3CVR - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE FULL LENGTH IPAH3

Authors :   Y. Zhu, F. Shao

Date :   19 Apr 08 (Deposition) - 11 Nov 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Leucine Rich Repeat And Alpha Fold, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhu, H. Li, L. Hu, J. Wang, Y. Zhou, Z. Pang, L. Liu, F. Shao
Structure Of A Shigella Effector Reveals A New Class Of Ubiquitin Ligases
Nat. Struct. Mol. Biol. V. 15 1302 2008
PubMed-ID: 18997779 | Reference-DOI: 10.1038/NSMB.1517

Molecule 1 - INVASION PLASMID ANTIGEN
	Chains	:	A
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	IPAH_3
	Organism Scientific	:	SHIGELLA FLEXNERI 2A
	Organism Taxid	:	198214
	Strain	:	301
	Synonym	:	UBIQUITIN E3 LIGASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 16)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3CVR)

(no "SS Bond" information available for 3CVR)

Asymmetric Unit

No.	Residues
1	Pro A:257	-	Asp A:258
2	Pro A:279	-	Leu A:280
3	Phe A:288	-	Pro A:289
4	Asn A:327	-	Thr A:328
5	Thr A:328	-	Ser A:329
6	Ser A:329	-	Gly A:330
7	Asp A:389	-	Asn A:390

(no "SAP(SNP)/Variant" information available for 3CVR)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	IPA3_SHIFL	121-142 101-120 81-100 161-182	4	A:121-142 A:101-120 A:81-100 A:161-182

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	IPA3_SHIFL	121-142 101-120 81-100 161-182	4	A:121-142 A:101-120 A:81-100 A:161-182

Biological Unit 2 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	IPA3_SHIFL	121-142 101-120 81-100 161-182	8	A:121-142 A:101-120 A:81-100 A:161-182

(no "Exon" information available for 3CVR)

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:477
 aligned with IPA3_SHIFL | Q83RJ4 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:537
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       
           IPA3_SHIFL    25 TYADYFSAWDKWEKQALPGENRNEAVSLLKECLINQFSELQLNRLNLSSLPDNLPPQITVLEITQNALISLPELPASLEYLDACDNRLSTLPELPASLKHLDVDNNQLTMLPELPALLEYINADNNQLTMLPELPTSLEVLSVRNNQLTFLPELPESLEALDVSTNLLESLPAVPVRNHHSEETEIFFRCRENRITHIPENILSLDPTCTIILEDNPLSSRIRESLSQQTAQPDYHGPRIYFSMSDGQQNTLHRPLADAVTAWFPENKQSDVSQIWHAFEHEEHANTFSAFLDRLSDTVSARNTSGFREQVAAWLEKLSTSAELRQQSFAVAADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREMFRLEILEDIARDKVRTLHFVDEIEVYLAFQTMLAEKLQLSTAVKEMRFYGVSGVTANDLRTAEAMVRSREENEFTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEMLENEYSQRVADRLKASGLSGDADAEREAGAQVMRETEQQIYRQVTDEVLALRL 561
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cvrA01 A:25-279 Ribonuclease Inhibitor                                                                                                                                                                                                                        ----------     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                                  --------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...eee..................eee.................eee.................eee.................eee.................eee.................eee.............--------..eeee.........hhhhhhh...eeee......hhhhhhhhhhhhhh..---.eee...----------..hhhhhh...-----hhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----------------------------------.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------LRR  PDB: A:81-100  LRR  PDB: A:101-120 LRR  PDB: A:121-142   ------------------LRR  PDB: A:161-182   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvr A  25 TYADYFSAWDKWEKQALPGENRNEAVSLLKECLINQFSELQLNRLNLSSLPDNLPPQITVLEITQNALISLPELPASLEYLDACDNRLSTLPELPASLKHLDVDNNQLTmLPELPALLEYINADNNQLTmLPELPTSLEVLSVRNNQLTFLPELPESLEALDVSTNLLESLPAVP--------TEIFFRCRENRITHIPENILSLDPTCTIILEDNPLSSRIRESLSQQTAQPD---PRIYFSm----------PLADAVTAWFP-----DVSQIWHAFEHEEHANTFSAFLDRLSDTVSARNTSGFREQVAAWLEKLSASAELRQQSFAVAADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREmFRLEILEDIARDKVRTLHFVDEIEVYLAFQTmLAEKLQLSTAVKEmRFYGVSGVTANDLRTAEAmVRSREENEFTDWFSLWGPWHAVLKRTEADRWALAEEQKY----------------------------------mRETEQQIYRQLTDEVLALRL 561
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    |    -   |   214       224       234       244       254   |   264   |     -    |  284    |    -|      304       314       324       334       344       354       364       374       384       394       404       414       424       434       444   |   454       464  |    474       484       494       504 |       -         -         -      |544       554       
                                                                                                                                       134-MSE             154-MSE                                      199      208                                               258 262     |        279       289   295                                                                                                        402-MSE                         434-MSE       448-MSE            467-MSE                                506                                541-MSE                
                                                                                                                                                                                                                                                                             268-MSE

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 '\|'

(no "SCOP Domain" information available for 3CVR)

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)

Shigella flexneri 2a. Organism_taxid: 198214. Strain: 301. (1)

3cvrA01

A:25-279

(no "Pfam Domain" information available for 3CVR)

Asymmetric Unit(hide GO term definitions)

Chain A (IPA3_SHIFL | Q83RJ4)

molecular function
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
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:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	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:0030430	host cell cytoplasm	The cytoplasm of a host cell.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 3cvr)

	Cis Peptide Bonds
		Asn A:327 - Thr A:328	[ RasMol ]
		Asp A:389 - Asn A:390	[ RasMol ]
		Phe A:288 - Pro A:289	[ RasMol ]
		Pro A:257 - Asp A:258	[ RasMol ]
		Pro A:279 - Leu A:280	[ RasMol ]
		Ser A:329 - Gly A:330	[ RasMol ]
		Thr A:328 - Ser A:329	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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