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PDBsum entry 3bbp

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protein ligands metals Protein-protein interface(s) links
Protein transport/splicing PDB id
3bbp
Jmol
Contents
Protein chains
161 a.a. *
38 a.a. *
37 a.a. *
30 a.a. *
Ligands
GTP ×3
Metals
_MG ×3
* Residue conservation analysis
PDB id:
3bbp
Name: Protein transport/splicing
Title: Rab6-gtp:gcc185 rab binding domain complex
Structure: Ras-related protein rab-6a. Chain: a, b, c. Synonym: rab-6. Engineered: yes. Mutation: yes. Grip and coiled-coil domain-containing protein 2. Chain: d, e, f. Fragment: unp residues 1446-1511. Synonym: golgi coiled-coil protein gcc185, ran-binding
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rab6a, rab6. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: gcc2, kiaa0336, ranbp2l4.
Resolution:
3.00Å     R-factor:   0.228     R-free:   0.268
Authors: A.Schweizer Burguete,T.D.Fenn,A.T.Brunger,S.R.Pfeffer
Key ref:
A.S.Burguete et al. (2008). Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185. Cell, 132, 286-298. PubMed id: 18243103 DOI: 10.1016/j.cell.2007.11.048
Date:
09-Nov-07     Release date:   05-Feb-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P20340  (RAB6A_HUMAN) -  Ras-related protein Rab-6A
Seq:
Struc:
208 a.a.
161 a.a.*
Protein chain
Pfam   ArchSchema ?
Q8IWJ2  (GCC2_HUMAN) -  GRIP and coiled-coil domain-containing protein 2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1684 a.a.
38 a.a.
Protein chain
Pfam   ArchSchema ?
Q8IWJ2  (GCC2_HUMAN) -  GRIP and coiled-coil domain-containing protein 2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1684 a.a.
37 a.a.
Protein chain
Pfam   ArchSchema ?
Q8IWJ2  (GCC2_HUMAN) -  GRIP and coiled-coil domain-containing protein 2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1684 a.a.
30 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   7 terms 
  Biological process     minus-end-directed organelle transport along microtubule   11 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
DOI no: 10.1016/j.cell.2007.11.048 Cell 132:286-298 (2008)
PubMed id: 18243103  
 
 
Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185.
A.S.Burguete, T.D.Fenn, A.T.Brunger, S.R.Pfeffer.
 
  ABSTRACT  
 
GCC185 is a large coiled-coil protein at the trans Golgi network that is required for receipt of transport vesicles inbound from late endosomes and for anchoring noncentrosomal microtubules that emanate from the Golgi. Here, we demonstrate that recruitment of GCC185 to the Golgi is mediated by two Golgi-localized small GTPases of the Rab and Arl families. GCC185 binds Rab6, and mutation of residues needed for Rab binding abolishes Golgi localization. The crystal structure of Rab6 bound to the GCC185 Rab-binding domain reveals that Rab6 recognizes a two-fold symmetric surface on a coiled coil immediately adjacent to a C-terminal GRIP domain. Unexpectedly, Rab6 binding promotes association of Arl1 with the GRIP domain. We present a structure-derived model for dual GTPase membrane attachment that highlights the potential ability of Rab GTPases to reach binding partners at a significant distance from the membrane via their unstructured and membrane-anchored, hypervariable domains.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Accessible Hydrophobic Residues in the Predicted Coiled Coil Are Critical for Rab Binding
(A) Helical wheel projection of a coiled coil predicted for GCC185 residues 1579–1606. Residues in registers “a–g” were predicted by the Paircoil program. Residues at positions “a” and “d” lie in the dimer interface. Boxed residues are candidates for binding interactions with Rab GTPases.
(B and C) Effect of alanine substitutions on Rab binding. Reactions contained wild-type or mutant GST-C-110 ([B] 3 μM, [C] 2 μM) and ^35S-GTPγS-preloaded GTPases ([B] 170 pmol Rab9-His, [C] 190 pmol His-Rab6). Data are mean ± SD.
(D) Mass determination of untagged RBD-87 I1588A/L1595A by multiple angle static light scattering. The gel filtration elution profile of the protein (black line) and molecular mass (gray line) are shown. Polydispersity of the peak was 1.001.
Figure 4.
Figure 4. Structure of the Rab6-GCC185 Complex
(A) Ribbon representation of the GCC185 Rab-binding domain dimer (green) and Rab6 (blue) bound to GTP (stick model) and magnesium (sphere). Switch I and II regions of Rab6 (Chattopadhyay et al., 2000) are colored yellow and orange respectively.
(B) View of the Rab6-GCC185-binding interface. A single GCC185 helix (E) out of the two-fold symmetric coiled coil is shown for clarity. Each helix contacts switch regions from two opposed Rab6 molecules A and B. Rab6 switch I and II (including W67) are colored yellow and orange, respectively. Protein backbone (α-carbon trace) and side chains involved in polar and hydrophobic interactions are shown. Carbonyl oxygens are shown for A44, I48, and I1588, and C-Cα bonds have been added to simplify the figure. An anomalous difference Fourier density map of the selenomethionine-substituted crystal (pink, contoured at 6σ) is shown for GCC185.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2008, 132, 286-298) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21378754 X.Hou, N.Hagemann, S.Schoebel, W.Blankenfeldt, R.S.Goody, K.S.Erdmann, and A.Itzen (2011).
A structural basis for Lowe syndrome caused by mutations in the Rab-binding domain of OCRL1.
  EMBO J, 30, 1659-1670.
PDB code: 3qbt
20534488 A.Mishra, S.Eathiraj, S.Corvera, and D.G.Lambright (2010).
Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1).
  Proc Natl Acad Sci U S A, 107, 10866-10871.
PDB code: 3mjh
20227882 B.Goud, and P.A.Gleeson (2010).
TGN golgins, Rabs and cytoskeleton: regulating the Golgi trafficking highways.
  Trends Cell Biol, 20, 329-336.  
19575650 I.M.Yu, and F.M.Hughson (2010).
Tethering factors as organizers of intracellular vesicular traffic.
  Annu Rev Cell Dev Biol, 26, 137-156.  
20610657 J.Jing, J.R.Junutula, C.Wu, J.Burden, H.Matern, A.A.Peden, and R.Prekeris (2010).
FIP1/RCP binding to Golgin-97 regulates retrograde transport from recycling endosomes to the trans-Golgi network.
  Mol Biol Cell, 21, 3041-3053.  
20235548 K.W.Kaufmann, G.H.Lemmon, S.L.Deluca, J.H.Sheehan, and J.Meiler (2010).
Practically useful: what the Rosetta protein modeling suite can do for you.
  Biochemistry, 49, 2987-2998.  
20213668 R.J.Falconer, A.Penkova, I.Jelesarov, and B.M.Collins (2010).
Survey of the year 2008: applications of isothermal titration calorimetry.
  J Mol Recognit, 23, 395-413.  
20100911 S.Pankiv, E.A.Alemu, A.Brech, J.A.Bruun, T.Lamark, A.Overvatn, G.Bjørkøy, and T.Johansen (2010).
FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport.
  J Cell Biol, 188, 253-269.  
20163571 T.Starr, Y.Sun, N.Wilkins, and B.Storrie (2010).
Rab33b and Rab6 are functionally overlapping regulators of Golgi homeostasis and trafficking.
  Traffic, 11, 626-636.  
19889643 Y.Fujioka, N.N.Noda, H.Nakatogawa, Y.Ohsumi, and F.Inagaki (2010).
Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its functional significance in autophagy.
  J Biol Chem, 285, 1508-1515.
PDB codes: 3a7o 3a7p
19490533 A.Osterrieder, C.M.Carvalho, M.Latijnhouwers, J.N.Johansen, C.Stubbs, S.Botchway, and C.Hawes (2009).
Fluorescence lifetime imaging of interactions between golgi tethering factors and small GTPases in plants.
  Traffic, 10, 1034-1046.  
19816566 A.R.Lipinski, J.Heymann, C.Meissner, A.Karlas, V.Brinkmann, T.F.Meyer, and D.Heuer (2009).
Rab6 and Rab11 regulate Chlamydia trachomatis development and golgin-84-dependent Golgi fragmentation.
  PLoS Pathog, 5, e1000615.  
19805030 E.Arnaud, J.Zenker, A.S.de Preux Charles, C.Stendel, A.Roos, J.J.Médard, N.Tricaud, J.Weis, U.Suter, J.Senderek, and R.Chrast (2009).
SH3TC2/KIAA1985 protein is required for proper myelination and the integrity of the node of Ranvier in the peripheral nervous system.
  Proc Natl Acad Sci U S A, 106, 17528-17533.  
19490898 E.J.Espinosa, M.Calero, K.Sridevi, and S.R.Pfeffer (2009).
RhoBTB3: a Rho GTPase-family ATPase required for endosome to Golgi transport.
  Cell, 137, 938-948.  
19887069 E.Sztul, and V.Lupashin (2009).
Role of vesicle tethering factors in the ER-Golgi membrane traffic.
  FEBS Lett, 583, 3770-3783.  
19508857 F.A.Barr (2009).
Rab GTPase function in Golgi trafficking.
  Semin Cell Dev Biol, 20, 780-783.  
19703403 F.J.Houghton, P.L.Chew, S.Lodeho, B.Goud, and P.A.Gleeson (2009).
The localization of the Golgin GCC185 is independent of Rab6A/A' and Arl1.
  Cell, 138, 787-794.  
18946081 G.L.Hayes, F.C.Brown, A.K.Haas, R.M.Nottingham, F.A.Barr, and S.R.Pfeffer (2009).
Multiple Rab GTPase binding sites in GCC185 suggest a model for vesicle tethering at the trans-Golgi.
  Mol Biol Cell, 20, 209-217.  
19603039 H.Stenmark (2009).
Rab GTPases as coordinators of vesicle traffic.
  Nat Rev Mol Cell Biol, 10, 513-525.  
19508854 I.B.Ramirez, and M.Lowe (2009).
Golgins and GRASPs: holding the Golgi together.
  Semin Cell Dev Biol, 20, 770-779.  
19443190 J.Gruenberg (2009).
Viruses and endosome membrane dynamics.
  Curr Opin Cell Biol, 21, 582-588.  
19153612 J.Mazelova, L.Astuto-Gribble, H.Inoue, B.M.Tam, E.Schonteich, R.Prekeris, O.L.Moritz, P.A.Randazzo, and D.Deretic (2009).
Ciliary targeting motif VxPx directs assembly of a trafficking module through Arf4.
  EMBO J, 28, 183-192.  
19454595 J.N.Johansen, C.M.Chow, I.Moore, and C.Hawes (2009).
AtRAB-H1b and AtRAB-H1c GTPases, homologues of the yeast Ypt6, target reporter proteins to the Golgi when expressed in Nicotiana tabacum and Arabidopsis thaliana.
  J Exp Bot, 60, 3179-3193.  
19224922 K.Nishimoto-Morita, H.W.Shin, H.Mitsuhashi, M.Kitamura, Q.Zhang, L.Johannes, and K.Nakayama (2009).
Differential Effects of Depletion of ARL1 and ARFRP1 on Membrane Trafficking between the trans-Golgi Network and Endosomes.
  J Biol Chem, 284, 10583-10592.  
19681135 M.Al-Dosari, and F.S.Alkuraya (2009).
A novel missense mutation in SCYL1BP1 produces geroderma osteodysplastica phenotype indistinguishable from that caused by nullimorphic mutations.
  Am J Med Genet A, 149, 2093-2098.  
19797081 M.Sumakovic, J.Hegermann, L.Luo, S.J.Husson, K.Schwarze, C.Olendrowitz, L.Schoofs, J.Richmond, and S.Eimer (2009).
UNC-108/RAB-2 and its effector RIC-19 are involved in dense core vesicle maturation in Caenorhabditis elegans.
  J Cell Biol, 186, 897-914.  
19522756 M.T.Lee, A.Mishra, and D.G.Lambright (2009).
Structural mechanisms for regulation of membrane traffic by rab GTPases.
  Traffic, 10, 1377-1389.  
19864631 R.Das, I.André, Y.Shen, Y.Wu, A.Lemak, S.Bansal, C.H.Arrowsmith, T.Szyperski, and D.Baker (2009).
Simultaneous prediction of protein folding and docking at high resolution.
  Proc Natl Acad Sci U S A, 106, 18978-18983.  
19706500 R.M.Nottingham, and S.R.Pfeffer (2009).
Defining the boundaries: Rab GEFs and GAPs.
  Proc Natl Acad Sci U S A, 106, 14185-14186.  
19141279 R.Recacha, A.Boulet, F.Jollivet, S.Monier, A.Houdusse, B.Goud, and A.R.Khan (2009).
Structural basis for recruitment of Rab6-interacting protein 1 to Golgi via a RUN domain.
  Structure, 17, 21-30.
PDB code: 3cwz
19349576 S.Pfeffer (2009).
Suzanne Pfeffer: sorting through membrane trafficking. Interview by Caitlin Sedwick.
  J Cell Biol, 185, 4-5.  
19879268 S.R.Pfeffer (2009).
Multiple routes of protein transport from endosomes to the trans Golgi network.
  FEBS Lett, 583, 3811-3816.  
19644450 T.Isabet, G.Montagnac, K.Regazzoni, B.Raynal, F.El Khadali, P.England, M.Franco, P.Chavrier, A.Houdusse, and J.Ménétrey (2009).
The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4.
  EMBO J, 28, 2835-2845.
PDB code: 2w83
19414022 Y.An, C.Y.Chen, B.Moyer, P.Rotkiewicz, M.A.Elsliger, A.Godzik, I.A.Wilson, and W.E.Balch (2009).
Structural and functional analysis of the globular head domain of p115 provides insight into membrane tethering.
  J Mol Biol, 391, 26-41.
PDB codes: 3gq2 3grl
19109890 L.Johannes, and V.Popoff (2008).
Tracing the retrograde route in protein trafficking.
  Cell, 135, 1175-1187.  
19001129 R.Sinka, A.K.Gillingham, V.Kondylis, and S.Munro (2008).
Golgi coiled-coil proteins contain multiple binding sites for Rab family G proteins.
  J Cell Biol, 183, 607-615.  
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 code is shown on the right.