PDBsum entry 3gj8

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protein ligands metals Protein-protein interface(s) links
Transport protein PDB id
Protein chains
204 a.a. *
27 a.a. *
26 a.a. *
GDP ×2
_MG ×4
_ZN ×2
Waters ×548
* Residue conservation analysis
PDB id:
Name: Transport protein
Title: Crystal structure of human rangdp-nup153znf34 complex
Structure: Gtp-binding nuclear protein ran. Chain: a, c. Synonym: gtpase ran, ras-related nuclear protein, ras-like protein tc4, androgen receptor-associated protein 24. Engineered: yes. Mutation: yes. Nuclear pore complex protein nup153. Chain: b, d. Fragment: nup153 - zinc finger module 34: unp residues 790-
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ran, ara24, ok/sw-cl.81. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: bl21(de3)-ril. Rattus norvegicus. Rat.
1.82Å     R-factor:   0.172     R-free:   0.203
Authors: J.R.Partridge,T.U.Schwartz
Key ref:
J.R.Partridge and T.U.Schwartz (2009). Crystallographic and biochemical analysis of the Ran-binding zinc finger domain. J Mol Biol, 391, 375-389. PubMed id: 19505478 DOI: 10.1016/j.jmb.2009.06.011
07-Mar-09     Release date:   04-Aug-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P62826  (RAN_HUMAN) -  GTP-binding nuclear protein Ran
216 a.a.
204 a.a.*
Protein chain
Pfam   ArchSchema ?
P49791  (NU153_RAT) -  Nuclear pore complex protein Nup153
1468 a.a.
27 a.a.
Protein chain
Pfam   ArchSchema ?
P49791  (NU153_RAT) -  Nuclear pore complex protein Nup153
1468 a.a.
26 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   9 terms 
  Biological process     viral reproduction   27 terms 
  Biochemical function     nucleotide binding     9 terms  


DOI no: 10.1016/j.jmb.2009.06.011 J Mol Biol 391:375-389 (2009)
PubMed id: 19505478  
Crystallographic and biochemical analysis of the Ran-binding zinc finger domain.
J.R.Partridge, T.U.Schwartz.
The nuclear pore complex (NPC) resides in circular openings within the nuclear envelope and serves as the sole conduit to facilitate nucleocytoplasmic transport in eukaryotes. The asymmetric distribution of the small G protein Ran across the nuclear envelope regulates directionality of protein transport. Ran interacts with the NPC of metazoa via two asymmetrically localized components, Nup153 at the nuclear face and Nup358 at the cytoplasmic face. Both nucleoporins contain a stretch of distinct, Ran-binding zinc finger domains. Here, we present six crystal structures of Nup153-zinc fingers in complex with Ran and a 1.48 A crystal structure of RanGDP. Crystal engineering allowed us to obtain well diffracting crystals so that all ZnF-Ran complex structures are refined to high resolution. Each of the four zinc finger modules of Nup153 binds one Ran molecule in apparently non-allosteric fashion. The affinity is measurably higher for RanGDP than for RanGTP and varies modestly between the individual zinc fingers. By microcalorimetric and mutational analysis, we determined that one specific hydrogen bond accounts for most of the differences in the binding affinity of individual zinc fingers. Genomic analysis reveals that only in animals do NPCs contain Ran-binding zinc fingers. We speculate that these organisms evolved a mechanism to maintain a high local concentration of Ran at the vicinity of the NPC, using this zinc finger domain as a sink.
  Selected figure(s)  
Figure 3.
Fig. 3. Crystallographic lattice formed in the crystallization of the Nup153-ZnF•RanGDP complex. Residues highlighted in red indicate contacts between neighboring Ran molecules down a single plane of the P2[1] lattice. This plane represents the smallest crystallographic interface and was chosen for crystal engineering to stabilize packing, in hopes of improving diffraction. The enlarged 3D image on the right depicts residues binding at the interface. Thr32′ and His53 make a single hydrogen bond, mirrored across a 2-fold symmetrical face as indicated. A clash between Phe35′ and Pro58, though tolerated, was theorized to partially counteract the strong interaction between Thr32′ and His53. A point-mutation of Phe35′ to serine stabilizes the crystal contact and increases the resolution of our crystallographic experiments by 1 Å.
Figure 5.
Fig. 5. A surface representation of RanGDP or RanGTP, grey, with or without Nup153-ZnF, blue ribbon. Residues involved in intermolecular contacts are colored orange. (a) The ZnF•RanGDP complex. Lys38^Ran and Thr42^Ran, located in the switch I region, form conserved H bonds with the ZnF, and are known to undergo significant conformational changes upon binding GTP. Both residues are positioned to interact with ZnF in this conformation. (b) The RanGDP interaction surface in the absence of ZnF. (c) RanGTP in the absence of modeled ZnF. Lys38^Ran and Thr42^Ran are displaced by up to 30 Å, and are no longer able to interact with Nup153-ZnF in this conformation.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 391, 375-389) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21189294 K.Tamura, Y.Fukao, M.Iwamoto, T.Haraguchi, and I.Hara-Nishimura (2010).
Identification and characterization of nuclear pore complex components in Arabidopsis thaliana.
  Plant Cell, 22, 4084-4097.  
20739938 R.D.Makde, J.R.England, H.P.Yennawar, and S.Tan (2010).
Structure of RCC1 chromatin factor bound to the nucleosome core particle.
  Nature, 467, 562-566.
PDB code: 3mvd
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.  
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