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Asym./Biol. Unit (Jmol Viewer)

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Title :   RICIN A-CHAIN (RECOMBINANT) AT 100K

Authors :   K. Watanabe, H. Motoshima

Date :   10 Dec 02 (Deposition) - 03 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

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

Reference :   K. Watanabe, H. Motoshima
Ricin A-Chain (Recombinant) At 100K
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RICIN
	Chains	:	A
	EC Number	:	3.2.2.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK223-3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	CASTOR BEAN
	Organism Scientific	:	RICINUS COMMUNIS
	Organism Taxid	:	3988
	Synonym	:	RICIN A-CHAIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:17 , GLN A:19 , HIS A:65 , HOH A:427 , HOH A:568 , HOH A:776	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	PHE A:119 , GLY A:120 , ASN A:122 , ARG A:125 , HOH A:530 , HOH A:641	BINDING SITE FOR RESIDUE SO4 A 302
3	AC3	SOFTWARE	THR A:13 , ALA A:14 , GLY A:15 , HIS A:65 , ASN A:141 , GLY A:142 , GLU A:145 , GLU A:146 , ASN A:195 , ARG A:197 , HOH A:413 , HOH A:460 , HOH A:480 , HOH A:484 , HOH A:494 , HOH A:502 , HOH A:571 , HOH A:619	BINDING SITE FOR RESIDUE TRE A 304
4	AC4	SOFTWARE	ARG A:48 , VAL A:49 , GLY A:50 , LEU A:51 , SER A:89 , ASN A:113 , TYR A:115 , SER A:155 , HOH A:453 , HOH A:466 , HOH A:528 , HOH A:556 , HOH A:602 , HOH A:603 , HOH A:622 , HOH A:625 , HOH A:643 , HOH A:654 , HOH A:799	BINDING SITE FOR RESIDUE TRE A 305

(no "SS Bond" information available for 1J1M)

(no "Cis Peptide Bond" information available for 1J1M)

(no "SAP(SNP)/Variant" information available for 1J1M)

Asymmetric/Biological 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.	RICI_RICCO	207-223	1	A:172-188

(no "Exon" information available for 1J1M)

Asymmetric/Biological 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:262
 aligned with RICI_RICCO | P02879 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:262
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
           RICI_RICCO    41 YPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF 302
               SCOP domains d1j1ma_ A: Ricin A-chain                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1j1mA01 A:6-179 Ricin (A subunit), domain 1                                                                                                                                   1j1mA02 A:180-267 Ricin (A Subunit), domain 2                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh....ee..ee........hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhhhhhh.....eeee.....hhhhhhhhhh........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.hhhh.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j1m A   6 YPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLREDIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF 267
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265

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/Biological 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: Ricin A-chain (36)

Castor bean (Ricinus communis) [TaxId: 3988] (36)

d1j1ma_

Asymmetric/Biological 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)

Castor bean (Ricinus communis) (28)

1j1mA01

A:6-179

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

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

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

Castor bean (Ricinus communis) (28)

1j1mA02

A:180-267

(no "Pfam Domain" information available for 1J1M)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RICI_RICCO | P02879)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0031640	killing of cells of other organism	Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
	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.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (2, 2)

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Gene Ontology (9, 9)

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