1N86

Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and GHRPLDK peptide ligands.

Summary for 1N86

• Entry DOI: 10.2210/pdb1n86/pdb
• Related: 1FZC 1N73 1N8E
• Descriptor: Fibrin alpha/alpha-E chain, Fibrin beta chain, Fibrin gamma chain, ... (8 entities in total)
• Functional Keywords: cross-linked fibrin, protein-peptide complex, blood clotting
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 172795.37

Authors

Yang, Z.,Pandi, L.,Doolittle, R.F. (deposition date: 2002-11-19, release date: 2003-01-07, Last modification date: 2024-11-06)

Primary citation

Yang, Z.,Pandi, L.,Doolittle, R.F.
The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface.
Biochemistry, 41:15610-15617, 2002

PubMed Abstract: The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that of lamprey, corresponds to the B-knob exposed by thrombin. The structure was determined by molecular replacement, a recently determined structure of lamprey fragment D being used as a search model. GHRPam was found in both the gamma- and beta-chain holes. Unlike the situation with fragment D, the crystal packing of the cross-linked double-D structure exhibits two different D-D interfaces, each gamma-chain facing gamma-chains on two other molecules. One of these (interface I) involves the asymmetric interface observed in all other D fragments and related structures. The other (interface II) encompasses a completely different set of residues. The two abutments differ in that interface I results in an "in line" arrangement of abutting molecules and the interface II in a "zigzag" arrangement. So far as can be determined (the electron density could only be traced on one side of the cross-links), it is the gamma-chains of the newly observed zigzag units (interface II) that are joined by the reciprocal epsilon-amino-gamma-glutamyl cross-links. Auspiciously, the same novel D-D interface was observed in two lower-resolution crystal structures of human double-D preparations that had been crystallized under unusual circumstances. These observations show that double-D structures are linked in a way that is sufficiently flexible to accommodate different D-D interfaces under different circumstances.

PubMed: 12501189
DOI: 10.1021/bi026666i

Experimental method

X-RAY DIFFRACTION (3.2 Å)