2NZ1	Viral Protein Cytokine	date	Nov 22, 2006
title	Viral Chemokine Binding Protein M3 From Murine Gammaherpesvi Complex With The Cc-Chemokine Ccl2mcp-1
authors	J.M.Alexander-Brett, D.H.Fremont
compound		source
Molecule: Hypothetical Protein Gammahv.M3 Chain: A, B, X Synonym: M3 Protein Engineered: Yes		Organism_scientific: Murid Herpesvirus 4 Organism_common: Murine Herpesvirus 68 Organism_taxid: 33708 Gene: Gammahv.M3, M3 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_cell_line: Sf9 Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pfb-1
Molecule: Small Inducible Cytokine A2 Chain: D, E, Y Synonym: Ccl2, Monocyte Chemotactic Protein 1, Mcp-1, Monoc Chemoattractant Protein 1, Monocyte Chemotactic And Activat Factor, Mcaf, Monocyte Secretory Protein Je, Hc11; Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ccl2, Mcp1, Scya2 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Plys S Expression_system_vector_type: Plasmid Expression_system_plasmid: Paed-4
symmetry	Space Group: P 31 2 1	R_factor 0.231 R_Free 0.300
crystal cell	length a length b length c angle alpha angle beta angle gamma 99.240 99.240 243.460 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.50 Å
Gene Ontology	Chain Function Process Component D, Y, E G-protein coupled receptor b... protein kinase activity receptor binding cytokine activity chemokine activity heparin binding CCR2 chemokine receptor bind... MAPK cascade angiogenesis response to hypoxia positive regulation of endot... monocyte chemotaxis protein phosphorylation cellular calcium ion homeost... chemotaxis inflammatory response humoral immune response activation of signaling prot... cytoskeleton organization cell adhesion signal transduction cell surface receptor signal... transforming growth factor b... G-protein coupled receptor s... G-protein coupled receptor s... JAK-STAT cascade aging regulation of cell shape response to heat response to wounding response to mechanical stimu... response to bacterium organ morphogenesis response to gamma radiation regulation of vascular endot... positive regulation of macro... response to activity negative regulation of angio... viral genome replication cytokine-mediated signaling ... cellular homeostasis neutrophil chemotaxis endoplasmic reticulum unfold... organ regeneration lipopolysaccharide-mediated ... response to lipopolysacchari... response to progesterone sti... response to vitamin B3 helper T cell extravasation response to drug response to amino acid stimu... protein kinase B signaling c... negative regulation of neuro... astrocyte cell migration cellular protein metabolic p... cellular response to fibrobl... response to ethanol response to antibiotic vascular endothelial growth ... macrophage chemotaxis lymphocyte chemotaxis positive regulation of synap... positive regulation of T cel... response to glucocorticoid s... positive regulation of nitri... maternal process involved in... chemokine-mediated signaling... cellular response to lipopol... cellular response to interfe... cellular response to interle... cellular response to tumor n... cellular response to organic... positive regulation of immun... positive regulation of apopt... negative regulation of natur... extracellular region extracellular space cytoplasm neuronal cell body
Primary reference	Dual GPCR and GAG mimicry by the M3 chemokine decoy receptor., Alexander-Brett JM, Fremont DH, J Exp Med. 2007 Dec 24;204(13):3157-72. Epub 2007 Dec 10. PMID:18070938

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (223 Kb) [Save to disk] Biological Unit Coordinates (2nz1.pdb1.gz) 147 Kb Biological Unit Coordinates (2nz1.pdb2.gz) 145 Kb CSU: Contacts of Structural Units for 2NZ1 Likely Quarternary Molecular Structure file(s) for 2NZ1 Structure Factors (1415 Kb) Retrieve 2NZ1 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2NZ1 from S2C, [Save to disk] Re-refined 2nz1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2NZ1 in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2NZ1

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2NZ1, from MSDmotif at EBI Fold representative 2nz1 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2nz1_A] [2nz1_B] [2nz1_D] [2nz1_E] [2nz1_X] [2nz1_Y] SWISS-PROT database: [P13500] [O41925] Domain organization of [CCL2_HUMAN] [O41925_MHV68] by SWISSPFAM Domain found in 2NZ1: [SCY ] by SMART Alignments of the sequence of 2NZ1 with the sequences similar proteins can be viewed for 2NZ1's classification [CCL2_HUMAN] [O41925_MHV68] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CCL2_HUMAN] [O41925_MHV68] at ProtoMap. Click on the Cluster number.

Other resources with information on 2NZ1

Community annotation for 2NZ1 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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