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Protein

Neuropilin-1

Gene

Nrp1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Receptor involved in the development of the cardiovascular system, in angiogenesis, in the formation of certain neuronal circuits and in organogenesis outside the nervous system. It mediates the chemorepulsant activity of semaphorins. It binds to semaphorin 3A, the PLGF-2 isoform of PGF, the VEGF-165 isoform of VEGF and VEGF-B. Coexpression with KDR results in increased VEGF-165 binding to KDR as well as increased chemotaxis. It may regulate VEGF-induced angiogenesis (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi195 – 1951CalciumBy similarity
Metal bindingi209 – 2091CalciumBy similarity
Metal bindingi250 – 2501CalciumBy similarity

GO - Molecular functioni

  • heparin binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • semaphorin receptor activity Source: RGD
  • vascular endothelial growth factor-activated receptor activity Source: RGD

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Receptor

Keywords - Biological processi

Angiogenesis, Differentiation, Neurogenesis

Keywords - Ligandi

Calcium, Heparin-binding, Metal-binding

Enzyme and pathway databases

ReactomeiR-RNO-194306. Neurophilin interactions with VEGF and VEGFR.
R-RNO-399954. Sema3A PAK dependent Axon repulsion.
R-RNO-399955. SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion.
R-RNO-399956. CRMPs in Sema3A signaling.
R-RNO-445144. Signal transduction by L1.

Names & Taxonomyi

Protein namesi
Recommended name:
Neuropilin-1
Alternative name(s):
Vascular endothelial cell growth factor 165 receptor
CD_antigen: CD304
Gene namesi
Name:Nrp1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 19

Organism-specific databases

RGDi621588. Nrp1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini22 – 855834ExtracellularSequence analysisAdd
BLAST
Transmembranei856 – 88025HelicalSequence analysisAdd
BLAST
Topological domaini881 – 92242CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • axon Source: RGD
  • cell surface Source: RGD
  • cytosol Source: Ensembl
  • early endosome Source: Ensembl
  • extracellular space Source: Ensembl
  • focal adhesion Source: Ensembl
  • growth cone Source: RGD
  • integral component of membrane Source: RGD
  • neurofilament Source: Ensembl
  • neuronal cell body Source: RGD
  • plasma membrane Source: Ensembl
  • sorting endosome Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL3309098.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2121Sequence analysisAdd
BLAST
Chaini22 – 922901Neuropilin-1PRO_0000021861Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi27 ↔ 541 Publication
Disulfide bondi82 ↔ 1041 Publication
Disulfide bondi147 ↔ 173By similarity
Glycosylationi150 – 1501N-linked (GlcNAc...)Sequence analysis
Disulfide bondi206 ↔ 228By similarity
Glycosylationi261 – 2611N-linked (GlcNAc...)Sequence analysis
Disulfide bondi275 ↔ 4241 Publication
Glycosylationi300 – 3001N-linked (GlcNAc...)Sequence analysis
Disulfide bondi431 ↔ 5831 Publication
Glycosylationi522 – 5221N-linked (GlcNAc...)Sequence analysis
Glycosylationi612 – 6121O-linked (Xyl...) (chondroitin sulfate); alternateBy similarity
Glycosylationi612 – 6121O-linked (Xyl...) (heparan sulfate); alternateBy similarity
Glycosylationi841 – 8411N-linked (GlcNAc...)Sequence analysis
Modified residuei893 – 8931PhosphoserineBy similarity

Keywords - PTMi

Disulfide bond, Glycoprotein, Heparan sulfate, Phosphoprotein, Proteoglycan

Proteomic databases

PaxDbiQ9QWJ9.
PRIDEiQ9QWJ9.

PTM databases

iPTMnetiQ9QWJ9.
PhosphoSiteiQ9QWJ9.
SwissPalmiQ9QWJ9.

Expressioni

Tissue specificityi

Found in the embryonic nervous system.

Gene expression databases

GenevisibleiQ9QWJ9. RN.

Interactioni

Subunit structurei

Homodimer, and heterodimer with NRP2. Binds PLXNB1. Interacts with FER (By similarity).By similarity

Protein-protein interaction databases

BioGridi251596. 1 interaction.
DIPiDIP-44935N.
IntActiQ9QWJ9. 1 interaction.
MINTiMINT-1542085.
STRINGi10116.ENSRNOP00000014492.

Structurei

Secondary structure

1
922
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni281 – 2833Combined sources
Helixi288 – 2903Combined sources
Beta strandi291 – 2944Combined sources
Helixi299 – 3013Combined sources
Helixi303 – 3053Combined sources
Beta strandi326 – 34217Combined sources
Turni347 – 3493Combined sources
Beta strandi352 – 36817Combined sources
Beta strandi385 – 3895Combined sources
Beta strandi391 – 41424Combined sources
Beta strandi417 – 4248Combined sources
Helixi426 – 4283Combined sources
Beta strandi429 – 4313Combined sources
Beta strandi432 – 4343Combined sources
Turni437 – 4393Combined sources
Helixi442 – 4443Combined sources
Beta strandi445 – 4495Combined sources
Helixi459 – 4624Combined sources
Turni464 – 4663Combined sources
Beta strandi467 – 4693Combined sources
Beta strandi471 – 4733Combined sources
Beta strandi485 – 50117Combined sources
Beta strandi503 – 5053Combined sources
Beta strandi508 – 5103Combined sources
Beta strandi512 – 52514Combined sources
Beta strandi534 – 5374Combined sources
Beta strandi544 – 5474Combined sources
Beta strandi550 – 57021Combined sources
Beta strandi573 – 58311Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ORXX-ray2.40A273-586[»]
2ORZX-ray2.15A273-586[»]
ProteinModelPortaliQ9QWJ9.
SMRiQ9QWJ9. Positions 145-586.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9QWJ9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini27 – 141115CUB 1PROSITE-ProRule annotationAdd
BLAST
Domaini147 – 265119CUB 2PROSITE-ProRule annotationAdd
BLAST
Domaini275 – 424150F5/8 type C 1PROSITE-ProRule annotationAdd
BLAST
Domaini431 – 583153F5/8 type C 2PROSITE-ProRule annotationAdd
BLAST
Domaini645 – 811167MAMPROSITE-ProRule annotationAdd
BLAST

Domaini

The tandem CUB domains mediate binding to semaphorin, while the tandem F5/8 domains are responsible for heparin and VEGF binding.By similarity

Sequence similaritiesi

Belongs to the neuropilin family.Curated
Contains 2 CUB domains.PROSITE-ProRule annotation
Contains 2 F5/8 type C domains.PROSITE-ProRule annotation
Contains 1 MAM domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IE8T. Eukaryota.
ENOG410YRBE. LUCA.
GeneTreeiENSGT00760000119073.
HOGENOMiHOG000039978.
HOVERGENiHBG000502.
InParanoidiQ9QWJ9.
KOiK06724.
OMAiCWHNGMS.
OrthoDBiEOG7ZWD1D.
PhylomeDBiQ9QWJ9.
TreeFamiTF316506.

Family and domain databases

Gene3Di2.60.120.260. 2 hits.
2.60.120.290. 2 hits.
InterProiIPR013320. ConA-like_dom.
IPR000859. CUB_dom.
IPR000421. FA58C.
IPR008979. Galactose-bd-like.
IPR000998. MAM_dom.
IPR014648. Neuropilin.
IPR022579. Neuropilin_C.
IPR027146. NRP1.
[Graphical view]
PANTHERiPTHR10127:SF654. PTHR10127:SF654. 1 hit.
PfamiPF00431. CUB. 2 hits.
PF11980. DUF3481. 1 hit.
PF00754. F5_F8_type_C. 2 hits.
PF00629. MAM. 1 hit.
[Graphical view]
PIRSFiPIRSF036960. Neuropilin. 1 hit.
PRINTSiPR00020. MAMDOMAIN.
SMARTiSM00042. CUB. 2 hits.
SM00231. FA58C. 2 hits.
SM00137. MAM. 1 hit.
[Graphical view]
SUPFAMiSSF49785. SSF49785. 2 hits.
SSF49854. SSF49854. 2 hits.
SSF49899. SSF49899. 1 hit.
PROSITEiPS01180. CUB. 2 hits.
PS01285. FA58C_1. 2 hits.
PS01286. FA58C_2. 2 hits.
PS50022. FA58C_3. 2 hits.
PS00740. MAM_1. 1 hit.
PS50060. MAM_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9QWJ9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERGLPLLCA TLALALALAG AFRSDKCGGT IKIENPGYLT SPGYPHSYHP
60 70 80 90 100
SEKCEWLIQA PEPYQRIMIN FNPHFDLEDR DCKYDYVEVI DGENEGGRLW
110 120 130 140 150
GKFCGKIAPS PVVSSGPFLF IKFVSDYETH GAGFSIRYEI FKRGPECSQN
160 170 180 190 200
YTAPTGVIKS PGFPEKYPNS LECTYIIFAP KMSEIILEFE SFDLEQDSNP
210 220 230 240 250
PGGVFCRYDR LEIWDGFPEV GPHIGRYCGQ KTPGRIRSSS GILSMVFYTD
260 270 280 290 300
SAIAKEGFSA NYSVLQSSIS EDFKCMEALG MESGEIHSDQ ITASSQYGTN
310 320 330 340 350
WSVERSRLNY PENGWTPGED SYREWIQVDL GLLRFVTAVG TQGAISKETK
360 370 380 390 400
KKYYVKTYRV DISSNGEDWI TLKEGNKAII FQGNTNPTDV VFGVFPKPLI
410 420 430 440 450
TRFVRIKPAS WETGISMRFE VYGCKITDYP CSGMLGMVSG LISDSQITAS
460 470 480 490 500
NQGDRNWMPE NIRLVTSRTG WALPPSPHPY INEWLQVDLG DEKIVRGVII
510 520 530 540 550
QGGKHRENKV FMRKFKIAYS NNGSDWKMIM DDSKRKAKSF EGNNNYDTPE
560 570 580 590 600
LRAFTPLSTR FIRIYPERAT HSGLGLRMEL LGCEVEVPTA GPTTPNGNPV
610 620 630 640 650
DECDDDQANC HSGTGDDFQL TGGTTVLATE KPTIIDSTIQ SEFPTYGFNC
660 670 680 690 700
EFGWGSHKTF CHWEHDSHAQ LRWRVLTSKT GPIQDHTGDG NFIYSQADEN
710 720 730 740 750
QKGKVARLVS PVVYSQSSAH CMTFWYHMSG SHVGTLRVKL HYQKPEEYDQ
760 770 780 790 800
LVWMVVGHQG DHWKEGRVLL HKSLKLYQVI FEGEIGKGNL GGIAVDDISI
810 820 830 840 850
NNHIPQEDCA KPTDLDKKNT EIKIDETGST PGYEEGKGDK NISRKPGNVL
860 870 880 890 900
KTLDPILITI IAMSALGVLL GAVCGVVLYC ACWHNGMSER NLSALENYNF
910 920
ELVDGVKLKK DKLNPQSNYS EA
Length:922
Mass (Da):103,082
Last modified:May 1, 2000 - v1
Checksum:iCC6F82AD098B0F2E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF016296 mRNA. Translation: AAC53337.1.
BC085689 mRNA. Translation: AAH85689.1.
RefSeqiNP_659566.1. NM_145098.2.
XP_006255887.1. XM_006255825.2.
XP_008770820.1. XM_008772598.1.
UniGeneiRn.10815.
Rn.165344.

Genome annotation databases

EnsembliENSRNOT00000014492; ENSRNOP00000014492; ENSRNOG00000010744.
ENSRNOT00000080465; ENSRNOP00000075034; ENSRNOG00000010744.
GeneIDi246331.
KEGGirno:246331.
UCSCiRGD:621588. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF016296 mRNA. Translation: AAC53337.1.
BC085689 mRNA. Translation: AAH85689.1.
RefSeqiNP_659566.1. NM_145098.2.
XP_006255887.1. XM_006255825.2.
XP_008770820.1. XM_008772598.1.
UniGeneiRn.10815.
Rn.165344.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ORXX-ray2.40A273-586[»]
2ORZX-ray2.15A273-586[»]
ProteinModelPortaliQ9QWJ9.
SMRiQ9QWJ9. Positions 145-586.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi251596. 1 interaction.
DIPiDIP-44935N.
IntActiQ9QWJ9. 1 interaction.
MINTiMINT-1542085.
STRINGi10116.ENSRNOP00000014492.

Chemistry

ChEMBLiCHEMBL3309098.

PTM databases

iPTMnetiQ9QWJ9.
PhosphoSiteiQ9QWJ9.
SwissPalmiQ9QWJ9.

Proteomic databases

PaxDbiQ9QWJ9.
PRIDEiQ9QWJ9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000014492; ENSRNOP00000014492; ENSRNOG00000010744.
ENSRNOT00000080465; ENSRNOP00000075034; ENSRNOG00000010744.
GeneIDi246331.
KEGGirno:246331.
UCSCiRGD:621588. rat.

Organism-specific databases

CTDi8829.
RGDi621588. Nrp1.

Phylogenomic databases

eggNOGiENOG410IE8T. Eukaryota.
ENOG410YRBE. LUCA.
GeneTreeiENSGT00760000119073.
HOGENOMiHOG000039978.
HOVERGENiHBG000502.
InParanoidiQ9QWJ9.
KOiK06724.
OMAiCWHNGMS.
OrthoDBiEOG7ZWD1D.
PhylomeDBiQ9QWJ9.
TreeFamiTF316506.

Enzyme and pathway databases

ReactomeiR-RNO-194306. Neurophilin interactions with VEGF and VEGFR.
R-RNO-399954. Sema3A PAK dependent Axon repulsion.
R-RNO-399955. SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion.
R-RNO-399956. CRMPs in Sema3A signaling.
R-RNO-445144. Signal transduction by L1.

Miscellaneous databases

EvolutionaryTraceiQ9QWJ9.
PROiQ9QWJ9.

Gene expression databases

GenevisibleiQ9QWJ9. RN.

Family and domain databases

Gene3Di2.60.120.260. 2 hits.
2.60.120.290. 2 hits.
InterProiIPR013320. ConA-like_dom.
IPR000859. CUB_dom.
IPR000421. FA58C.
IPR008979. Galactose-bd-like.
IPR000998. MAM_dom.
IPR014648. Neuropilin.
IPR022579. Neuropilin_C.
IPR027146. NRP1.
[Graphical view]
PANTHERiPTHR10127:SF654. PTHR10127:SF654. 1 hit.
PfamiPF00431. CUB. 2 hits.
PF11980. DUF3481. 1 hit.
PF00754. F5_F8_type_C. 2 hits.
PF00629. MAM. 1 hit.
[Graphical view]
PIRSFiPIRSF036960. Neuropilin. 1 hit.
PRINTSiPR00020. MAMDOMAIN.
SMARTiSM00042. CUB. 2 hits.
SM00231. FA58C. 2 hits.
SM00137. MAM. 1 hit.
[Graphical view]
SUPFAMiSSF49785. SSF49785. 2 hits.
SSF49854. SSF49854. 2 hits.
SSF49899. SSF49899. 1 hit.
PROSITEiPS01180. CUB. 2 hits.
PS01285. FA58C_1. 2 hits.
PS01286. FA58C_2. 2 hits.
PS50022. FA58C_3. 2 hits.
PS00740. MAM_1. 1 hit.
PS50060. MAM_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Sprague-Dawley.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Kidney.
  3. Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 273-586 IN COMPLEX WITH VEGF FRAGMENT, HEPARIN-BINDING, DISULFIDE BONDS.

Entry informationi

Entry nameiNRP1_RAT
AccessioniPrimary (citable) accession number: Q9QWJ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: May 1, 2000
Last modified: June 8, 2016
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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.