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Protein

Nigrin b

Gene
N/A
Organism
Sambucus nigra (European elder)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Non-toxic type 2 RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA.
The B chain is a galactose-specific lectin that facilitates the binding of nigrin b to the cell membrane that precedes endocytosis.

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei188 – 1881By similarity

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

Names & Taxonomyi

Protein namesi
Recommended name:
Nigrin b
Alternative name(s):
Agglutinin V
SNAV
Cleaved into the following 2 chains:
Alternative name(s):
rRNA N-glycosidase
OrganismiSambucus nigra (European elder)
Taxonomic identifieri4202 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridscampanulidsDipsacalesAdoxaceaeSambucus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 25251 PublicationAdd
BLAST
Chaini26 – 297272Nigrin b A chainPRO_0000030744Add
BLAST
Chaini298 – 563266Nigrin b B chainPRO_0000030745Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi221 – 2211N-linked (GlcNAc...)Sequence analysis
Disulfide bondi274 ↔ 302Interchain (between B and A chains)PROSITE-ProRule annotation
Disulfide bondi319 ↔ 338PROSITE-ProRule annotation
Disulfide bondi360 ↔ 377PROSITE-ProRule annotation
Glycosylationi368 – 3681N-linked (GlcNAc...)Sequence analysis
Glycosylationi376 – 3761N-linked (GlcNAc...)Sequence analysis
Disulfide bondi448 ↔ 463PROSITE-ProRule annotation
Glycosylationi483 – 4831N-linked (GlcNAc...)Sequence analysis
Disulfide bondi489 ↔ 506PROSITE-ProRule annotation
Glycosylationi537 – 5371N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Interactioni

Subunit structurei

Disulfide-linked dimer of A and B chains.

Structurei

Secondary structure

1
563
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi308 – 3136Combined sources
Helixi315 – 3173Combined sources
Beta strandi319 – 3224Combined sources
Helixi323 – 3253Combined sources
Beta strandi332 – 3365Combined sources
Helixi342 – 3443Combined sources
Beta strandi346 – 3483Combined sources
Beta strandi354 – 3563Combined sources
Beta strandi359 – 3679Combined sources
Beta strandi371 – 3755Combined sources
Turni377 – 3793Combined sources
Helixi382 – 3843Combined sources
Turni398 – 4003Combined sources
Beta strandi403 – 4053Combined sources
Beta strandi407 – 4104Combined sources
Beta strandi416 – 4183Combined sources
Helixi424 – 4263Combined sources
Beta strandi429 – 4324Combined sources
Beta strandi437 – 4426Combined sources
Helixi444 – 4463Combined sources
Beta strandi448 – 4503Combined sources
Beta strandi459 – 4613Combined sources
Helixi468 – 4703Combined sources
Beta strandi472 – 4743Combined sources
Beta strandi480 – 4823Combined sources
Beta strandi485 – 49612Combined sources
Beta strandi500 – 5056Combined sources
Helixi510 – 5123Combined sources
Turni525 – 5273Combined sources
Beta strandi530 – 5334Combined sources
Helixi534 – 5363Combined sources
Helixi538 – 5403Combined sources
Beta strandi543 – 5464Combined sources
Helixi552 – 5543Combined sources
Beta strandi557 – 5604Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3C9ZX-ray1.35A306-563[»]
3CA0X-ray1.95A306-563[»]
3CA1X-ray1.55A306-563[»]
3CA3X-ray1.55A306-563[»]
3CA4X-ray1.55A306-563[»]
3CA5X-ray1.55A306-563[»]
3CA6X-ray1.40A306-563[»]
3CAHX-ray1.55A306-563[»]
ProteinModelPortaliP33183.
SMRiP33183. Positions 26-274, 299-560.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP33183.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini305 – 431127Ricin B-type lectin 1PROSITE-ProRule annotationAdd
BLAST
Repeati316 – 356411-alphaAdd
BLAST
Repeati357 – 397411-betaAdd
BLAST
Repeati400 – 432331-gammaAdd
BLAST
Domaini434 – 559126Ricin B-type lectin 2PROSITE-ProRule annotationAdd
BLAST
Repeati445 – 482382-alphaAdd
BLAST
Repeati486 – 524392-betaAdd
BLAST
Repeati527 – 554282-gammaAdd
BLAST

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.

P33183-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRVVAAAMLY FYIVVLAICS VGIQGIDYPS VSFNLDGAKS ATYRDFLSNL
60 70 80 90 100
RKTVATGTYE VNGLPVLRRE SEVQVKSRFV LVPLTNYNGN TVTLAVDVTN
110 120 130 140 150
LYVVAFSGNA NSYFFKDATE VQKSNLFVGT KQNTLSFTGN YDNLETAANT
160 170 180 190 200
RRESIELGPS PLDGAITSLY HGDSVARSLL VVIQMVSEAA RFRYIEQEVR
210 220 230 240 250
RSLQQATSFT PNALMLSMEN NWSSMSLEIQ QAGNNVSPFF GTVQLLNYDH
260 270 280 290 300
THRLVDNFEE LYKITGIAIL LFRCSSPSND NAIRMPLDLA GEDNKYNDGE
310 320 330 340 350
TCTLRTSFTR NIVGRDGLCV DVRNGYDTDG TPLQLWPCGT QRNQRWTFDS
360 370 380 390 400
DDTIRSMGKC MTANGLNNGS NIVIFNCSTA AENAIKWEVP IDGSIINPSS
410 420 430 440 450
GLVMTAPRAA SRTILLLEDN IYAASQGWTV TNNVKPIVAS IVGYKEMCLQ
460 470 480 490 500
SNGENNGVWM EDCEATSLQQ QWALYGDRTI RVNSTRGLCV TTNGYNSKDL
510 520 530 540 550
IIILKCQGLP SQRWFFNSDG AIVNPKSRHV MDVRASNVSL REIIIFPATG
560
NPNQQWVTQV LPS
Length:563
Mass (Da):62,300
Last modified:December 5, 2001 - v2
Checksum:iF250CBE24621BF14
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti39 – 391K → V AA sequence (PubMed:8400135).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U41299 mRNA. Translation: AAB39475.1.
PIRiS37382.
S37383.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U41299 mRNA. Translation: AAB39475.1.
PIRiS37382.
S37383.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3C9ZX-ray1.35A306-563[»]
3CA0X-ray1.95A306-563[»]
3CA1X-ray1.55A306-563[»]
3CA3X-ray1.55A306-563[»]
3CA4X-ray1.55A306-563[»]
3CA5X-ray1.55A306-563[»]
3CA6X-ray1.40A306-563[»]
3CAHX-ray1.55A306-563[»]
ProteinModelPortaliP33183.
SMRiP33183. Positions 26-274, 299-560.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP33183.

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...

Publicationsi

  1. "Characterization and molecular cloning of Sambucus nigra agglutinin V (nigrin b), a GalNAc-specific type-2 ribosome-inactivating protein from the bark of elderberry (Sambucus nigra)."
    Van Damme E.J., Barre A., Rouge P., Van Leuven F., Peumans W.J.
    Eur. J. Biochem. 237:505-513(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Bark.
  2. "Isolation and partial characterization of nigrin b, a non-toxic novel type 2 ribosome-inactivating protein from the bark of Sambucus nigra L."
    Girbes T., Citores L., Ferreras J.M., Rojo M.A., Iglesias R., Munoz R., Arias F.J., Calonge M., Garcia J.R., Mendez E.
    Plant Mol. Biol. 22:1181-1186(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 26-49 AND 298-321.
    Tissue: Bark.

Entry informationi

Entry nameiNIGB_SAMNI
AccessioniPrimary (citable) accession number: P33183
Secondary accession number(s): P33184, P93542
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: December 5, 2001
Last modified: October 14, 2015
This is version 90 of the entry and version 2 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. 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.