5FT2 - JenaLib

Title :   SUB-TOMOGRAM AVERAGING OF LASSA VIRUS GLYCOPROTEIN SPIKE FROM VIRUS-LIKE PARTICLES AT PH 5

Authors :   S. Li, S. Zhaoyang, R. Pryce, M. L. Parsy, S. K. Fehling, K. Schlie, C. A. S W. Garten, T. A. Bowden, T. Strecker, J. T. Huiskonen

Date :   09 Jan 16 (Deposition) - 02 Mar 16 (Release) - 02 Mar 16 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   16.40

Chains :   Asym./Biol. Unit : B

Keywords :   Cell Adhesion, Membrane Protein, Glycoprotein, Receptor Binding, Membrane Fusion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Li, Z. Sun, R. Pryce, M. Parsy, S. K. Fehling, K. Schlie, C. A. Siebert W. Garten, T. A. Bowden, T. Strecker, J. T. Huiskonen
Acidic Ph-Induced Conformations And Lamp1 Binding Of The Lassa Virus Glycoprotein Spike.
Plos Pathog. V. 12 5418 2016
PubMed-ID: 26849049 | Reference-DOI: 10.1371/JOURNAL.PPAT.1005418
(for further references see the PDB file header)

Compounds

Molecule 1 - PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX
	Chains	:	B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Fragment	:	RECEPTOR BINDING DOMAIN, UNP RESIDUES 75-237
	Organism Common	:	LASSA MAMMARENAVIRUS, LASV
	Organism Scientific	:	LASSA VIRUS
	Organism Taxid	:	11622
	Strain	:	JOSIAH
	Synonym	:	GP1

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN B:89 , ASN B:109 , SER B:171 , SER B:216 , GLN B:218 , HOH B:406	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 301 THROUGH NAG B 302 BOUND TO ASN B 109
2	AC2	SOFTWARE	ASN B:119	BINDING SITE FOR MONO-SACCHARIDE NAG B 304 BOUND TO ASN B 119
3	AC3	SOFTWARE	ASN B:114 , HIS B:115 , LYS B:116 , MET B:153 , SER B:154 , ASN B:167 , TYR B:219	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 305 THROUGH NAG B 306 BOUND TO ASN B 167
4	AC4	SOFTWARE	THR B:101 , LEU B:103 , HIS B:131 , GLY B:160 , ASN B:224 , HOH B:404	BINDING SITE FOR MONO-SACCHARIDE NAG B 303 BOUND TO ASN B 224

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain B from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee......eeeeeee.............hhhhhhhhhhhhhhhhhhh...........eeeeeee..eeeeeee....hhhhhhhh..hhhhhhhhhhhhhh.....eeee......eeee....eeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ft2 B  81 TMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPS 237
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ft2)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5ft2
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GLYC_LASSJ \| P08669
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GLYC_LASSJ \| P08669
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description