1JL5 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   NOVEL MOLECULAR ARCHITECTURE OF YOPM-A LEUCINE-RICH EFFECTOR PROTEIN FROM YERSINIA PESTIS

Authors :   A. G. Evdokimov, D. E. Anderson, K. M. Routzahn, D. S. Waugh

Date :   15 Jul 01 (Deposition) - 10 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Leucine-Rich Repeat, Molecular Pathogenesis, Effector Protein, Virulence Factor, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Evdokimov, D. E. Anderson, K. M. Routzahn, D. S. Waugh
Unusual Molecular Architecture Of The Yersinia Pestis Cytotoxin Yopm: A Leucine-Rich Repeat Protein With The Shortest Repeating Unit.
J. Mol. Biol. V. 312 807 2001
PubMed-ID: 11575934 | Reference-DOI: 10.1006/JMBI.2001.4973
(for further references see the PDB file header)

Molecule 1 - OUTER PROTEIN YOPM
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	MODIFIED PMAL
	Gene	:	YOPM
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	CA	5	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:5 , HOH A:9 , HOH A:28 , ASN A:1246 , ASP A:1266 , ASN A:1326	BINDING SITE FOR RESIDUE CA A 2001
2	AC2	SOFTWARE	HOH A:1 , HOH A:2 , HOH A:8 , HOH A:18 , ASP A:1266 , ASN A:1307 , GLU A:1308	BINDING SITE FOR RESIDUE CA A 2002
3	AC3	SOFTWARE	HOH A:27 , HOH A:189 , HOH A:292 , HOH A:316 , ASN A:1162 , ASN A:1182	BINDING SITE FOR RESIDUE CA A 2003
4	AC4	SOFTWARE	HOH A:232 , HOH A:392 , GLU A:1274 , GLU A:1294	BINDING SITE FOR RESIDUE CA A 2004
5	AC5	SOFTWARE	HOH A:76 , GLU A:1059	BINDING SITE FOR RESIDUE CA A 2005

(no "SS Bond" information available for 1JL5)

(no "Cis Peptide Bond" information available for 1JL5)

(no "SAP(SNP)/Variant" information available for 1JL5)

Asymmetric Unit (1, 11)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	YOPM_YERPE	132-153 92-113 174-195 154-173 216-237 196-215 258-279 238-257 318-339 298-317 358-379	11	A:1132-1153 A:1092-1113 A:1174-1195 A:1154-1173 A:1216-1237 A:1196-1215 A:1258-1279 A:1238-1257 A:1318-1339 A:1298-1317 A:1358-1379

Biological Unit 1 (1, 44)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	YOPM_YERPE	132-153 92-113 174-195 154-173 216-237 196-215 258-279 238-257 318-339 298-317 358-379	44	A:1132-1153 A:1092-1113 A:1174-1195 A:1154-1173 A:1216-1237 A:1196-1215 A:1258-1279 A:1238-1257 A:1318-1339 A:1298-1317 A:1358-1379

(no "Exon" information available for 1JL5)

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:353
 aligned with YOPM_YERPE | P17778 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:353
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383   
          YOPM_YERPE     34 KSKTEYYNAWSEWERNAPPGNGEQREMAVSRLRDCLDRQAHELELNNLGLSSLPELPPHLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNNQLEELPELQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLCDLPPSLEELNVSNNKLIELPALPPRLERLIASFNHLAEVPELPQNLKQLHVEYNPLREFPDIPESVEDLRMNS  386
               SCOP domains d1jl5a_ A: Leucine rich effector protein YopM                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1jl5A00 A:1034-1386 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) TTSSLRR-1jl5A05 A:1034-1063   --------------------------------------------------------------------LRR_1-1jl5A01        --------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_7-1jl5A02    ----------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_7-1jl5A03    ----------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_7-1jl5A04    ----------------------------------------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..eee.................eee.................eee.................eee...................eee.................eee...................eee.................eee...................eee.................eee.................eee.......ee........eee.......ee........eee.................eee.................eee.................eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------LRR  PDB: A:1092-1113 ------------------LRR  PDB: A:1132-1153 LRR  PDB: A:1154-117LRR  PDB: A:1174-1195 LRR  PDB: A:1196-121LRR  PDB: A:1216-1237 LRR  PDB: A:1238-125LRR  PDB: A:1258-1279 ------------------LRR  PDB: A:1298-131LRR  PDB: A:1318-1339 ------------------LRR  PDB: A:1358-1379 ------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jl5 A 1034 KSKTEYYNAWSEWERNAPPGNGEQREMAVSRLRDCLDRQAHELELNNLGLSSLPELPPHLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNNQLEELPELQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLCDLPPSLEELNVSNNKLIELPALPPRLERLIASFNHLAEVPELPQNLKQLHVEYNPLREFPDIPESVEDLRMNS 1386
                                  1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (112)

Superfamily: L domain-like (93)

Family: Leucine rich effector protein YopM (2)

Protein domain: Leucine rich effector protein YopM (2)

Yersinia pestis [TaxId: 632] (2)

d1jl5a_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Horseshoe (92)

Topology: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (73)

Homologous Superfamily: Ribonuclease Inhibitor (73)

Yersinia pestis. Organism_taxid: 632. (2)

1jl5A00

A:1034-1386

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LRR (77)

Family: LRR_1 (20)

Yersinia pestis (1)

LRR_1-1jl5A01

A:1132-1152

Family: LRR_7 (15)

Yersinia pestis (1)

2a	LRR_7-1jl5A02	A:1317-1333
2b	LRR_7-1jl5A03	A:1317-1333
2c	LRR_7-1jl5A04	A:1317-1333

Clan: no clan defined [family: TTSSLRR] (1)

Family: TTSSLRR (1)

Yersinia pestis (1)

TTSSLRR-1jl5A05

A:1034-1063

Asymmetric Unit(hide GO term definitions)

Chain A (YOPM_YERPE | P17778)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jl5)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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)

Access by PDB/NDB ID
	1jl5
		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
	YOPM_YERPE \| P17778
		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

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
	YOPM_YERPE \| P17778
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	YOPM_YERPE \| P17778	:	1g9u

1g9u	1G9U IS THE COMPANION STRUCTURE - SAME PUBLICATION. TWO DIFFERENT SPACEGROUPS, SAME TETRAMERIC ORGANIZATION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 11)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (3, 5)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File