3J0R - JenaLib

Title :   MODEL OF A TYPE III SECRETION SYSTEM NEEDLE BASED ON A 7 ANGSTROM RESOLUTION CRYOEM MAP

Authors :   T. Fujii, M. Cheung, A. Blanco, T. Kato, A. J. Blocker, K. Namba

Date :   03 Nov 11 (Deposition) - 29 Feb 12 (Release) - 04 Apr 12 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   7.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (22x)

Keywords :   Helical Assembly, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Fujii, M. Cheung, A. Blanco, T. Kato, A. J. Blocker, K. Namba
Structure Of A Type Iii Secretion Needle At 7-A Resolution Provides Insights Into Its Assembly And Signaling Mechanisms.
Proc. Natl. Acad. Sci. Usa V. 109 4461 2012
PubMed-ID: 22388746 | Reference-DOI: 10.1073/PNAS.1116126109

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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:82
 aligned with MXIH_SHIFL | P0A223 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:82
                                    11        21        31        41        51        61        71        81  
            MXIH_SHIFL    2 SVTVPNDDWTLSSLSETFDDGTQTLQGELTLALDKLAKNPSNPQLLAEYQSKLSEYTLYRNAQSNTVKVIKDVDAAIIQNFR 83
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  3j0r A  2 SVTVPNDDWTLSSLSETFDDGTQTLQGELTLALDKLAKNPSNPQLLAEYQSKLSEYTLYRNAQSNTVKVIKDVDAAIIQNFR 83
                                    11        21        31        41        51        61        71        81

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 (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A (MXIH_SHIFL | P0A223)

molecular function
	GO:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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
(no "Ligands, Modified Residues, Ions" information available for 3j0r)

	Sites
(no "Sites" information available for 3j0r)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3j0r)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3j0r
		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
	MXIH_SHIFL \| P0A223
		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
	MXIH_SHIFL \| P0A223
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description