Primary Citation PubMed: 15502812
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Recognition of interaction interface residues in low-resolution structures of protein assemblies solely from the positions of C(alpha) atoms.
(2009) PLoS One 4
PubMed: 19214247 | PubMedCentral: PMC2641018 | DOI: 10.1371/journal.pone.0004476
PDB ID Description 1ffk Ribosomal unit 2akh SECYEG ribosomal unit 2esg Complex of IgA and serum albumin 2bcw Ribosomal protein 1xi4 Clathrin coat Discussion An approach has been developed to identify ... he buried and exposed residues in proteins solely based on the positions of Cα atoms.
Publication Year: 2009
Single-molecule analysis of a molecular disassemblase reveals the mechanism of Hsc70-driven clathrin uncoating.
(2011) Nat Struct Mol Biol 18
PubMed: 21278753 | PubMedCentral: PMC3056279 | DOI: 10.1038/nsmb.1985
Conservation of light chain polymorphism in three mammalian species J Biol Chem 1988 263 16688 16695 3267234 25 Boll W Sequence requirements for the recognition of tyrosine-based endocytic signals by ... lathrin AP-2 complexes EMBO J 1996 15 5789 5795 8918456 26 Gallusser A Kirchhausen T The beta 1 and beta 2 subunits of the AP complexes are the clathrin coat assembly components EMBO J 1993 12 5237 5244 8262066 27 Aitken CE Marshall RA Puglisi JD An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments Biophys J 2008 94 1826 1835 17921203 28 Kerssemakers JWJ Assembly dynamics of microtubules at molecular resolution Nature 2006 442 709 712 16799566 Figure 1 A clathrin coat with views of a vertex before and after formation of an uncoating intermediate ( a ) Schematic representation of clathrin triskelions in a D6-barrel lattice (PDB 1XI4).
Publication Year: 2011
Modeling symmetric macromolecular structures in Rosetta3.
(2011) PLoS One 6
PubMed: 21731614 | PubMedCentral: PMC3120754 | DOI: 10.1371/journal.pone.0020450
As an example, a clathrin cage (pdb id 1xi4) exhibits D 6 symmetry; D symmetry provides additional interface variety that leads to more stability as well as improved allosteric control.
Protein-protein interactions in clathrin vesicular assembly: radial distribution of evolutionary constraints in interfaces.
(2012) PLoS One 7
PubMed: 22384024 | PubMedCentral: PMC3285160 | DOI: 10.1371/journal.pone.0031445
PDB ID Description Resolution Organism Clathrins 1xi4 Clathrin D6 coat 8 Å bovine 1xi5 Clathrin coat with auxillin J domain 8 Å bovine 1b89 Clathrin heavy chain proximal leg 2.6 ... 5; Bovine 1c9i Beta propeller with peptides 2.9 Å rat 1bpo Heavy chain terminal domain 2.6 Å rat 1utc Terminal domain with amphiphysin peptide 2.3 Å Bovine 1c9l Beta-propeller with peptide 2.9 Rat Adaptor proteins 1ky6 AP2 α-appendage with Epsin peptide 2 Å Mouse 1ky7 AP2 α-appendage with amph peptide 2.1 Å Mouse 1kyu AP2 α-appendage with EPS15 DPF pep 1.8 Å Mouse 1kyd AP2 α-appendage with Epsin peptide 2 Å Mouse 1kyf AP2 α-appendage with EPS15 DPF pep 1.2 Å Mouse 1qts AP-2 adaptor α-appendage 1.4 Å Mouse 1qtp AP-2 adaptor α-appendage 1.6 Mouse 1gyu AP-1 adaptor γ-appendage 1.81 Mouse 1gyv AP-1 adaptor γ-appendage mutant 1.71 Mouse 2vj0 AP2 α-appendage in complex with FXDNF from amph & WVXF from synaptojanin 1.6 Mouse & synthetic 1gyw AP1 γ-appendage A753D mutant 2.4 Mouse 2iv8 β1 of AP2 with β-arrestin peptide 2.8 Human 1w63 AP1 adaptor core 4 Mouse & rat 1w80 α-adaptin of Ap2 with 2 peptides from synaptojanin 170 1.9 Mouse & synthetic 2g30 β-appendage of AP2 with ARH peptide 1.6 Human & synthetic 2ivg β-appendage of AP2 with EPS15 peptide 1.9 Human 2vgl AP-2 adaptor core 2.6 Rat, human & mouse 1e42 β2 of AP2 1.7 Human 1b9k α of AP2 1.9 Mouse Listed are the cryo-EM fitted models or the structures of the components of CCV determined using X-ray crystallography.
Chain Chain in Complex for 1xi4 Chain in Complex for 1xi5 A AEFJB ACFN B BCDK BCD C CDLB CDA D DCEMF DECB E EADHNF EDH F FADEGO FAGHR G GFPIH GHIF H HEGQ HEFM I IGHR IGH J JA - K KB - L LC - M MD MHEF N NE NACF O OF - P PG - Q QH - R RI RFAGH Clathrin coat structures (with and without auxillin; 1xi5 and 1xi4 respectively) were dissected into smaller subcomplexes by identifying near neighbors of the chains that are designated in the structures by letters A to I for clathrin heavy chains and J to R for clathrin light chains.
The complex structures (PDb IDs 1xi4 & 1xi5) were then divided into smaller sub-complexes that were treated as independent structures to recognize interface residues.
g002 Figure 2 Structure of Clathrin coat (PDB ID : 1xi4).
t003 Table 3 Interface residues of clathrin heavy chains as predicted from low resolution structure of clathrin coat (PDB Id 1xi4).
Figure 5a shows the comparison of conservation scores for predicted interface residues and non-interface surface exposed residues of clathrin heavy chains of the clathrin coat structure (PDB ID 1xi4) while that in case of adaptins is shown in the Figure 5b (for AP1 chains) and 5c (for Ap2 chains).
Publication Year: 2012
The role of structural bioinformatics resources in the era of integrative structural biology.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 23633580 | PubMedCentral: PMC3640467 | DOI: 10.1107/S0907444913001157
of structures 86785 76355 † 9727 † 520 Highest resolution X-ray structure 0.48 ( 3nir ) Length of longest observed polymer chains Protein 3040 (... 3vkh ) 828 ( 2vda ) 1630 ( 3iyv and 1xi4 ) RNA 3206 ( 3o5h and 3o58 ) 111 ( 2lkr ) 3352 ( 3izf ) DNA 347 ( 1zbb ) 42 ( 2f1q ) 4896 ( 2ymf ) PDB entry with the highest number of Polymer residues 89160 (split over 4fy1 , 4fy2 , 4fy3 , 4fy4 , 4fy5 , 4fy6 , 4fy7 , 4fy8 , 4fy9 , 4fya ) Macromolecular atoms 717805 (split over 1voq , 1vor , 1vos , 1vou , 1vov , 1vow , 1vox , 1voy , 1voz , 1vp0 ) Macromolecular chains 480 (split over 4fy1 , 4fy2 , 4fy3 , 4fy4 , 4fy5 , 4fy6 , 4fy7 , 4fy8 , 4fy9 , 4fya ) No.
Publication Year: 2013
Hsc70-induced changes in clathrin-auxilin cage structure suggest a role for clathrin light chains in cage disassembly.
(2013) Traffic 14
PubMed: 23710728 | PubMedCentral: PMC3776051 | DOI: 10.1111/tra.12085
Two barrel models, calculated from the available pdb coordinates 1XI4 and 1XI5 11 – 19 , were tested.
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