PDBsum entry 2v7n

Immune system

PDB id: 2v7n

Contents

Protein chains

213 a.a. *

214 a.a. *

Waters ×540

* Residue conservation analysis

PDB id:

2v7n

Name:

Immune system

Title:

Unusual twinning in crystals of the cits binding antibody fab fragment f3p4

Structure:

Immunoglobulin light chain. Chain: a, c, e, g. Fragment: fab fragment, residues 1-255. Synonym: vk3. Engineered: yes. Other_details: synthetic gene, derived from phage display of the human combinatorial antibody library (hucal). Immunoglobulin heavy chain. Chain: b, d, f, h.

Source:

Synthetic construct. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.92Å R-factor: 0.155 R-free: 0.202

Authors:

D.Frey,T.Huber,A.Plueckthun,M.G.Gruetter

Key ref:

D.Frey et al. (2008). Structure of the recombinant antibody Fab fragment f3p4. Acta Crystallogr D Biol Crystallogr, 64, 636-643. PubMed id: 18560151 DOI: 10.1107/S0907444908007282

Date:

31-Jul-07 Release date: 17-Jun-08

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Protein chains

No UniProt id for this chain

Struc: 214 a.a.

DOI no: 10.1107/S0907444908007282

Acta Crystallogr D Biol Crystallogr 64:636-643 (2008)

PubMed id: 18560151

Structure of the recombinant antibody Fab fragment f3p4.

D.Frey, T.Huber, A.Plückthun, M.G.Grütter.

ABSTRACT

The structure of the antibody Fab fragment f3p4, which was selected from a subset of the synthetic HuCAL antibody library to bind the sodium citrate symporter CitS, is described at 1.92 A resolution. Comparison with computational models revealed deviations in a few framework positions and in the binding loops. The crystals belong to space group P2(1)2(1)2 and contain four molecules in the asymmetric unit, with unit-cell parameters a=102.77, b=185.92, c=102.97 A. These particular unit-cell parameters allowed pseudo-merohedral twinning; interestingly, the twinning law relates a twofold screw axis to a twofold axis.

Selected figure(s)

Figure 5.
Figure 5 Structure of CDR-L3. A superposition of the main-chain atoms (for clarity, carbonyl O atoms are omitted from the figure) of CDR-L3 of the Fab fragment f3p4 (grey) with typical members of the V[ ]and V[ ]families is shown. In V[ ]members CDR-L3 adopts a hairpin-like structure (magenta; PDB code 8fab ). In V[ ]members, which predominantly have a proline at position L136 (Kabat L95), the CDR-L3 has an -loop conformation (yellow; PDB code 1ay1 ). The conformation of the CDR-L3 of Fab fragment f3p4 is an intermediate conformation, but is also present in naturally occurring antibodies with a proline residue at L136 (Kabat L95; green; PDB code 1c1e ). The compared molecules have an equal number of residues in CDR-L3 and all C^ atoms of L106-L140 (Kabat L88-99) were used for the superposition.

Figure 7.
Figure 7 Surface representation of the binding region. C^ traces of CDR-H1, CDR-H2, CDR-H3, CDR-L1, CDR-L2 and CDR-L3 are shown and coloured red, green, blue, cyan, magenta and yellow, respectively. Residues Arg H108 (Kabat H94) and Asp H137 (Kabat H101) forming the conserved hydrogen bonds as well as the solvent-exposed residue Tyr L40 (Kabat L32) are shown in stick representation.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 636-643) copyright 2008.

Figures were selected by an automated process.