Primary Citation PubMed: 14645856
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Non-EST based prediction of exon skipping and intron retention events using Pfam information.
(2005) Nucleic Acids Res 33
PubMed: 16204458 | PubMedCentral: PMC1243800 | DOI: 10.1093/nar/gki870
( C ) BAR domain PF03114 as an example: The exon junctions of BIN1 (NM_139345) are mapped to the secondary structure of the BAR domain using the known structure (PDB 1uru) of CG8604-PA (Swiss-Prot Q9Y... 92) as a template.
Publication Year: 2005
ProFAT: a web-based tool for the functional annotation of protein sequences.
(2006) BMC Bioinformatics 7
PubMed: 17059594 | PubMedCentral: PMC1636073 | DOI: 10.1186/1471-2105-7-466
Threader identified the two structures of Amphiphysin ([PDB: 1URU ]) and Arfaptin2 ([PDB: 1I49 ]), which are both members of the BAR domain family with nearly 90% confidence.
Publication Year: 2006
Structure of the APPL1 BAR-PH domain and characterization of its interaction with Rab5.
(2007) EMBO J 26
PubMed: 17581628 | PubMedCentral: PMC1933402 | DOI: 10.1038/sj.emboj.7601771
For instance, using 150 Cα atoms of the common helical regions, the r.m.s.d. values between the dimer of APPL1 BAR and 1I4T, 1URU, and 1ZWW were 3.7, 3.8, and 4.4 Å, respectively, whil... those among 1I4T, 1URU, and 1ZWW range between 2.4 and 2.6 Å.
Although the overall folding of APPL1 BAR domain is similar to previously reported BAR domain 3D structures (i.e., arfaptin2, PDB file 1I4T; amphiphysin, 1URU; and endophilin, 1ZWW), those structures are in general more similar to each other than to the APPL1 BAR domain.
Publication Year: 2007
Missing-in-metastasis and IRSp53 deform PI(4,5)P2-rich membranes by an inverse BAR domain-like mechanism.
(2007) J Cell Biol 176
PubMed: 17371834 | PubMedCentral: PMC2064081 | DOI: 10.1083/jcb.200609176
(A) Structures of amphiphysin BAR domain (left; Protein Data Bank ID: 1URU) and MIM/IMD (right; Protein Data Bank ID: 2D1L).
An introduction to molecular replacement.
(2008) Acta Crystallogr D Biol Crystallogr 64
PubMed: 18094461 | PubMedCentral: PMC2394790 | DOI: 10.1107/S0907444907051554
( c ) An elongated monomer, 217 residues, ∼25 × 25 × 110 Å, space group P 3 1 21, PDB code 1uru .
Publication Year: 2008
Stacked sets of parallel, in-register beta-strands of beta2-microglobulin in amyloid fibrils revealed by site-directed spin labeling and chemical labeling.
(2010) J Biol Chem 285
PubMed: 20335170 | PubMedCentral: PMC2878032 | DOI: 10.1074/jbc.M110.117234
A , the crystal structure of the amphiphysin dimer indicates the positions at which spin labels were introduced (Protein Data Bank code 1URU ( 31 )).
Publication Year: 2010
Defining the functional domain of programmed cell death 10 through its interactions with phosphatidylinositol-3,4,5-trisphosphate.
(2010) PLoS One 5
PubMed: 20668527 | PubMedCentral: PMC2909203 | DOI: 10.1371/journal.pone.0011740
This distribution of lysine residues is seen in protein structures that interact with inositolphosphate ligands, including Drosophila melanogaster amphiphysin (PDB code 1URU) , endophilin-A1 BAR domai... (PDB code 1ZWW), CIP4 (Cdc42-interacting protein-4), F-BAR domain (PDB code 2EFK), and IMD domain from IRSp53/missing-in-metastasis (PDB code 1Y2O)  –  .
Dissecting BAR domain function in the yeast Amphiphysins Rvs161 and Rvs167 during endocytosis.
(2010) Mol Biol Cell 21
PubMed: 20610658 | PubMedCentral: PMC2929998 | DOI: 10.1091/mbc.E10-03-0181
The Drosophila amphiphysin BAR domain homodimer structure (RCSB: 1uru) was used as a template to generate a homology model of Rvs161-Rvs167 BAR domain heterodimer.
To gain insight into the potential structural effects of these mutations, we manually generated a homology model of the Rvs161-Rvs167 BAR domain heterodimer guided by the DmAmph BAR domain crystal structure (PDB: 1URU) and sequence alignment ( Figure 3 ).
A high precision survey of the molecular dynamics of mammalian clathrin-mediated endocytosis.
(2011) PLoS Biol 9
PubMed: 21445324 | PubMedCentral: PMC3062526 | DOI: 10.1371/journal.pbio.1000604
Endophilin: http://www.rcsb.org/pdb/explore/explore.do?structureId=2C08 Amphiphysin: http://www.rcsb.org/pdb/explore/explore.do?structureId=1URU APPL: http://www.rcsb.org/pdb/explore/explore.do?struct... reId=2Q12 SNX9: http://www.rcsb.org/pdb/explore/explore.do?structureId=3DYT Syndapin: http://www.rcsb.org/pdb/explore/explore.do?structureId=3HAI FCHo2: http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0O Supporting Information Figure S1 The canonical model of CME.
Publication Year: 2011
The eisosome core is composed of BAR domain proteins.
(2011) Mol Biol Cell 22
PubMed: 21593205 | PubMedCentral: PMC3128537 | DOI: 10.1091/mbc.E10-12-1021
Structural modeling Homology model for the monomer of Pil1 was built using five different BAR/N-BAR domains as structural templates (1URU, 2RAJ, 2Q13, 2FIC, and 1I49).
We used the program Modeller ( Marti-Renom et al. , 2000 ), using five BAR domain crystal structures as templates: Drosophila melanogaster amphiphysin (1uru) and the human proteins sorting nexin 9 (2raj), APPL1 (adaptor protein containing pleckstrin homology [PH] domain, PTB domain, and leucine zipper motif 1) (2q13), Bin1 (2fic), and Arfaptin 2 (1i49).
Dimer assembly was manually built using Coot based on the crystal structure of the amphiphysin BAR domain from D. melanogaster as reference (1URU) ( Peter et al. , 2004 ).
The modeled monomer was sequentially superimposed onto chains A and B of the Drosophila amphiphysin dimer (1URU).
Membrane fission is promoted by insertion of amphipathic helices and is restricted by crescent BAR domains.
(2012) Cell 149
PubMed: 22464325 | PubMedCentral: PMC3465558 | DOI: 10.1016/j.cell.2012.01.047
Figure S1 Predicted Membrane-Shaping Effects of Hydrophobic Insertions and Crescent-like Scaffolds, Related to Figure 1 (A) Structures of Epsin ENTH domain (PDB: 1h0a), Amphiphysin BAR... domain (PDB: 1uru), and endophilin BAR domain (PDB: 2c08) ( Ford et al., 2002; Gallop et al., 2006; Peter et al., 2004 ).
Publication Year: 2012
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