PDBsum entry 2adj

Immune system

PDB id: 2adj

Contents

Protein chains

211 a.a. *

214 a.a. *

Metals

_CA

Waters ×30

* Residue conservation analysis

PDB id:

2adj

Name:

Immune system

Title:

Crystal structure of monoclonal anti-cd4 antibody q425 in complex with calcium

Structure:

Q425 fab light chain. Chain: a. Q425 fab heavy chain. Chain: b

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Other_details: hydridoma. Other_details: hydridoma

Biol. unit:

Dimer (from PQS)

Resolution:

2.90Å R-factor: 0.213 R-free: 0.300

Authors:

T.Zhou,D.H.Hamer,W.A.Hendrickson,Q.J.Sattentau,P.D.Kwong

Key ref:

T.Zhou et al. (2005). Interfacial metal and antibody recognition. Proc Natl Acad Sci U S A, 102, 14575-14580. PubMed id: 16195378 DOI: 10.1073/pnas.0507267102

Date:

20-Jul-05 Release date: 20-Sep-05

Protein chain

Q58EU4  (Q58EU4_MOUSE) -

Protein chain

No UniProt id for this chain

Struc: 214 a.a.

DOI no: 10.1073/pnas.0507267102

Proc Natl Acad Sci U S A 102:14575-14580 (2005)

PubMed id: 16195378

Interfacial metal and antibody recognition.

T.Zhou, D.H.Hamer, W.A.Hendrickson, Q.J.Sattentau, P.D.Kwong.

ABSTRACT

The unique ligation properties of metal ions are widely exploited by proteins, with approximately one-third of all proteins estimated to be metalloproteins. Although antibodies use various mechanisms for recognition, to our knowledge, none has ever been characterized that uses an interfacial metal. We previously described a family of CD4-reactive antibodies, the archetype being Q425. CD4:Q425 engagement does not interfere with CD4:HIV-1 gp120 envelope glycoprotein binding, but it blocks subsequent steps required for viral entry. Here, we use surface-plasmon resonance to show that Q425 requires calcium for recognition of CD4. Specifically, Q425 binding of calcium resulted in a 55,000-fold enhancement in affinity for CD4. X-ray crystallographic analyses of Q425 in the presence of Ca(2+), Ba(2+), or EDTA revealed an exposed metal-binding site, partially coordinated by five atoms contributed from four antibody complementarity-determining regions. The results suggest that Q425 recognition of CD4 involves direct ligation of antigen by the Q425-held calcium, with calcium binding each ligating atom of CD4 with approximately 1.5 kcal/mol of binding energy. This energetic contribution, which is greater than that from a typical protein atom, demonstrates how interfacial metal ligation can play a unique role in antigen recognition.

Selected figure(s)

Figure 4.
Fig. 4. Structure of Fab Q425. (A) Overall structure. The Q425:Ba^2+ complex is shown in ribbon representation, with Ba^2+ ion in red, heavy chain in orange, and light chain in blue. Contoured in green at 6 is the rigid-body difference Fourier (Ba^2+ vs. EDTA; see details in Materials and Methods), marking the position of the Ba^2+ ion. (B) Q425:Ca^2+ structure, showing details of the Ca^2+ binding site. A close-up of the Q425-calcium binding site is shown in an orientation related to A by a 90° rotation around a horizontal axis. The Ca^2+ ion is colored purple, oxygen atoms are colored red, nitrogen atoms are in dark blue, carbon atoms of the heavy chain are in yellow, and carbon atoms of the light chain are in blue. Coordinating ligands are side-chain oxygens from Asn (residue 100a from the CDR H3), Asp (residue 32 from the CDR L1), and Glu (residue 50 from the CDR L2), as well as the backbone carbonyl of residue 92 (in the CDR L3). Ligand distances are shown in Å. (C) Q425:EDTA structure, showing details of the same site shown in B but in the presence of 10 mM EDTA.

Figure 5.
Fig. 5. Calcium dependence of other Q425-like Abs binding to CD4. CD4 was immobilized on a CM5 chip, and the binding of Q425, Q428, and Q4116 IgG was tested. Sensorgrams are shown for Q425, Q428, and Q4116 in the presence of 2.5 mM Ca^2+ and also in the presence of 1 mM EDTA. IgG (144 nM) was passed over the chip starting at 80 s and allowed to associate for 170 s, with the dissociation followed for 5 min.

Figures were selected by an automated process.