PDBsum entry: 1n86

Blood clotting

PDB id: 1n86

Contents

Protein chains

74 a.a. *

307 a.a. *

295 a.a. *

Ligands

GLY-PRO-ARG ×2

GLY-HIS-ARG-PRO ×2

NDG ×4

MAN

Metals

_CA ×4

* Residue conservation analysis

PDB id:

1n86

Name:

Blood clotting

Title:

Crystal structure of human d-dimer from cross-linked fibrin complexed with gpr and ghrpldk peptide ligands.

Structure:

Fibrin alpha/alpha-e chain. Chain: a, d. Fragment: double-d alpha chain. Fibrin beta chain. Chain: b, e. Fragment: double-d beta chain. Fibrin gamma chain. Chain: c, f. Fragment: double-d gamma chain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Other_details: fibrinogen from blood bank plasma. Synthetic: yes. Other_details: synthetic peptide matching portion of human fibrin alpha chain. Fibrin beta chain

Biol. unit:

Pentamer (from PQS)

Resolution:

3.20Å R-factor: 0.226 R-free: 0.289

Authors:

Z.Yang,L.Pandi,R.F.Doolittle

Key ref:

Z.Yang et al. (2002). 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. PubMed id: 12501189 DOI: 10.1021/bi026666i

Date:

19-Nov-02 Release date: 07-Jan-03

Protein chains

P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain

Seq: 866 a.a.

Struc: 74 a.a.

Protein chains

P02675  (FIBB_HUMAN) -  Fibrinogen beta chain

Seq: 491 a.a.

Struc: 307 a.a.

Protein chains

P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain

Seq: 453 a.a.

Struc: 295 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular space (2 terms)
• Biological process: signal transduction (3 terms)
• Biochemical function: receptor binding (2 terms)

DOI no: 10.1021/bi026666i

Biochemistry 41:15610-15617 (2002)

PubMed id: 12501189

The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface.

Z.Yang, L.Pandi, R.F.Doolittle.

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.