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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SAPORIN-L1 FROM SAPONARIA OFFICINALIS

Authors :   M. Ho, M. B. Sturm, S. C. Almo, V. L. Schramm

Date :   20 May 09 (Deposition) - 08 Dec 09 (Release) - 21 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.49

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

Keywords :   Transition State Analogue, Ribosome Inactivating Proteins, Rips, Hydrolase, Plant Defense, Protein Synthesis Inhibitor, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Ho, M. B. Sturm, S. C. Almo, V. L. Schramm
Transition State Analogues In Structures Of Ricin And Saporin Ribosome-Inactivating Proteins.
Proc. Natl. Acad. Sci. Usa V. 106 20276 2009
PubMed-ID: 19920175 | Reference-DOI: 10.1073/PNAS.0911606106

Molecule 1 - VACUOLAR SAPORIN
	Chains	:	A, B
	EC Number	:	3.2.2.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	COMMON SOAPWORT
	Organism Scientific	:	SAPONARIA OFFICINALIS
	Organism Taxid	:	3572

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3HIS)

(no "Site" information available for 3HIS)

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

Asymmetric Unit

No.	Residues
1	Arg A:44	-	Pro A:45
2	Gly A:47	-	Pro A:48
3	Pro A:48	-	Pro A:49
4	Glu A:196	-	Pro A:197
5	Arg B:44	-	Pro B:45
6	Gly B:47	-	Pro B:48
7	Pro B:48	-	Pro B:49
8	Glu B:196	-	Pro B:197

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

(no "PROSITE Motif" information available for 3HIS)

(no "Exon" information available for 3HIS)

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:257
 aligned with Q2QEH4_SAPOF | Q2QEH4 from UniProtKB/TrEMBL  Length:299

    Alignment length:257
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       
         Q2QEH4_SAPOF    22 VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 278
               SCOP domains d3hisa_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hisA01 A:1-176 Ricin (A subunit), domain 1                                                                                                                                     3hisA02 A:177-257 Ricin (A Subunit), domain 2                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh......................eeeeeee....eeeeeee.....eeeeeee.....eeeee......hhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh.hhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.........eeeee.hhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3his A   1 VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with Q2QEH4_SAPOF | Q2QEH4 from UniProtKB/TrEMBL  Length:299

    Alignment length:257
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       
         Q2QEH4_SAPOF    22 VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 278
               SCOP domains d3hisb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hisB01 B:1-176 Ricin (A subunit), domain 1                                                                                                                                     3hisB02 B:177-257 Ricin (A Subunit), domain 2                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh......................eeeeeeee..eeeeeeee.....eeeeeee.....eeeee......hhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh.hhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.........eeeeehhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3his B   1 VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVD 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

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) (23004)

Fold: Ribosome inactivating proteins (RIP) (180)

Superfamily: Ribosome inactivating proteins (RIP) (180)

Family: automated matches (9)

Protein domain: automated matches (9)

Common soapwort (Saponaria officinalis) [TaxId: 3572] (5)

1a	d3hisa_	A:
1b	d3hisb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Ricin (A subunit); domain 1 (112)

Homologous Superfamily: Ricin (A subunit), domain 1 (112)

Common soapwort (Saponaria officinalis) (6)

1a	3hisA01	A:1-176
1b	3hisB01	B:1-176

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Ricin (A Subunit), domain 2 (112)

Homologous Superfamily: Ricin (A Subunit), domain 2 (112)

Common soapwort (Saponaria officinalis) (6)

2a	3hisA02	A:177-257
2b	3hisB02	B:177-257

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q2QEH4_SAPOF | Q2QEH4)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0030598	rRNA N-glycosylase activity	Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

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

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

	Cis Peptide Bonds
		Arg A:44 - Pro A:45	[ RasMol ]
		Arg B:44 - Pro B:45	[ RasMol ]
		Glu A:196 - Pro A:197	[ RasMol ]
		Glu B:196 - Pro B:197	[ RasMol ]
		Gly A:47 - Pro A:48	[ RasMol ]
		Gly B:47 - Pro B:48	[ RasMol ]
		Pro A:48 - Pro A:49	[ RasMol ]
		Pro B:48 - Pro B:49	[ RasMol ]

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

Jmol
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	3his
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		Orientation in Membranes	:	OPM
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	3.2.2.22
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UniProtKB/TrEMBL
	Q2QEH4_SAPOF \| Q2QEH4	:	3hiq 3hit 3hiv 3hiw

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (2, 4)

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Gene Ontology (4, 4)

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