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PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces.

(2010) Nucleic Acids Res 38

PubMed: 20008102 | PubMedCentral: PMC2847225 | DOI: 10.1093/nar/gkp1158

The protein complexes 1dfj (K7; chain E), 1dzi (N154, Y157, Q215, D219, L220, T221, E256, H258; chain A), and 2nmb (Y2, I3; chain B) were excluded because the corresponding experimental data associate... to the residues shown between parentheses could not be found in the BID database ( 40 ).

Publication Year: 2010

A role for specific collagen motifs during wound healing and inflammatory response of fibroblasts in the teleost fish gilthead seabream.

(2011) Mol Immunol 48

PubMed: 21232799 | PubMedCentral: PMC3048961 | DOI: 10.1016/j.molimm.2010.12.004

Models of the GFOGER, GLOGEN and CRP motifs were obtained by modifying side-chains in the collagen part of the ITGA2 I-domain in complex with the GFOGER motif (PDB code 1DZI) ( Emsley et al., 2000 ), ... sing ad hoc scripts developed for CNS ( Brunger et al., 1998 ).

Publication Year: 2011

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

(2009) J Appl Crystallogr 42

PubMed: 22477769 | PubMedCentral: PMC3246819 | DOI: 10.1107/S0021889809008784

Table 1 Data set selection and re-refinement PDB entries (January 2007) 41277 X-ray structure models 35003 X-ray + 2.70 resolution 29541 X-ray + experimental data (SF) 20889 X-ray + SF + R -free set 1... 877 X-ray + SF + usable R -free set 16807 Re-refined structure models 15034 Improved structure models 10046 Table 2 Status flag schemes for R -free set selection encountered in deposited reflection files at the wwPDB Scheme Working set R -free set Example PDB entry † 1 o f 1aa6 (1dzi) 2 0 1 101m (1a4i) 3 1 1 1a8d 4 Positive integer 0 1b7d 5 Positive real number 0.00 1c3c 6 1.0 0.0 1a27 † PDB identifiers in parentheses are examples of reversed usage of the scheme.

Publication Year: 2009

Complex structure of engineered modular domains defining molecular interaction between ICAM-1 and integrin LFA-1.

(2012) PLoS One 7

PubMed: 22956999 | PubMedCentral: PMC3431320 | DOI: 10.1371/journal.pone.0044124

(E) In comparison to the previous open structures of the I domains of different α subunits, α M (1IDO; blue) [27] and α 2 (1DZI; green) [28] , the α7-helix in our struc... ure (3TCX; magenta) shows a comparable extent of downward displacement, away from the closed structure seen in the wild-type α L I domain (3F74; yellow) [44] .

Structure Alignments and Analysis Previous structures of the α M (1IDO) [27] , α 2 (1DZI) [28] , and α L (3F74) [44] I domains were superimposed to the α L I domain of our structure (3TCX) based on residues in the α6-helix (α M : 278–288; α 2 : 294–304; α L : 268–278) ( Fig. 1C ).

Publication Year: 2012

Polyproline and triple helix motifs in host-pathogen recognition.

(2012) Curr Protein Pept Sci 13

PubMed: 23305370 | PubMedCentral: PMC3707005 | DOI: null

These complexes are formed with integrin alpha 2 I domain (PDB code 1dzi) [ 81 ], CNA (2f6a) [ 82 ], SPARC (2v53) [ 83 ], DDR2 discoidin domain (2wuh) [ 84 ], MASP-1 CUB2 domain (3pob) [ 85 ], Von Wil... ebrand factor A3 domain (4dmu) [ 86 ], matrix metalloproteinase 1 (4auo) [ 87 ] and the chaperone Hsp47/SERPINH1 (4awr) [ 88 ].

Panels A-G refer to complexes of triple helices with integrin alpha 2 I domain (PDB code 1dzi), CNA (2f6a), SPARC (2v53), DDR2 discoidin domain (2wuh), MASP-1 CUB2 domain (3pob), Von Willebrand factor A3 domain (4dmu), matrix metalloproteinase 1 (4auo), and the chaperone Hsp47/SERPINH1 (4awr) respectively.

Publication Year: 2012

Early chordate origin of the vertebrate integrin ?I domains.

(2014) PLoS One 9

PubMed: 25409021 | PubMedCentral: PMC4237329 | DOI: 10.1371/journal.pone.0112064

In order to evaluate the potential of the lamprey αI domain sequences for binding collagen, structures were modeled for the three lamprey αI domains with GFOGER triple-helical peptide ... ased on the α2I complex structure (1DZI; [15] ) and a wider set of known X-ray structures of αI domains was used to optimize the alignments for structure modeling.

The collagen binding integrins and those that recognize leukocytes also have recognizable differences, having the αC helix containing a key tyrosine residue (Y285 in the α2I domain; 1AOX) and present only in the collagen receptor αI domains [14] – an easy-to-scan sequence feature observable in alignments ( Fig. 2 ; [26] , [27] ), observed in the ligand-free structures of the α1I and α2I domains but unraveled (Y285 moves by over 17 Å forming a hydrogen bond with S316; 1DZI) after the conformational changes accompanying ligand binding.

Structure of the α2I domain without (B) (PDB code: 1AOX; [14] ) and with (C) bound GFOGER tripeptide (PDB code: 1DZI; [15] ).

The first X-ray structures of integrins deposited within the Protein Data Bank (PDB; [10] ) have focused on the αI domain in human integrin α subunits: e.g. αM (PDB code: 1IDO and 1JLM; [11] , [12] ) and αL (1LFA; [13] ) of the immune system type; and α2 without (PDB code: 1A0X; [14] ) and with (1DZI; [15] ) collagen-like triple-helical GFOGER peptide bound.

g005 Figure 5 Views of (A, C) the structure of the α2I domain with bound GFOGER tripeptide (PDB code: 1DZI) and (B, D) a model constructed for lamprey Pma_f3 αI domain; (C) and (D) are rotated approximately 180° from the view in (A) and (B).

A simple C program, Surf2, was written to identify interactions between the α2I domain and the GFOGER tripeptide and structural water molecules (PDB code: 1DZI), and between the α1I domain NMR structure and GLOGEN tripeptide (PDB code: 3M32) and apo-form of the α1I domain (PDB code: 1PT6; [79] ).

Publication Year: 2014