2X6M	Immune System	date	Feb 18, 2010
title	Structure Of A Single Domain Camelid Antibody Fragment In Complex With A C-Terminal Peptide Of Alpha-Synuclein
authors	E.Degenst, T.Guilliams, J.Wellens, E.M.O'Day, C.A.Waudby, S.Meeha M.Dumoulin, S.T.D.Hsu, N.Cremades, K.H.G.Verschueren, E.Pardon J.Steyaert, J.Christodoulou, C.M.Dobson
compound		source
Molecule: Heavy Chain Variable Domain From Dromedary Chain: A Engineered: Yes Other_details: Engineered From Immunised Dromedary		Organism_scientific: Camelus Dromedarius Organism_common: Dromedary Organism_taxid: 9838 Tissue: Blood Cell: Lymphocyte Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Wk6 Expression_system_vector: Phen6
Molecule: Alpha-Synuclein Peptide Chain: B Fragment: C-Terminal Fragment Of Alpha-Synuclein, Residues		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: C 2 2 21	R_factor 0.15634 R_Free 0.20258
crystal cell	length a length b length c angle alpha angle beta angle gamma 60.170 63.120 62.870 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.62 Å
Gene Ontology	Chain Function Process Component B magnesium ion binding fatty acid binding copper ion binding calcium ion binding protein binding phospholipid binding microtubule binding ferrous iron binding zinc ion binding oxidoreductase activity kinesin binding enzyme binding protein domain specific bind... Hsp70 protein binding histone binding identical protein binding alpha-tubulin binding cysteine-type endopeptidase ... phospholipase binding dynein binding metal ion binding protein N-terminus binding tau protein binding beta-tubulin binding phosphoprotein binding phospholipase D inhibitor ac... microglial cell activation positive regulation of recep... negative regulation of prote... positive regulation of neuro... synaptic transmission, dopam... fatty acid metabolic process... neutral lipid metabolic proc... phospholipid metabolic proce... activation of cysteine-type ... mitochondrial membrane organ... synaptic transmission aging cell death adult locomotory behavior response to iron(II) ion regulation of phospholipase ... negative regulation of plate... regulation of glutamate secr... regulation of dopamine secre... cellular membrane organizati... negative regulation of micro... receptor internalization protein destabilization response to magnesium ion negative regulation of trans... response to lipopolysacchari... negative regulation of monoo... positive regulation of pepti... response to interferon-gamma... cellular response to oxidati... negative regulation of histo... regulation of locomotion response to cocaine dopamine biosynthetic proces... dopamine metabolic process response to drug mitochondrial ATP synthesis ... regulation of macrophage act... negative regulation of apopt... negative regulation of cyste... extracellular fibril organiz... negative regulation of neuro... cellular response to fibrobl... positive regulation of endoc... negative regulation of exocy... negative regulation of dopam... regulation of neurotransmitt... behavioral response to cocai... regulation of neuronal synap... regulation of long-term neur... synaptic vesicle endocytosis... synaptic vesicle transport positive regulation of synap... synapse organization regulation of acyl-CoA biosy... positive regulation of relea... dopamine uptake involved in ... negative regulation of dopam... negative regulation of serot... negative regulation of norep... calcium ion homeostasis oxidation-reduction process regulation of excitatory pos... long-term synaptic potentiat... positive regulation of inosi... negative regulation of throm... response to interleukin-1 cellular response to copper ... cellular response to epineph... positive regulation of prote... extracellular region nucleus nuclear outer membrane cytoplasm mitochondrion rough endoplasmic reticulum Golgi apparatus cytosol ribosome cytoskeleton plasma membrane cell cortex synaptic vesicle actin cytoskeleton membrane inclusion body cell junction axon growth cone cytoplasmic vesicle membrane... platelet alpha granule membr... terminal bouton fibril intracellular membrane-bound... axon terminus synapse perinuclear region of cytopl...
Primary reference	Structure and properties of a complex of alpha-synuclein and a single-domain camelid antibody., De Genst EJ, Guilliams T, Wellens J, O'Day EM, Waudby CA, Meehan S, Dumoulin M, Hsu ST, Cremades N, Verschueren KH, Pardon E, Wyns L, Steyaert J, Christodoulou J, Dobson CM, J Mol Biol. 2010 Sep 17;402(2):326-43. Epub 2010 Jul 8. PMID:20620148

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk] Biological Unit Coordinates (2x6m.pdb1.gz) 26 Kb CSU: Contacts of Structural Units for 2X6M Structure Factors (187 Kb) Retrieve 2X6M in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2X6M from S2C, [Save to disk] Re-refined 2x6m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2X6M 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.

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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 2X6M, from MSDmotif at EBI Fold representative 2x6m from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2x6m_A] [2x6m_B] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 2X6M with the sequences similar proteins can be viewed for 2X6M's classification 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 at ProtoMap. Click on the Cluster number.

Other resources with information on 2X6M

Community annotation for 2X6M at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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