PDBsum entry 1ml0

Immune system

PDB id: 1ml0

Contents

Protein chains

371 a.a.

64 a.a. *

Waters ×43

* Residue conservation analysis

PDB id:

1ml0

Name:

Immune system

Title:

Viral chemokine binding protein m3 from murine gammaherpesvirus68 in complex with the p8a variant of cc-chemokine mcp-1

Structure:

M3 protein. Chain: a. Engineered: yes. Small inducible cytokine. Chain: d. Synonym: ccl2, monocyte chemotactic protein 1, mcp-1, monocyte chemotactic protein 1, mcp-1, monocyte chemoattractant protein-1, monocyte chemotactic and activating factor, mcaf, monocyte secretory protein je, hc11.

Source:

Murid herpesvirus 4. Murine herpesvirus 68. Organism_taxid: 33708. Gene: m3. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Homo sapiens. Human.

Biol. unit:

Dodecamer (from PDB file)

Resolution:

2.80Å R-factor: 0.201 R-free: 0.282

Authors:

J.M.Alexander,D.H.Fremont

Key ref:

J.M.Alexander et al. (2002). Structural basis of chemokine sequestration by a herpesvirus decoy receptor. Cell, 111, 343-356. PubMed id: 12419245 DOI: 10.1016/S0092-8674(02)01007-3

Date:

29-Aug-02 Release date: 13-Nov-02

Protein chain

O41925  (O41925_MHV68) -  M3 from Murid herpesvirus 4

Seq: 406 a.a.

Struc: 371 a.a.

Protein chain

P13500  (CCL2_HUMAN) -  C-C motif chemokine 2 from Homo sapiens

Seq: 99 a.a.

Struc: 64 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1016/S0092-8674(02)01007-3

Cell 111:343-356 (2002)

PubMed id: 12419245

Structural basis of chemokine sequestration by a herpesvirus decoy receptor.

J.M.Alexander, C.A.Nelson, V.van Berkel, E.K.Lau, J.M.Studts, T.J.Brett, S.H.Speck, T.M.Handel, H.W.Virgin, D.H.Fremont.

ABSTRACT

The M3 protein encoded by murine gamma herpesvirus68 (gamma HV68) functions as an immune system saboteur by the engagement of chemoattractant cytokines, thereby altering host antiviral inflammatory responses. Here we report the crystal structures of M3 both alone and in complex with the CC chemokine MCP-1. M3 is a two-domain beta sandwich protein with a unique sequence and topology, forming a tightly packed anti-parallel dimer. The stoichiometry of the MCP-1:M3 complex is 2:2, with two monomeric chemokines embedded at distal ends of the preassociated M3 dimer. Conformational flexibility and electrostatic complementation are both used by M3 to achieve high-affinity and broad-spectrum chemokine engagement. M3 also employs structural mimicry to promiscuously sequester chemokines, engaging conservative structural elements associated with both chemokine homodimerization and binding to G protein-coupled receptors.

Selected figure(s)

Figure 5.
Figure 5. Promiscuous Chemokine Binding Facilitated by M3 Conformational Plasticity and Electrostatic Complementation(A) Comparison of the chemokine binding clefts of M3 alone and the M3/MCP-1 complex. The top image depicts the open and closed niches found in the preassociated asymmetric homodimer, viewed looking edgewise into the binding sites. Chemokine contact residues highlighted in blue (CTD) and cyan (NTD) and the corresponding loops that create the binding cleft are labeled. The middle image is a cartoon depicting the asymmetric conformation of M3 alone and the symmetric dimer formed in complex with chemokine. Below is the edgewise view of the M3 chemokine binding cleft with MCP-1 bound, depicted in magenta.(B) Electrostatic complementarity between M3 and chemokines. On the right is the surface electrostatic potentials of the asymmetric M3 dimer (upper image) and the symmetric M3/MCP-1(P8A) complex (lower image). The view is rotated 90° relative to the edgewise orientation seen in (A). Negative and positive electrostatic potentials are mapped to the surfaces in red and blue for ± 15 KeV using GRASP. In the lower image, M3 and the chemokines are pulled apart to show their matched surfaces and charge potentials.

Figure 6.
Figure 6. Structural Mimicry of Chemokine Dimer Formation and GPCR Receptor Binding(A) Tube and surface representations of the M3 sequestration of MCP-1(P8A). M3 NTD and CTD loops are depicted in cyan, and the chemokine in magenta. Cys residues are in yellow. Directly below is the same view depicting the MCP-1 (P8A) surface engaged by M3, with the intensity of the magenta surface increased for shorter contact distances between 2.5 and 4 Å. The acidic NTD s2b-s3 loop, which engages the N-loop region, and the CTD A-B loop, which forms an anti-parallel β interaction with the N-terminal segment of MCP-1, are shown as cyan tubes with their side chains displayed.(B) CC-chemokine homodimerization as observed for MCP-1 (1DOK). Displayed is the homodimer of MCP-1 with the magenta monomer oriented as MCP-1(P8A) in (A). The dimer is formed dominantly by the anti-parallel β interaction between N-terminal regions. Below is the contact surface, highlighting the role of MCP-1 Pro8, which is situated above the chemokine invariant Cys12-Cys52 disulfide bond in precisely the same location as M3 ProP272 in the M3/MCP-1(P8A) complex.(C) Displayed is the NMR structure of dimeric IL-8 in complex with a modified peptide from the N terminus of the IL-8 receptor CXCR-1 (1ILQ). The CXC dimer is displayed in magenta and blue and is formed through the extended sheet formed between monomer β1-strands. The CXCR-1 receptor fragment also binds to the N-terminal chemokine region in an anti-parallel fashion, with Pro29 similarly packed on top of the Cys12-Cys52 disulfide bond. Further, this receptor fragment also engages the N-loop region with a highly acidic cluster of residues, very similar in location to where the M3 NTD s2b-s3 loop engages MCP-1(P8A).

The above figures are reprinted by permission from Cell Press: Cell (2002, 111, 343-356) copyright 2002.

Figures were selected by an automated process.