Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Ricin

Gene
N/A
Organism
Ricinus communis (Castor bean)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).

Catalytic activityi

Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei50Carbohydrate; via amide nitrogen1
Binding sitei85Carbohydrate; via amide nitrogen1
Active sitei2121
Binding sitei324Carbohydrate; via carbonyl oxygenBy similarity1
Binding sitei349Carbohydrate1
Binding sitei354Carbohydrate1
Binding sitei360Carbohydrate1
Binding sitei409CarbohydrateBy similarity1
Binding sitei449CarbohydrateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi115 – 116AMP2
Nucleotide bindingi156 – 158AMP3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein synthesis inhibitor, Toxin

Keywords - Biological processi

Plant defense

Keywords - Ligandi

Lectin, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18749.
BRENDAi3.2.2.22. 1204.

Protein family/group databases

CAZyiCBM13. Carbohydrate-Binding Module Family 13.

Names & Taxonomyi

Protein namesi
Recommended name:
Ricin
Cleaved into the following 3 chains:
Alternative name(s):
rRNA N-glycosidase
OrganismiRicinus communis (Castor bean)
Taxonomic identifieri3988 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsMalpighialesEuphorbiaceaeAcalyphoideaeAcalypheaeRicinus

Subcellular locationi

GO - Cellular componenti

  • endoplasmic reticulum Source: UniProtKB
Complete GO annotation...

Pathology & Biotechi

Biotechnological usei

A deglycosylated A chain may be linked to monoclonal antibodies to produce immunotoxins exploited in cancer treatment. However, a point mutation should be introduced to eliminate vascular leak syndrome, a side effect resulting from endothelial damage.

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi83R → A: No effect on the toxic activity but suppresses the vascular leak syndrome. 1 Publication1
Mutagenesisi109L → A or M: No effect on the toxic activity or the vascular leak syndrome. 1 Publication1
Mutagenesisi110D → A, E or N: Suppresses the toxic activity. 1 Publication1
Mutagenesisi111V → A or M: No effect on the toxic activity or the vascular leak syndrome. 1 Publication1
Mutagenesisi132N → A: No effect on the toxic activity but Suppresses the vascular leak syndrome. 1 Publication1

Protein family/group databases

Allergomei2803. Ric c RIP.

Chemistry databases

ChEMBLiCHEMBL4756.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 351 PublicationAdd BLAST35
ChainiPRO_000003074136 – 302Ricin A chainAdd BLAST267
PeptideiPRO_0000030742303 – 314Linker peptide1 PublicationAdd BLAST12
ChainiPRO_0000030743315 – 576Ricin B chainAdd BLAST262

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
GlycosylationiCAR_00008045N-linked (GlcNAc...)1 Publication1
GlycosylationiCAR_000081271N-linked (GlcNAc...); partial1 Publication1
Disulfide bondi294 ↔ 318Interchain (between A and B chains)
Disulfide bondi334 ↔ 353
Disulfide bondi377 ↔ 394
Glycosylationi409N-linked (GlcNAc...)Combined sources1
Glycosylationi449N-linked (GlcNAc...)Combined sources1
Disulfide bondi465 ↔ 478
Disulfide bondi504 ↔ 521

Keywords - PTMi

Disulfide bond, Glycoprotein

PTM databases

UniCarbKBiP02879.

Interactioni

Subunit structurei

Disulfide-linked dimer of A and B chains.

Protein-protein interaction databases

BioGridi1022023. 2 interactors.
DIPiDIP-46421N.
IntActiP02879. 2 interactors.
MINTiMINT-8391414.

Chemistry databases

BindingDBiP02879.

Structurei

Secondary structure

1576
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi43 – 48Combined sources6
Helixi53 – 67Combined sources15
Beta strandi72 – 74Combined sources3
Beta strandi77 – 79Combined sources3
Turni83 – 85Combined sources3
Helixi88 – 90Combined sources3
Beta strandi91 – 98Combined sources8
Beta strandi100 – 102Combined sources3
Beta strandi104 – 110Combined sources7
Turni111 – 113Combined sources3
Beta strandi116 – 121Combined sources6
Beta strandi124 – 127Combined sources4
Helixi133 – 139Combined sources7
Turni140 – 145Combined sources6
Beta strandi147 – 151Combined sources5
Helixi158 – 165Combined sources8
Turni166 – 168Combined sources3
Helixi169 – 171Combined sources3
Helixi176 – 188Combined sources13
Helixi189 – 191Combined sources3
Helixi196 – 215Combined sources20
Helixi217 – 228Combined sources12
Helixi237 – 254Combined sources18
Beta strandi260 – 268Combined sources9
Beta strandi270 – 272Combined sources3
Beta strandi274 – 279Combined sources6
Helixi280 – 283Combined sources4
Turni284 – 286Combined sources3
Beta strandi298 – 300Combined sources3
Helixi330 – 332Combined sources3
Beta strandi334 – 337Combined sources4
Helixi338 – 340Combined sources3
Beta strandi347 – 351Combined sources5
Helixi359 – 361Combined sources3
Beta strandi363 – 365Combined sources3
Beta strandi369 – 373Combined sources5
Beta strandi376 – 381Combined sources6
Beta strandi388 – 393Combined sources6
Turni394 – 396Combined sources3
Helixi399 – 401Combined sources3
Beta strandi412 – 414Combined sources3
Turni415 – 418Combined sources4
Beta strandi419 – 422Combined sources4
Beta strandi433 – 436Combined sources4
Helixi441 – 443Combined sources3
Beta strandi454 – 459Combined sources6
Helixi461 – 463Combined sources3
Beta strandi465 – 469Combined sources5
Beta strandi472 – 476Combined sources5
Turni480 – 483Combined sources4
Beta strandi487 – 489Combined sources3
Beta strandi495 – 497Combined sources3
Beta strandi503 – 507Combined sources5
Beta strandi516 – 521Combined sources6
Helixi526 – 528Combined sources3
Turni541 – 543Combined sources3
Beta strandi546 – 549Combined sources4
Helixi550 – 552Combined sources3
Helixi554 – 556Combined sources3
Beta strandi559 – 562Combined sources4
Helixi568 – 570Combined sources3
Beta strandi573 – 575Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BR5X-ray2.50A36-302[»]
1BR6X-ray2.30A36-302[»]
1IFSX-ray2.00A38-298[»]
1IFTX-ray1.80A38-298[»]
1IFUX-ray2.40A38-298[»]
1IL3X-ray2.80A36-302[»]
1IL4X-ray2.60A36-302[»]
1IL5X-ray2.80A/B36-302[»]
1IL9X-ray3.10A36-302[»]
1J1MX-ray1.50A36-302[»]
1OBSX-ray2.20A36-302[»]
1OBTX-ray2.80A36-302[»]
1RTCX-ray2.30A36-302[»]
1UQ4X-ray1.90A40-302[»]
1UQ5X-ray1.40A40-302[»]
2AAIX-ray2.50A36-302[»]
B315-576[»]
2P8NX-ray1.94A36-302[»]
2PJOX-ray1.80A36-302[»]
2R2XX-ray2.40A36-302[»]
2R3DX-ray2.09A36-302[»]
2VC3X-ray1.60A36-302[»]
2VC4X-ray1.39A36-302[»]
3BJGX-ray2.14A36-302[»]
3EJ5X-ray2.50X40-296[»]
3HIOX-ray2.00A36-302[»]
3LC9X-ray2.28A36-233[»]
3MK9X-ray2.08A36-233[»]
3PX8X-ray1.29X39-296[»]
3PX9X-ray1.89X39-296[»]
3RTIX-ray2.80A36-302[»]
B315-576[»]
3RTJX-ray3.00A36-302[»]
B315-576[»]
3SRPX-ray2.14A36-302[»]
4ESIX-ray1.87A36-302[»]
4HUOX-ray1.52X36-302[»]
4HUPX-ray1.70X36-302[»]
4HV3X-ray1.54A36-302[»]
4HV7X-ray1.87X36-302[»]
4IMVX-ray2.25A36-233[»]
4KUCX-ray2.79A/I36-302[»]
4LGPX-ray2.40A/C36-296[»]
4LGRX-ray1.65A40-294[»]
4LGSX-ray2.70A39-301[»]
4LHJX-ray1.80A39-297[»]
4LHQX-ray2.30A/C39-298[»]
4MX1X-ray1.59A36-302[»]
4MX5X-ray1.52X36-302[»]
4Q2VX-ray2.20A36-302[»]
4Z9KX-ray1.50A39-296[»]
5DDZX-ray1.50A36-302[»]
5E1HX-ray2.03A40-297[»]
5SV3X-ray2.73B/D36-233[»]
ProteinModelPortaliP02879.
SMRiP02879.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP02879.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini321 – 448Ricin B-type lectin 1PROSITE-ProRule annotationAdd BLAST128
Repeati331 – 3731-alphaAdd BLAST43
Repeati374 – 4141-betaAdd BLAST41
Repeati417 – 4491-gammaAdd BLAST33
Domaini451 – 575Ricin B-type lectin 2PROSITE-ProRule annotationAdd BLAST125
Repeati462 – 4972-alphaAdd BLAST36
Repeati501 – 5402-betaAdd BLAST40
Repeati543 – 5702-gammaAdd BLAST28

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni43 – 45Carbohydrate bindingBy similarity3
Regioni176 – 181Carbohydrate binding6
Regioni230 – 232Carbohydrate binding3
Regioni336 – 340Carbohydrate binding5
Regioni548 – 551Carbohydrate binding4
Regioni565 – 569Carbohydrate binding5

Domaini

The B chain is composed of two domains, each domain consists of 3 homologous subdomains (alpha, beta, gamma).

Sequence similaritiesi

In the N-terminal section; belongs to the ribosome-inactivating protein family. Type 2 RIP subfamily.Curated
Contains 2 ricin B-type lectin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal

Family and domain databases

Gene3Di3.40.420.10. 1 hit.
4.10.470.10. 1 hit.
InterProiIPR001574. Ribosome_inactivat_prot.
IPR017988. Ribosome_inactivat_prot_CS.
IPR016138. Ribosome_inactivat_prot_sub1.
IPR016139. Ribosome_inactivat_prot_sub2.
IPR017989. Ribosome_inactivat_prot_subgr.
IPR000772. Ricin_B_lectin.
[Graphical view]
PfamiPF00652. Ricin_B_lectin. 2 hits.
PF00161. RIP. 1 hit.
[Graphical view]
PRINTSiPR00396. SHIGARICIN.
SMARTiSM00458. RICIN. 2 hits.
[Graphical view]
SUPFAMiSSF50370. SSF50370. 2 hits.
SSF56371. SSF56371. 1 hit.
PROSITEiPS50231. RICIN_B_LECTIN. 2 hits.
PS00275. SHIGA_RICIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P02879-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKPGGNTIVI WMYAVATWLC FGSTSGWSFT LEDNNIFPKQ YPIINFTTAG
60 70 80 90 100
ATVQSYTNFI RAVRGRLTTG ADVRHEIPVL PNRVGLPINQ RFILVELSNH
110 120 130 140 150
AELSVTLALD VTNAYVVGYR AGNSAYFFHP DNQEDAEAIT HLFTDVQNRY
160 170 180 190 200
TFAFGGNYDR LEQLAGNLRE NIELGNGPLE EAISALYYYS TGGTQLPTLA
210 220 230 240 250
RSFIICIQMI SEAARFQYIE GEMRTRIRYN RRSAPDPSVI TLENSWGRLS
260 270 280 290 300
TAIQESNQGA FASPIQLQRR NGSKFSVYDV SILIPIIALM VYRCAPPPSS
310 320 330 340 350
QFSLLIRPVV PNFNADVCMD PEPIVRIVGR NGLCVDVRDG RFHNGNAIQL
360 370 380 390 400
WPCKSNTDAN QLWTLKRDNT IRSNGKCLTT YGYSPGVYVM IYDCNTAATD
410 420 430 440 450
ATRWQIWDNG TIINPRSSLV LAATSGNSGT TLTVQTNIYA VSQGWLPTNN
460 470 480 490 500
TQPFVTTIVG LYGLCLQANS GQVWIEDCSS EKAEQQWALY ADGSIRPQQN
510 520 530 540 550
RDNCLTSDSN IRETVVKILS CGPASSGQRW MFKNDGTILN LYSGLVLDVR
560 570
ASDPSLKQII LYPLHGDPNQ IWLPLF
Length:576
Mass (Da):64,091
Last modified:August 13, 1987 - v1
Checksum:iC14C4B77A8B5470D
GO

Sequence cautioni

The sequence described in Ref. 4 differs from that shown. High number of conflicts with the sequence translated from DNA.Curated
The sequence described in Ref. 5 differs from that shown. High number of conflicts with the sequence translated from DNA.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti76E → D in CAA26230 (PubMed:3838723).Curated1
Sequence conflicti551A → R in CAA26230 (PubMed:3838723).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03179 Genomic DNA. Translation: CAA26939.1.
X52908 Genomic DNA. Translation: CAA37095.1.
X02388 mRNA. Translation: CAA26230.1.
PIRiA24041. RLCSD.
RefSeqiNP_001310630.1. NM_001323701.1.

Genome annotation databases

GeneIDi8261245.
KEGGircu:8261245.

Cross-referencesi

Web resourcesi

Protein Spotlight

Baneful beans - Issue 31 of February 2003

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03179 Genomic DNA. Translation: CAA26939.1.
X52908 Genomic DNA. Translation: CAA37095.1.
X02388 mRNA. Translation: CAA26230.1.
PIRiA24041. RLCSD.
RefSeqiNP_001310630.1. NM_001323701.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BR5X-ray2.50A36-302[»]
1BR6X-ray2.30A36-302[»]
1IFSX-ray2.00A38-298[»]
1IFTX-ray1.80A38-298[»]
1IFUX-ray2.40A38-298[»]
1IL3X-ray2.80A36-302[»]
1IL4X-ray2.60A36-302[»]
1IL5X-ray2.80A/B36-302[»]
1IL9X-ray3.10A36-302[»]
1J1MX-ray1.50A36-302[»]
1OBSX-ray2.20A36-302[»]
1OBTX-ray2.80A36-302[»]
1RTCX-ray2.30A36-302[»]
1UQ4X-ray1.90A40-302[»]
1UQ5X-ray1.40A40-302[»]
2AAIX-ray2.50A36-302[»]
B315-576[»]
2P8NX-ray1.94A36-302[»]
2PJOX-ray1.80A36-302[»]
2R2XX-ray2.40A36-302[»]
2R3DX-ray2.09A36-302[»]
2VC3X-ray1.60A36-302[»]
2VC4X-ray1.39A36-302[»]
3BJGX-ray2.14A36-302[»]
3EJ5X-ray2.50X40-296[»]
3HIOX-ray2.00A36-302[»]
3LC9X-ray2.28A36-233[»]
3MK9X-ray2.08A36-233[»]
3PX8X-ray1.29X39-296[»]
3PX9X-ray1.89X39-296[»]
3RTIX-ray2.80A36-302[»]
B315-576[»]
3RTJX-ray3.00A36-302[»]
B315-576[»]
3SRPX-ray2.14A36-302[»]
4ESIX-ray1.87A36-302[»]
4HUOX-ray1.52X36-302[»]
4HUPX-ray1.70X36-302[»]
4HV3X-ray1.54A36-302[»]
4HV7X-ray1.87X36-302[»]
4IMVX-ray2.25A36-233[»]
4KUCX-ray2.79A/I36-302[»]
4LGPX-ray2.40A/C36-296[»]
4LGRX-ray1.65A40-294[»]
4LGSX-ray2.70A39-301[»]
4LHJX-ray1.80A39-297[»]
4LHQX-ray2.30A/C39-298[»]
4MX1X-ray1.59A36-302[»]
4MX5X-ray1.52X36-302[»]
4Q2VX-ray2.20A36-302[»]
4Z9KX-ray1.50A39-296[»]
5DDZX-ray1.50A36-302[»]
5E1HX-ray2.03A40-297[»]
5SV3X-ray2.73B/D36-233[»]
ProteinModelPortaliP02879.
SMRiP02879.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1022023. 2 interactors.
DIPiDIP-46421N.
IntActiP02879. 2 interactors.
MINTiMINT-8391414.

Chemistry databases

BindingDBiP02879.
ChEMBLiCHEMBL4756.

Protein family/group databases

Allergomei2803. Ric c RIP.
CAZyiCBM13. Carbohydrate-Binding Module Family 13.

PTM databases

UniCarbKBiP02879.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi8261245.
KEGGircu:8261245.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18749.
BRENDAi3.2.2.22. 1204.

Miscellaneous databases

EvolutionaryTraceiP02879.
PROiP02879.

Family and domain databases

Gene3Di3.40.420.10. 1 hit.
4.10.470.10. 1 hit.
InterProiIPR001574. Ribosome_inactivat_prot.
IPR017988. Ribosome_inactivat_prot_CS.
IPR016138. Ribosome_inactivat_prot_sub1.
IPR016139. Ribosome_inactivat_prot_sub2.
IPR017989. Ribosome_inactivat_prot_subgr.
IPR000772. Ricin_B_lectin.
[Graphical view]
PfamiPF00652. Ricin_B_lectin. 2 hits.
PF00161. RIP. 1 hit.
[Graphical view]
PRINTSiPR00396. SHIGARICIN.
SMARTiSM00458. RICIN. 2 hits.
[Graphical view]
SUPFAMiSSF50370. SSF50370. 2 hits.
SSF56371. SSF56371. 1 hit.
PROSITEiPS50231. RICIN_B_LECTIN. 2 hits.
PS00275. SHIGA_RICIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRICI_RICCO
AccessioniPrimary (citable) accession number: P02879
Secondary accession number(s): P02880
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: August 13, 1987
Last modified: November 30, 2016
This is version 163 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.