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PDB ID Mentions in PubMed Central Article count: 3

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PDB ID Mentions in PubMed Central

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Structure of the N-terminal region of complement factor H and conformational implications of disease-linked sequence variations.

(2008) J Biol Chem 283

PubMed: 18252712 | PubMedCentral: PMC2276370 | DOI: 10.1074/jbc.M709587200

The atomic coordinates and structure factors (codes 2RLP and 2RLQ) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick... NJ ( http://www.rcsb.org/ ).

b PDB accession codes 2RLP and 2RLQ respectively.

Factor H modules RCA-CCP (PDB code (81)) FH1 FH2 FH3 FH 1 (2RLP) FH 2 (2RLQ) 3.12 (59); 27 FH 3 (2RLQ) 3.00 (54); 22 1.80 (55); 20 FB 1 (2OK5) 4.13 (64); 20 2.34 (55); 19 2.04 (51); 32 FB 2 (2OK5) 3.35 (60); 20 2.20 (57); 24 1.80 (58); 25 FB 3 (2OK5) 3.38 (58); 23 1.91 (57); 23 1.30 (56); 26 C4BPα 1 (2A55) 2.23 (60); 27 3.48 (69); 24 3.24 (61); 19 C4BPα 2 (2A55) 3.22 (58); 22 1.81 (57); 31 1.70 (57); 24 CR1 15 (1GKN) 1.98 (58); 26 3.03 (59); 20 2.76 (55); 18 CR1 16 (1GKN) 3.38 (58); 24 1.57 (58); 28 1.67 (57); 24 CR1 17 (1GKG) 2.74 (58); 26 2.31 (58); 36 2.12 (57); 32 DAF 1 (1OK3) 2.48 (60); 22 2.54 (59); 15 2.59 (59); 17 DAF 2 (1OK3) 2.22 (61); 31 2.92 (60); 21 2.80 (59); 20 DAF 3 (1H03) 3.31 (58); 22 1.59 (58); 29 1.54 (57); 34 DAF 4 (1H03) 2.68 (58); 28 1.91 (57); 25 1.63 (58); 31 MCP 1 (2CKL) 2.56 (60); 23 2.73 (58); 20 2.73 (58); 22 MCP 2 (2CKL) 3.32 (53); 27 1.77 (59); 36 1.63 (56); 34 VCP 1 (1G40) 3.41 (61); 27 3.09 (59); 24 2.82 (60); 21 VCP 2 (1G40) 3.33 (58); 22 2.44 (57); 39 2.04 (56); 28 VCP 3 (1G40) 2.79 (58); 30 2.57 (58); 30 2.47 (56); 35 VCP 4 (1G40) 3.06 (58); 25 2.21 (55); 21 2.29 (58); 38 The elongated nature of FH1-3 reflects small intermodular tilt angles (see Fig. 4, G and H ).

Publication Year: 2008


The central portion of factor H (modules 10-15) is compact and contains a structurally deviant CCP module.

(2010) J Mol Biol 395

PubMed: 19835885 | PubMedCentral: PMC2806952 | DOI: 10.1016/j.jmb.2009.10.010

Discussion The structural biology of the N-terminal and C-terminal regions of fH that encompas the known binding sites for its principal protein and carbohydrate ligands, has been studied extensively;... the medium-resolution or high-resolution structures of all eight N-terminal CCPs have been experimentally determined {in fragments: fH1–2 [Protein Data Bank (PDB) ID 2RLP ], fH2–3 (PDB ID 2RLQ ), fH1–4 (PDB ID 2WII ), and fH5 and fH6–8 (PDB ID 2UWN )} by NMR or crystallography, as have structures of four of the C-terminal six modules [fH15–16 (PDB ID 1HFH ) and fH19–20 (PDB IDs 2BZM and 2G7I )].

Publication Year: 2010


Contribution of the CR domain to P-selectin lectin domain allostery by regulating the orientation of the EGF domain.

(2015) PLoS One 10

PubMed: 25675100 | PubMedCentral: PMC4326174 | DOI: 10.1371/journal.pone.0118083

( C ) Conformational comparison between modeled P-selectin CR1 domain upon 2RLQ template ( cyan ) and crystallized E-selectin CR1 domain ( purple ), three disulfide bonds were highlighted in CPK and l... corice , respectively.

The orientation of the CR domain to the EGF domain was determined through sequence alignment between P-selectin and the 2RLQ template and followed structural superposition.

However, only the modeled structures based on the 2RLQ and 1OK3 templates showed low ratios of unreasonable structures ( S1 Table , gray boxes ) according to stereochemistry rationality, and the disulfide bond distributions in templates 2G7I and 2RLQ ( B ) were similar with that found in the P-selectin CR domain ( A ) ( S2 Table ).

Firstly, the sequence alignment of both EGF domain and CR1 domain with that of 2RLQ was performed, then the structures of P-LE and modeled CR1 domain were superposed to x-ray crystal 2RLQ, respectively, based on the backbone alignment of corresponding residues in aligned sequence, and finally the C-term of EGF domain and N-term of CR1 domain were covalently linked.

Furthermore, the 2RLQ template exhibited the highest sequence homology with the CR domain ( S1 Table , second column ) as well as with the C terminus of the EGF domain, which helped us to build a simulation system with reasonable settings regarding the CR domain orientation with respect to the EGF domain by combining sequence alignment and structure superposition between the P-selectin target and the template.

Integrated with the above three considerations, the structures of the P-selectin CR domains modeled based on the 2RLQ template were adopted in this study.

The modeled structures based on the 2RLQ template were chosen in this study by considering stereochemistry structure optimization ( S1 Table ) as well as the similarity of the disulfide bond distribution between P-selectin CR domains and the template ( S2 Table ).

( A ) Conformational consistency among the homology-modeled structures of the first CR domain of human P-selectin upon different templates, which was quantified using the backbone C α distances of every residue between the reference based on the template of 2RLQ and each of other five structures.

( B ) A typical conformation of the P-selectin first CR domain modeled based on the template of 2RLQ.

The first two CR domains of P-selectin were modeled using the homology model module in Molecular Operating Environment (MOE) based on six templates (PDB codes: 2G7I, 1RID, 1OK3, 1GKN, 2RLQ, 1PPQ), and the selection of templates was based on a combination of MOE (E-value ≤ 10 –12 ) and Blast (Blast-score ≥ 25) sequence homology searches [ 22 ].

Based on sequence homology searches by both MOE and Blast, six templates (PDB codes: 2G7I, 1RID, 1OK3, 1GKN, 2RLQ, 1PPQ) were chosen for the homology modeling of P-selectin CR domains.

Publication Year: 2015