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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)DescriptionActionsGraphical viewLength
Active sitei188By similarity1

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)DescriptionActionsGraphical viewLength
Signal peptidei1 – 251 PublicationAdd BLAST25
ChainiPRO_000003074426 – 297Nigrin b A chainAdd BLAST272
ChainiPRO_0000030745298 – 563Nigrin b B chainAdd BLAST266

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi221N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi274 ↔ 302Interchain (between B and A chains)PROSITE-ProRule annotation
Disulfide bondi319 ↔ 338PROSITE-ProRule annotation
Disulfide bondi360 ↔ 377PROSITE-ProRule annotation
Glycosylationi368N-linked (GlcNAc...)Sequence analysis1
Glycosylationi376N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi448 ↔ 463PROSITE-ProRule annotation
Glycosylationi483N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi489 ↔ 506PROSITE-ProRule annotation
Glycosylationi537N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Disulfide bond, Glycoprotein

Interactioni

Subunit structurei

Disulfide-linked dimer of A and B chains.

Structurei

Secondary structure

1563
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi308 – 313Combined sources6
Helixi315 – 317Combined sources3
Beta strandi319 – 322Combined sources4
Helixi323 – 325Combined sources3
Beta strandi332 – 336Combined sources5
Helixi342 – 344Combined sources3
Beta strandi346 – 348Combined sources3
Beta strandi354 – 356Combined sources3
Beta strandi359 – 367Combined sources9
Beta strandi371 – 375Combined sources5
Turni377 – 379Combined sources3
Helixi382 – 384Combined sources3
Turni398 – 400Combined sources3
Beta strandi403 – 405Combined sources3
Beta strandi407 – 410Combined sources4
Beta strandi416 – 418Combined sources3
Helixi424 – 426Combined sources3
Beta strandi429 – 432Combined sources4
Beta strandi437 – 442Combined sources6
Helixi444 – 446Combined sources3
Beta strandi448 – 450Combined sources3
Beta strandi459 – 461Combined sources3
Helixi468 – 470Combined sources3
Beta strandi472 – 474Combined sources3
Beta strandi480 – 482Combined sources3
Beta strandi485 – 496Combined sources12
Beta strandi500 – 505Combined sources6
Helixi510 – 512Combined sources3
Turni525 – 527Combined sources3
Beta strandi530 – 533Combined sources4
Helixi534 – 536Combined sources3
Helixi538 – 540Combined sources3
Beta strandi543 – 546Combined sources4
Helixi552 – 554Combined sources3
Beta strandi557 – 560Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP33183.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini305 – 431Ricin B-type lectin 1PROSITE-ProRule annotationAdd BLAST127
Repeati316 – 3561-alphaAdd BLAST41
Repeati357 – 3971-betaAdd BLAST41
Repeati400 – 4321-gammaAdd BLAST33
Domaini434 – 559Ricin B-type lectin 2PROSITE-ProRule annotationAdd BLAST126
Repeati445 – 4822-alphaAdd BLAST38
Repeati486 – 5242-betaAdd BLAST39
Repeati527 – 5542-gammaAdd BLAST28

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)DescriptionActionsGraphical viewLength
Sequence conflicti39K → V AA sequence (PubMed:8400135).Curated1

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
PDB 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.
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...

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: November 2, 2016
This is version 92 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.