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Protein

RGM domain family member B

Gene

RGMB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Member of the repulsive guidance molecule (RGM) family that contributes to the patterning of the developing nervous system (By similarity). Acts as a bone morphogenetic protein (BMP) coreceptor that potentiates BMP signaling (By similarity). Promotes neuronal adhesion (By similarity). May inhibit neurite outgrowth.By similarity1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-HSA-373752. Netrin-1 signaling.

Names & Taxonomyi

Protein namesi
Recommended name:
RGM domain family member B
Alternative name(s):
DRG11-responsive axonal guidance and outgrowth of neurite
Short name:
DRAGON
Gene namesi
Name:RGMB
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:26896. RGMB.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi186 – 1861A → R: Severely impairs interaction with NEO1. 1 Publication
Mutagenesisi206 – 2061P → N: Introduces a N-linked glycan; changes interaction with NEO1 from a 2:2 to a 1:1 stoichiometry. 1 Publication

Organism-specific databases

PharmGKBiPA134868641.

Polymorphism and mutation databases

BioMutaiRGMB.
DMDMi327478562.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 4545Sequence analysisAdd
BLAST
Chaini46 – 413368RGM domain family member BPRO_0000030394Add
BLAST
Propeptidei414 – 43724Removed in mature formSequence analysisPRO_0000030395Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi120 – 1201N-linked (GlcNAc...)Sequence analysis
Disulfide bondi139 ↔ 2261 Publication
Disulfide bondi163 ↔ 3121 Publication
Glycosylationi383 – 3831N-linked (GlcNAc...)Sequence analysis
Lipidationi413 – 4131GPI-anchor amidated asparagineSequence analysis

Post-translational modificationi

GPI-anchored.By similarity
Autocatalytically cleaved at low pH; the two chains remain linked via two disulfide bonds.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei168 – 1692Cleavage; by autolysis

Keywords - PTMi

Autocatalytic cleavage, Disulfide bond, Glycoprotein, GPI-anchor, Lipoprotein

Proteomic databases

EPDiQ6NW40.
PaxDbiQ6NW40.
PeptideAtlasiQ6NW40.
PRIDEiQ6NW40.

PTM databases

iPTMnetiQ6NW40.

Expressioni

Gene expression databases

BgeeiQ6NW40.
CleanExiHS_RGMB.
ExpressionAtlasiQ6NW40. baseline and differential.
GenevisibleiQ6NW40. HS.

Organism-specific databases

HPAiHPA016993.

Interactioni

Subunit structurei

Homooligomer (By similarity). Interacts with DRGX (By similarity). Interacts with BMP2 and BMP4 (By similarity). Interacts with the BMP type I receptors ACVR1, BMPR1A and BMPR1B and with the BMP type II receptor ACVR2B (By similarity). The functional complex with its receptor NEO1/neogenin appears to be a heterotetramer with a 2:2 stoichiometry, RGM molecules acting as staples that brings two NEO1 receptors together without interacting themselves, this arrangement leads to activation of downstream signaling via RhoA.By similarity1 Publication

GO - Molecular functioni

Protein-protein interaction databases

DIPiDIP-61607N.
STRINGi9606.ENSP00000308219.

Structurei

Secondary structure

1
437
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi56 – 6712Combined sources
Helixi84 – 9512Combined sources
Turni96 – 1016Combined sources
Helixi103 – 11715Combined sources
Turni118 – 1203Combined sources
Beta strandi160 – 1667Combined sources
Beta strandi170 – 1723Combined sources
Beta strandi178 – 1803Combined sources
Beta strandi185 – 20521Combined sources
Beta strandi211 – 22010Combined sources
Turni224 – 2263Combined sources
Beta strandi230 – 2356Combined sources
Beta strandi248 – 2547Combined sources
Beta strandi257 – 2615Combined sources
Turni264 – 2674Combined sources
Beta strandi269 – 2735Combined sources
Helixi274 – 2763Combined sources
Beta strandi278 – 2858Combined sources
Beta strandi288 – 2969Combined sources
Helixi297 – 3004Combined sources
Helixi311 – 3144Combined sources
Helixi318 – 3203Combined sources
Helixi326 – 3338Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BQ6X-ray2.30C/E50-168[»]
D/F169-410[»]
4BQ7X-ray6.60C/E50-168[»]
D/F169-410[»]
4BQ8X-ray2.80B50-168[»]
C169-410[»]
4UHZX-ray2.85B53-136[»]
4UI0X-ray2.80C53-136[»]
4UI2X-ray3.15C50-168[»]
D169-410[»]
ProteinModelPortaliQ6NW40.
SMRiQ6NW40. Positions 52-324.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IFAH. Eukaryota.
ENOG410ZT7E. LUCA.
GeneTreeiENSGT00390000008488.
HOGENOMiHOG000013072.
HOVERGENiHBG057627.
InParanoidiQ6NW40.
KOiK06847.
PhylomeDBiQ6NW40.

Family and domain databases

InterProiIPR033608. DRAGON.
IPR009496. RGM_C.
IPR010536. RGM_N.
[Graphical view]
PANTHERiPTHR31428:SF5. PTHR31428:SF5. 1 hit.
PfamiPF06534. RGM_C. 1 hit.
PF06535. RGM_N. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q6NW40-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGLRAAPSSA AAAAAEVEQR RSPGLCPPPL ELLLLLLFSL GLLHAGDCQQ
60 70 80 90 100
PAQCRIQKCT TDFVSLTSHL NSAVDGFDSE FCKALRAYAG CTQRTSKACR
110 120 130 140 150
GNLVYHSAVL GISDLMSQRN CSKDGPTSST NPEVTHDPCN YHSHAGAREH
160 170 180 190 200
RRGDQNPPSY LFCGLFGDPH LRTFKDNFQT CKVEGAWPLI DNNYLSVQVT
210 220 230 240 250
NVPVVPGSSA TATNKITIIF KAHHECTDQK VYQAVTDDLP AAFVDGTTSG
260 270 280 290 300
GDSDAKSLRI VERESGHYVE MHARYIGTTV FVRQVGRYLT LAIRMPEDLA
310 320 330 340 350
MSYEESQDLQ LCVNGCPLSE RIDDGQGQVS AILGHSLPRT SLVQAWPGYT
360 370 380 390 400
LETANTQCHE KMPVKDIYFQ SCVFDLLTTG DANFTAAAHS ALEDVEALHP
410 420 430
RKERWHIFPS SGNGTPRGGS DLSVSLGLTC LILIVFL
Length:437
Mass (Da):47,547
Last modified:April 5, 2011 - v3
Checksum:i48C26166E68DCE5F
GO

Sequence cautioni

The sequence AAH67736.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence BAC11268.1 differs from that shown.Intron retention.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti22 – 221S → R in AAH67736 (PubMed:15489334).Curated
Sequence conflicti225 – 2251E → G in AAH67736 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK074887 mRNA. Translation: BAC11268.1. Sequence problems.
AC008522 Genomic DNA. No translation available.
BC067736 mRNA. Translation: AAH67736.1. Different initiation.
RefSeqiNP_001012779.2. NM_001012761.2.
UniGeneiHs.526902.

Genome annotation databases

EnsembliENST00000513185; ENSP00000423256; ENSG00000174136.
GeneIDi285704.
KEGGihsa:285704.
UCSCiuc063frq.1. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK074887 mRNA. Translation: BAC11268.1. Sequence problems.
AC008522 Genomic DNA. No translation available.
BC067736 mRNA. Translation: AAH67736.1. Different initiation.
RefSeqiNP_001012779.2. NM_001012761.2.
UniGeneiHs.526902.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BQ6X-ray2.30C/E50-168[»]
D/F169-410[»]
4BQ7X-ray6.60C/E50-168[»]
D/F169-410[»]
4BQ8X-ray2.80B50-168[»]
C169-410[»]
4UHZX-ray2.85B53-136[»]
4UI0X-ray2.80C53-136[»]
4UI2X-ray3.15C50-168[»]
D169-410[»]
ProteinModelPortaliQ6NW40.
SMRiQ6NW40. Positions 52-324.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-61607N.
STRINGi9606.ENSP00000308219.

PTM databases

iPTMnetiQ6NW40.

Polymorphism and mutation databases

BioMutaiRGMB.
DMDMi327478562.

Proteomic databases

EPDiQ6NW40.
PaxDbiQ6NW40.
PeptideAtlasiQ6NW40.
PRIDEiQ6NW40.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000513185; ENSP00000423256; ENSG00000174136.
GeneIDi285704.
KEGGihsa:285704.
UCSCiuc063frq.1. human.

Organism-specific databases

CTDi285704.
GeneCardsiRGMB.
H-InvDBHIX0005059.
HGNCiHGNC:26896. RGMB.
HPAiHPA016993.
MIMi612687. gene.
neXtProtiNX_Q6NW40.
PharmGKBiPA134868641.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IFAH. Eukaryota.
ENOG410ZT7E. LUCA.
GeneTreeiENSGT00390000008488.
HOGENOMiHOG000013072.
HOVERGENiHBG057627.
InParanoidiQ6NW40.
KOiK06847.
PhylomeDBiQ6NW40.

Enzyme and pathway databases

ReactomeiR-HSA-373752. Netrin-1 signaling.

Miscellaneous databases

ChiTaRSiRGMB. human.
GeneWikiiRGMB.
GenomeRNAii285704.
PROiQ6NW40.
SOURCEiSearch...

Gene expression databases

BgeeiQ6NW40.
CleanExiHS_RGMB.
ExpressionAtlasiQ6NW40. baseline and differential.
GenevisibleiQ6NW40. HS.

Family and domain databases

InterProiIPR033608. DRAGON.
IPR009496. RGM_C.
IPR010536. RGM_N.
[Graphical view]
PANTHERiPTHR31428:SF5. PTHR31428:SF5. 1 hit.
PfamiPF06534. RGM_C. 1 hit.
PF06535. RGM_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  2. "The DNA sequence and comparative analysis of human chromosome 5."
    Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.
    , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
    Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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: Placenta.
  4. "Repulsive guidance molecule b inhibits neurite growth and is increased after spinal cord injury."
    Liu X., Hashimoto M., Horii H., Yamaguchi A., Naito K., Yamashita T.
    Biochem. Biophys. Res. Commun. 382:795-800(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Structure of the repulsive guidance molecule (RGM)-neogenin signaling hub."
    Bell C.H., Healey E., van Erp S., Bishop B., Tang C., Gilbert R.J., Aricescu A.R., Pasterkamp R.J., Siebold C.
    Science 341:77-80(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 50-410 IN COMPLEX WITH MOUSE NEO1 RECEPTOR, AUTOCATALYTIC CLEAVAGE, MUTAGENESIS OF ALA-186 AND PRO-206, DISULFIDE BONDS.

Entry informationi

Entry nameiRGMB_HUMAN
AccessioniPrimary (citable) accession number: Q6NW40
Secondary accession number(s): D6R9A0, Q8NC92
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 16, 2004
Last sequence update: April 5, 2011
Last modified: July 6, 2016
This is version 96 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.