5I72 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE OLIGOMERIC FORM OF THE LASSA VIRUS MATRIX PROTEIN Z

Authors :   K. Hastie, M. Zandonatti, T. Liu, S. Li, V. Woods Jr, E. O. Saphire

Date :   16 Feb 16 (Deposition) - 09 Mar 16 (Release) - 04 May 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (6x)

Keywords :   Arenavirus, Lassa Virus, Matrix, Z, Oligomer, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Hastie, M. Zandonatti, T. Liu, S. Li, V. L. Woods, E. O. Saphire
Crystal Structure Of The Oligomeric Form Of Lassa Virus Matrix Protein Z.
J. Virol. V. 90 4556 2016
PubMed-ID: 26912609 | Reference-DOI: 10.1128/JVI.02896-15

Compounds

Molecule 1 - RING FINGER PROTEIN Z
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 25-77
	Organism Common	:	LASV
	Organism Scientific	:	LASSA VIRUS (STRAIN MOUSE/SIERRA LEONE/JOSIAH/1976)
	Organism Taxid	:	11622
	Strain	:	MOUSE/SIERRA LEONE/JOSIAH/1976
	Synonym	:	PROTEIN Z,ZINC-BINDING PROTEIN

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (6x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 4)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:31 , CYS A:34 , CYS A:50 , CYS A:53	binding site for residue ZN A 101
2	AC2	SOFTWARE	CYS A:44 , HIS A:47 , CYS A:64 , CYS A:67	binding site for residue ZN A 102
3	AC3	SOFTWARE	CYS B:31 , CYS B:34 , CYS B:50 , CYS B:53	binding site for residue ZN B 101
4	AC4	SOFTWARE	CYS B:44 , HIS B:47 , CYS B:64 , CYS B:67	binding site for residue ZN B 102

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric 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 A from PDB  Type:PROTEIN  Length:51
                                                                                  
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ................eee....eeehhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  5i72 A 25 HLGPQFCKSCWFENKGLVECNNHYLCLNCLTLLLSVSNRCPICKMPLPTKL 75
                                    34        44        54        64        74

Chain B from PDB  Type:PROTEIN  Length:53
                                                                                    
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ................eee....eeehhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  5i72 B 25 HLGPQFCKSCWFENKGLVECNNHYLCLNCLTLLLSVSNRCPICKMPLPTKLRP 77
                                    34        44        54        64        74

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 (14, 14)

Visualization

Interactive Views

Asymmetric 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
		ZN	[ 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 5i72)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	5i72
		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
	Z_LASSJ \| O73557
		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
	Z_LASSJ \| O73557
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description