain invasion motif (DIM), the α-helical solenoid domain, and their secondary structure elements are indicated.
(B) The structure of the Seh1•Nup85 heterodimer. The Nup85^DIM (magenta), the Nup85 α-helical solenoid domain (blue), the Nup85 αQ-αR connector (red), the Seh1 β propeller (yellow), the disordered Seh1 5CD loop (gray dots), and the Seh1 2CD loop (orange) are indicated; a 90° rotated view is shown on the right. Dotted lines represent disordered regions.
(C) Schematic representation of the Seh1•Nup85 interaction. The Seh1 2CD loop, the Nup85 αQ-αR connector, and the DIM region are highlighted in orange, red, and pink, respectively.
(D) The β propeller domain of Seh1 in complex with the Nup85^DIM. Seh1 is shown in yellow, and the six blades are indicated. The Nup85^DIM contributes one strand to blade 6 and three strands to blade 7, completing the β propeller.
(E) Schematic representation of the Seh1 β propeller and its interaction with the Nup85^DIM.
Figure 5.
Figure 5. Flexibility of the Seh1•Nup85 Hetero-Octamer
(A) The hetero-octamers of crystal forms 1 and 2 are related by an vert, similar 35° hinge motion around the center of the hetero-octamer. On the right, a schematic of the two conformations is shown, where Seh1 and Nup85 are displayed as balls and cylinders, respectively.
(B) Crystal form 3 harbors a heterododecamer in the asymmetric unit (small ribbon representation). The two interfaces between the heterotetramers are identical. In the upper two neighboring heterotetramers of crystal form 3 (boxed in the heterododecamer), one heterotetramer is rotated by vert, similar 80° around its long axis with respect to crystal form 1. For clarity, a stripe of black lines marks the relative orientations of the heterotetramers. The alignment of the different structures was based on the lower heterotetramer of crystal form 1.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2008, 32, 815-826) copyright 2008.  
  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.  
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.  
20926687 B.Fichtman, C.Ramos, B.Rasala, A.Harel, and D.J.Forbes (2010).
Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis.
  Mol Biol Cell, 21, 4197-4211.  
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.  
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.  
20144761 M.Capelson, Y.Liang, R.Schulte, W.Mair, U.Wagner, and M.W.Hetzer (2010).
Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes.
  Cell, 140, 372-383.  
  20354266 M.W.Hetzer (2010).
The role of the nuclear pore complex in aging of post-mitotic cells.
  Aging (Albany NY), 2, 74-75.  
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.  
20505070 S.L.Schmid, and M.G.Farquhar (2010).
The Palade symposium: celebrating cell biology at its best.
  Mol Biol Cell, 21, 2367-2370.  
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.  
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
19525551 J.A.DeGrasse, K.N.DuBois, D.Devos, T.N.Siegel, A.Sali, M.C.Field, M.P.Rout, and B.T.Chait (2009).
Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor.
  Mol Cell Proteomics, 8, 2119-2130.  
19208808 J.Napetschnig, S.A.Kassube, E.W.Debler, R.W.Wong, G.Blobel, and A.Hoelz (2009).
Structural and functional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19.
  Proc Natl Acad Sci U S A, 106, 3089-3094.
PDB codes: 3fmo 3fmp
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
19543230 M.Capelson, and M.W.Hetzer (2009).
The role of nuclear pores in gene regulation, development and disease.
  EMBO Rep, 10, 697-705.  
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
19596381 R.Peters (2009).
Functionalization of a nanopore: the nuclear pore complex paradigm.
  Biochim Biophys Acta, 1793, 1533-1539.  
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.  
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.