1QI7 - JenaLib

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Title :   THE CRYSTAL STRUCTURE AT 2.0 A OF SAPORIN SO6, A RIBOSOME INACTIVATING PROTEIN FROM SAPONARIA OFFICINALIS

Authors :   C. Savino, L. Federici, R. Ippoliti, E. Lendaro, D. Tsernoglou

Date :   08 Jun 99 (Deposition) - 05 Jun 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Ribosome Inactivating Protein, N-Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Savino, L. Federici, R. Ippoliti, E. Lendaro, D. Tsernoglou
The Crystal Structure Of Saporin So6 From Saponaria Officinalis And Its Interaction With The Ribosome.
Febs Lett. V. 470 239 2000
PubMed-ID: 10745075 | Reference-DOI: 10.1016/S0014-5793(00)01325-9

Molecule 1 - PROTEIN (N-GLYCOSIDASE)
	Cellular Location	:	CYTOPLASM
	Chains	:	A
	EC Number	:	3.2.2.22
	Organ	:	SEEDS
	Organism Common	:	COMMON SOAPWORT
	Organism Scientific	:	SAPONARIA OFFICINALIS
	Organism Taxid	:	3572

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:89 , LYS A:91 , THR A:95 , SER A:96 , ARG A:209	BINDING SITE FOR RESIDUE SO4 A 301

(no "SS Bond" information available for 1QI7)

Asymmetric Unit

No.	Residues
1	Phe A:191	-	Pro A:192

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_RIP6_SAPOF_001 *	E	72	D	RIP6_SAPOF	---	---	A	E	48	D
2	UniProt	VAR_RIP2_SAPOF_001 *	D	72	E	RIP2_SAPOF	---	---	A	E	48	E
3	UniProt	VAR_RIP6_SAPOF_002 *	R	115	K	RIP6_SAPOF	---	---	A	K	91	K
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_RIP6_SAPOF_001 *	E	72	D	RIP6_SAPOF	---	---	A	E	48	D
2	UniProt	VAR_RIP2_SAPOF_001 *	D	72	E	RIP2_SAPOF	---	---	A	E	48	E
3	UniProt	VAR_RIP6_SAPOF_002 *	R	115	K	RIP6_SAPOF	---	---	A	K	91	K
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_RIP6_SAPOF_001 *	E	72	D	RIP6_SAPOF	---	---	A	E	48	D
2	UniProt	VAR_RIP2_SAPOF_001 *	D	72	E	RIP2_SAPOF	---	---	A	E	48	E
3	UniProt	VAR_RIP6_SAPOF_002 *	R	115	K	RIP6_SAPOF	---	---	A	K	91	K
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIP2_SAPOF	195-211	1	A:171-187
1	SHIGA_RICIN	PS00275		RIP6_SAPOF	195-211	1	A:171-187

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIP2_SAPOF	195-211	1	A:171-187
1	SHIGA_RICIN	PS00275		RIP6_SAPOF	195-211	1	A:171-187

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIP2_SAPOF	195-211	2	A:171-187
1	SHIGA_RICIN	PS00275		RIP6_SAPOF	195-211	2	A:171-187

(no "Exon" information available for 1QI7)

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:253
 aligned with RIP2_SAPOF | P27559 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:253
                                    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   
           RIP2_SAPOF    25 VTSITLDLVNPTAGQYSSFVDKIRNNVKDPNLKYGGTDIAVIGPPSKDKFLRINFQSSRGTVSLGLKRDNLYVVAYLAMDNTNVNRAYYFKSEITSAELTALFPEATTANQKALEYTEDYQSIEKNAQITQGDKSRKELGLGIDLLLTFMEAVNKKARVVKNEARFLLIAIQMTAEVARFRYIQNLVTKNFPNKFDSDNKVIQFEVSWRKISTAIYGDAKNGVFNKDYDFGFGKVRQVKDLQMGLLMYLGKPK 277
               SCOP domains d1qi7a_ A: Saporin So6                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1qi7A01 A:1-178 Ricin (A subunit), domain 1                                                                                                                                       1qi7A02 A:179-250 Ricin (A Subunit), domain 2                           --- CATH domains
               Pfam domains ----RIP-1qi7A01 A:5-218                                                                                                                                                                                                   ----------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh.....................eeeeeeee..eeeeeeee.....eeeeeee.....eeeee.....hhhhhhhhh...hhh.eee.....hhhhhhhhhh......hhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....................hhhh........... Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------D------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qi7 A   1 VTSITLDLVNPTAGQYSSFVDKIRNNVKDPNLKYGGTDIAVIGPPSKEKFLRINFQSSRGTVSLGLKRDNLYVVAYLAMDNTNVNRAYYFKSEITSAELTALFPEATTANQKALEYTEDYQSIEKNAQITQGDKSRKELGLGIDLLLTFMEAVNKKARVVKNEARFLLIAIQMTAEVARFRYIQNLVTKNFPNKFDSDNKVIQFEVSWRKISTAIYGDAKNGVFNKDYDFGFGKVRQVKDLQMGLLMYLGKPK 253
                                    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 A from PDB  Type:PROTEIN  Length:253
 aligned with RIP6_SAPOF | P20656 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:253
                                    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   
           RIP6_SAPOF    25 VTSITLDLVNPTAGQYSSFVDKIRNNVKDPNLKYGGTDIAVIGPPSKEKFLRINFQSSRGTVSLGLKRDNLYVVAYLAMDNTNVNRAYYFRSEITSAESTALFPEATTANQKALEYTEDYQSIEKNAQITQGDQSRKELGLGIDLLSTSMEAVNKKARVVKDEARFLLIAIQMTAEAARFRYIQNLVIKNFPNKFNSENKVIQFEVNWKKISTAIYGDAKNGVFNKDYDFGFGKVRQVKDLQMGLLMYLGKPK 277
               SCOP domains d1qi7a_ A: Saporin So6                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1qi7A01 A:1-178 Ricin (A subunit), domain 1                                                                                                                                       1qi7A02 A:179-250 Ricin (A Subunit), domain 2                           --- CATH domains
               Pfam domains ----RIP-1qi7A01 A:5-218                                                                                                                                                                                                   ----------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh.....................eeeeeeee..eeeeeeee.....eeeeeee.....eeeee.....hhhhhhhhh...hhh.eee.....hhhhhhhhhh......hhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....................hhhh........... Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------D------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qi7 A   1 VTSITLDLVNPTAGQYSSFVDKIRNNVKDPNLKYGGTDIAVIGPPSKEKFLRINFQSSRGTVSLGLKRDNLYVVAYLAMDNTNVNRAYYFKSEITSAELTALFPEATTANQKALEYTEDYQSIEKNAQITQGDKSRKELGLGIDLLLTFMEAVNKKARVVKNEARFLLIAIQMTAEVARFRYIQNLVTKNFPNKFDSDNKVIQFEVSWRKISTAIYGDAKNGVFNKDYDFGFGKVRQVKDLQMGLLMYLGKPK 253
                                    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: Plant cytotoxins (166)

Protein domain: Saporin So6 (1)

Common soapwort (Saponaria officinalis) [TaxId: 3572] (1)

d1qi7a_

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RIP] (62)

Family: RIP (62)

Saponaria officinalis (Common soapwort) (1)

RIP-1qi7A01

A:5-218

Asymmetric Unit(hide GO term definitions)

Chain A (RIP2_SAPOF | P27559)

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.

Chain A (RIP6_SAPOF | P20656)

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.

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(no "Entries Sharing at Least One Protein Chain" available for 1QI7)

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Description

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Ligands, Modified Residues, Ions (1, 1)

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