PDBsum entry 1xf5

Immune system

PDB id: 1xf5

Contents

Protein chains

16 a.a.

220 a.a. *

218 a.a. *

71 a.a. *

67 a.a. *

Ligands

GLN-ILE-VAL-GLY-GLY-VAL-TYR-LEU

Waters ×446

* Residue conservation analysis

PDB id:

1xf5

Name:

Immune system

Title:

Complex hcv core-fab 19d9d6-protein l mutant (h74c, y64w)in space group p21212

Structure:

Capsid protein c. Chain: p, q. Fragment: residues 2-45. Synonym: core protein. Engineered: yes. Monoclonal antibody 19d9d6 light chain. Chain: a, c. Monoclonal antibody 19d9d6 heavy chain. Chain: b, d.

Source:

Synthetic: yes. Other_details: this sequence occurs naturally in hcv. Mus musculus. House mouse. Organism_taxid: 10090. Finegoldia magna. Organism_taxid: 334413. Strain: atcc 29328. Expressed in: escherichia coli.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.60Å R-factor: 0.201 R-free: 0.240

Authors:

R.Menez,N.G.Housden,S.Harrison,C.Jolivet-Reynaud,M.G.Gore,E.A.Stura

Key ref:

R.Ménez et al. (2005). Different crystal packing in Fab-protein L semi-disordered peptide complex. Acta Crystallogr D Biol Crystallogr, 61, 744-749. PubMed id: 15930632 DOI: 10.1107/S0907444905006724

Date:

14-Sep-04 Release date: 31-May-05

Protein chain

P26661  (POLG_HCVJ8) -  Genome polyprotein from Hepatitis C virus genotype 2b (isolate HC-J8)

Seq: 3033 a.a.

Struc: 16 a.a.

Protein chains

No UniProt id for this chain

Struc: 220 a.a.

Protein chains

No UniProt id for this chain

Struc: 218 a.a.

Protein chain

No UniProt id for this chain

Struc: 71 a.a.

Protein chain

No UniProt id for this chain

Struc: 67 a.a.

Enzyme reactions

• Enzyme class 2: Chain P: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chain P: E.C.3.4.21.98 - hepacivirin.
• Reaction: Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
• Enzyme class 4: Chain P: E.C.3.4.22.- - ?????
• Enzyme class 5: Chain P: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 6: Chain P: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444905006724

Acta Crystallogr D Biol Crystallogr 61:744-749 (2005)

PubMed id: 15930632

Different crystal packing in Fab-protein L semi-disordered peptide complex.

R.Ménez, N.G.Housden, S.Harrison, C.Jolivet-Reynaud, M.G.Gore, E.A.Stura.

ABSTRACT

Proteins and peptides with variable degrees of disorder are a challenge for protein crystallization. These may be completely disordered or just contain regions with a high degree of mobility that may be represented by a multitude of discretely defined conformations. These difficulties are not insurmountable, but it may be unreasonable to expect a clean result from a structural point of view. The complex between a murine monoclonal antibody (19D9D6) and a synthetic peptide that encompasses the first 45 residues of the core protein of Hepatitis C virus that is poorly structured in solution has been crystallized. In order to make the crystallization possible, use was made of a single immunoglobulin-binding domain of protein L from Peptostreptococcus magnus (PpL), a bacterial protein that can bind the variable region (Fv) of a large population of antibodies through its light chain with no interference with antibody-antigen recognition. Crystals were obtained in different space groups where the size of the cavity that accommodates the peptide is different, although many of the crystal contacts and the overall lattice are preserved. The peptide can be considered to be semi-disordered and the larger cavity accommodates a better ordered peptide than the smaller one. The lattice is of interest for the design of a scaffold system for the crystallization of peptide-tagged proteins since a cavity that accommodates a disordered entity might be able to host ordered proteins of the same size and shape as the cavity. Here, the differences between the lattices formed by this trimolecular complex are described and it is discussed how such a system may be adapted to the crystallization of peptide-tagged proteins.

Selected figure(s)

Figure 2.
Figure 2 Omit map of peptide 2-45 in the complex with Fab' 19D9D6 (blue) and PpL (not shown). The two peptides (red) do not adopt the same conformation and are not as well ordered within and outside the recognition site. Peptide P (a) is fully occupied and ordered while peptide Q (b) is not, possibly because of poor peptide availability.

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 744-749) copyright 2005.

Figure was selected by an automated process.