1ML0	Immune System	date	Aug 29, 2002
title	Viral Chemokine Binding Protein M3 From Murine Gammaherpesvi Complex With The P8a Variant Of Cc-Chemokine Mcp-1
authors	J.M.Alexander, D.H.Fremont
compound		source
Molecule: M3 Protein Chain: A Engineered: Yes		Organism_scientific: Murid Herpesvirus 4 Organism_common: Murine Herpesvirus 68 Organism_taxid: 33708 Gene: M3 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_cell_line: Sf9 Expression_system_vector_type: Baculovirus
Molecule: Small Inducible Cytokine Chain: D Synonym: Ccl2, Monocyte Chemotactic Protein 1, Mcp-1, Monoc Chemotactic Protein 1, Mcp-1, Monocyte Chemoattractant Prot Monocyte Chemotactic And Activating Factor, Mcaf, Monocyte Protein Je, Hc11; Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Monocyte Chemoattractant Protein 1 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 3 2 1	R_factor 0.201 R_Free 0.282
crystal cell	length a length b length c angle alpha angle beta angle gamma 99.200 99.200 78.900 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.80 Å
related structures	by homologous chain: 1DOL, 1DON, 1MKF
Gene Ontology	Chain Function Process Component D 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 negative regulation of apopt... response to amino acid stimu... protein kinase B signaling c... 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	Structural basis of chemokine sequestration by a herpesvirus decoy receptor., Alexander JM, Nelson CA, van Berkel V, Lau EK, Studts JM, Brett TJ, Speck SH, Handel TM, Virgin HW, Fremont DH, Cell 2002 Nov 1;111(3):343-56. PMID:12419245

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk] Biological Unit Coordinates (1ml0.pdb1.gz) 138 Kb Biological Unit Coordinates (1ml0.pdb2.gz) 409 Kb CSU: Contacts of Structural Units for 1ML0 Likely Quarternary Molecular Structure file(s) for 1ML0 Retrieve 1ML0 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1ML0 from S2C, [Save to disk]

View 1ML0 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 1ML0

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1ML0, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ml0a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1ml0d_, region D [Jmol] [rasmolscript] [script source] Fold representative 1ml0 from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ml0_A] [1ml0_D] SWISS-PROT database: [P13500] [O41925] Domain organization of [CCL2_HUMAN] [O41925_MHV68] by SWISSPFAM Domain found in 1ML0: [SCY ] by SMART Alignments of the sequence of 1ML0 with the sequences similar proteins can be viewed for 1ML0'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 1ML0

Community annotation for 1ML0 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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