Q96NA2 (RILP_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Rab-interacting lysosomal protein

Gene names

Name:	RILP
ORF Names:	PP10141

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	401 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Rab effector playing a role in late endocytic transport to degradative compartments. Involved in the regulation of lysosomal morphology and distribution. Induces recruitment of dynein-dynactin motor complexes to Rab7A-containing late endosome and lysosome compartments. Promotes centripetal migration of phagosomes and the fusion of phagosomes with the late endosomes and lysosomes. Ref.1 Ref.7 Ref.9 Ref.10
Subunit structure	Homodimer. Each subunit can interact with either RAB7A or RAB34. Interacts with CLN3. Ref.1 Ref.8 Ref.10 Ref.11 Ref.13 Ref.14
Subcellular location	Endomembrane system. Late endosome membrane. Lysosome membrane. Cytoplasmic vesicle › phagosome membrane. Note: Associated with late endosomal, lysosomal and phagosomal membranes. The interaction with RAB7A is necessary for its recruitment to phagosomes. Ref.1 Ref.9 Ref.10
Tissue specificity	Ubiquitous. Strongly expressed in fetal heart, heart, stomach, spleen, adrenal gland, thyroid gland, salivary gland, fetal liver, liver and lung. Poorly expressed in brain. Ref.1 Ref.6 Ref.10
Sequence similarities	Contains 1 RILP-like domain.

Ontologies

Keywords
Biological process	Protein transport Transport
Cellular component	Cytoplasmic vesicle Endosome Lysosome Membrane
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Coiled coil
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II Traceable author statement. Source: Reactome endosome to lysosome transport Inferred from mutant phenotype PubMed 18272684. Source: BHF-UCL protein transport Non-traceable author statement Ref.1. Source: UniProtKB
Cellular_component	late endosome Non-traceable author statement Ref.1. Source: UniProtKB late endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell lysosomal membrane Non-traceable author statement Ref.1. Source: UniProtKB mitochondrion Inferred from electronic annotation. Source: Compara phagocytic vesicle membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	Rab GTPase binding Traceable author statement Ref.1. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q96NA2-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q96NA2-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-210: Missing.
     211-213: WAT → MGA

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 401

401

Rab-interacting lysosomal protein

PRO_0000097339

Regions

Domain

236 – 270

35

RILP-like

Region

272 – 333

62

Necessary for the interaction with RAB7A and RAB34, lysosomal distribution and morphology

Coiled coil

75 – 181

107

Potential

Amino acid modifications

Modified residue

314

1

Phosphoserine Ref.12

Modified residue

315

1

Phosphoserine Ref.12

Natural variations

Alternative sequence

1 – 210

210

Missing in isoform 2.

VSP_016043

Alternative sequence

211 – 213

3

WAT → MGA in isoform 2.

VSP_016044

Natural variant

81

1

A → T. Ref.2
Corresponds to variant rs9909321 [ dbSNP | Ensembl ].

VAR_051321

Natural variant

281

1

R → Q.
Corresponds to variant rs34982553 [ dbSNP | Ensembl ].

VAR_034417

Experimental info

Mutagenesis

248

1

F → A: Strongly reduces dimerization and localization to late endosomal/lysosomal compartments. Ref.14

Mutagenesis

251

1

I → A: Abolishes dimerization, interaction with RAB7A and localization to late endosomal/lysosomal compartments. Ref.14

Mutagenesis

252

1

L → A: Abolishes interaction with RAB7A and localization to late endosomal/lysosomal compartments. Ref.14

Mutagenesis

255

1

R → A: Abolishes dimerization, interaction with RAB7A and localization to late endosomal/lysosomal compartments. Ref.14

Mutagenesis

258

1

L → A: Reduces dimerization, interaction with RAB7A and localization to late endosomal/lysosomal compartments. Ref.14

Mutagenesis

304

1

K → A: Abolishes interaction with RAB7A and localization to late endosomal/lysosomal compartments. Ref.14

Mutagenesis

305

1

M → A: Abolishes interaction with RAB7A and localization to late endosomal/lysosomal compartments. Ref.14

Mutagenesis

306

1

L → A: Abolishes interaction with RAB7A and localization to late endosomal/lysosomal compartments. Ref.14

Sequence conflict

284

1

G → S in CAC33443. Ref.1

Secondary structure

1

.

.

.

.

.

401

Helix Strand Turn

Details...

Helix

248 – 276

29

Helix

284 – 306

23

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 1057A1DAC2FFED94	FASTA	401	44,200
	10 20 30 40 50 60 MEPRRAAPGV PGWGSREAAG SASAAELVYH LAGALGTELQ DLARRFGPEA AAGLVPLVVR 70 80 90 100 110 120 ALELLEQAAV GPAPDSLQVS AQPAEQELRR LREENERLRR ELRAGPQEER ALLRQLKEVT 130 140 150 160 170 180 DRQRDELRAH NRDLRQRGQE TEALQEQLQR LLLVNAELRH KLAAMQTQLR AAQDRERERQ 190 200 210 220 230 240 QPGEAATPQA KERARGQAGR PGHQHGQEPE WATAGAGAPG NPEDPAEAAQ QLGRPSEAGQ 250 260 270 280 290 300 CRFSREEFEQ ILQERNELKA KVFLLKEELA YFQRELLTDH RVPGLLLEAM KVAVRKQRKK 310 320 330 340 350 360 IKAKMLGTPE EAESSEDEAG PWILLSDDKG DHPPPPESKI QSFFGLWYRG KAESSEDETS 370 380 390 400 SPAPSKLGGE EEAQPQSPAP DPPCSALHEH LCLGASAAPE A
	Isoform 2 [UniParc]. Checksum: 76673702E0FF4FFD	FASTA	191	20,726
	10 20 30 40 50 60 MGAAGAGAPG NPEDPAEAAQ QLGRPSEAGQ CRFSREEFEQ ILQERNELKA KVFLLKEELA 70 80 90 100 110 120 YFQRELLTDH RVPGLLLEAM KVAVRKQRKK IKAKMLGTPE EAESSEDEAG PWILLSDDKG 130 140 150 160 170 180 DHPPPPESKI QSFFGLWYRG KAESSEDETS SPAPSKLGGE EEAQPQSPAP DPPCSALHEH 190 LCLGASAAPE A

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Rab-interacting lysosomal protein (RILP): the Rab7 effector required for transport to lysosomes." Cantalupo G., Alifano P., Roberti V., Bruni C.B., Bucci C. EMBO J. 20:683-693(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION IN LATE ENDOCYTOSIS, INTERACTION WITH RAB7A, SUBCELLULAR LOCATION, TISSUE SPECIFICITY. Tissue: Cervix carcinoma.
[2]	"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] (ISOFORM 1), VARIANT THR-81. Tissue: Kidney and Thalamus.
[3]	"Large-scale cDNA transfection screening for genes related to cancer development and progression." Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X. , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J. Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
[4]	"Study of 100 skeletal muscle full length mRNA (Telethon project B41)." Frigimelica E., Lanfranchi G. Submitted (JUL-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Skeletal muscle.
[5]	"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] (ISOFORM 1). Tissue: Brain, Lung, Testis and Uterus.
[6]	"Expression analysis and chromosomal assignment of PRA1 and RILP genes." Bucci C., De Gregorio L., Bruni C.B. Biochem. Biophys. Res. Commun. 286:815-819(2001) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY.
[7]	"The Rab7 effector protein RILP controls lysosomal transport by inducing the recruitment of dynein-dynactin motors." Jordens I., Fernandez-Borja M., Marsman M., Dusseljee S., Janssen L., Calafat J., Janssen H., Wubbolts R., Neefjes J. Curr. Biol. 11:1680-1685(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN DYNEIN-DYNACTIN COMPLEX RECRUITMENT.
[8]	"Interorganellar regulation of lysosome positioning by the Golgi apparatus through Rab34 interaction with Rab-interacting lysosomal protein." Wang T., Hong W. Mol. Biol. Cell 13:4317-4332(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RAB34.
[9]	"Phagosomes fuse with late endosomes and/or lysosomes by extension of membrane protrusions along microtubules: role of Rab7 and RILP." Harrison R.E., Bucci C., Vieira O.V., Schroer T.A., Grinstein S. Mol. Cell. Biol. 23:6494-6506(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN PHAGOSOME MIGRATION AND PHAGOLYSOSOMAL FUSION, SUBCELLULAR LOCATION.
[10]	"A unique region of RILP distinguishes it from its related proteins in its regulation of lysosomal morphology and interaction with Rab7 and Rab34." Wang T., Wong K.K., Hong W. Mol. Biol. Cell 15:815-826(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN LYSOSOMAL MORPHOLOGY AND DISTRIBUTION, INTERACTION WITH RAB7A AND RAB34, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[11]	"The Rab-interacting lysosomal protein, a Rab7 and Rab34 effector, is capable of self-interaction." Colucci A.M.R., Campana M.C., Bellopede M., Bucci C. Biochem. Biophys. Res. Commun. 334:128-133(2005) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[12]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-314 AND SER-315, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[13]	"Neuronal ceroid lipofuscinosis protein CLN3 interacts with motor proteins and modifies location of late endosomal compartments." Uusi-Rauva K., Kyttala A., van der Kant R., Vesa J., Tanhuanpaa K., Neefjes J., Olkkonen V.M., Jalanko A. Cell. Mol. Life Sci. 69:2075-2089(2012) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH CLN3.
[14]	"Structural basis for recruitment of RILP by small GTPase Rab7." Wu M., Wang T., Loh E., Hong W., Song H. EMBO J. 24:1491-1501(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 244-308 IN COMPLEX WITH RAB7A, SUBUNIT, MUTAGENESIS OF PHE-248; ILE-251; LEU-252; ARG-255; LEU-258; LYS-304; MET-305 AND LEU-306.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ404317 mRNA. Translation: CAC33443.1.
AK055755 mRNA. Translation: BAB71003.1.
AK314767 mRNA. Translation: BAG37305.1.
AF370391 mRNA. Translation: AAQ15227.1.
AJ278711 mRNA. Translation: CAC82174.1.
BC004961 mRNA. Translation: AAH04961.1.
BC031621 mRNA. Translation: AAH31621.1.

IPI

IPI00289188.
IPI00654568.

RefSeq

NP_113618.2. NM_031430.2.

UniGene

Hs.534497.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1YHN	X-ray	3.00	B	244-308	[»]

ProteinModelPortal

Q96NA2.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q96NA2. 3 interactions.

STRING

9606.ENSP00000301336.

PTM databases

PhosphoSite

Q96NA2.

Polymorphism databases

DMDM

74732524.

Proteomic databases

PaxDb

Q96NA2.

PRIDE

Q96NA2.

Protocols and materials databases

DNASU

83547.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000301336; ENSP00000301336; ENSG00000167705.

GeneID

83547.

KEGG

hsa:83547.

UCSC

uc002ftd.3. human.

Organism-specific databases

CTD

83547.

GeneCards

GC17M001549.

HGNC

HGNC:30266. RILP.

HPA

HPA052041.

MIM

607848. gene.

neXtProt

NX_Q96NA2.

PharmGKB

PA134915969.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG28812.

HOGENOM

HOG000007529.

HOVERGEN

HBG082629.

InParanoid

Q96NA2.

KO

K13883.

OMA

KVAVKKQ.

OrthoDB

EOG415GDV.

PhylomeDB

Q96NA2.

Enzyme and pathway databases

Reactome

REACT_6900. Immune System.

Gene expression databases

ArrayExpress

Q96NA2.

Bgee

Q96NA2.

CleanEx

HS_RILP.

Genevestigator

Q96NA2.

GermOnline

ENSG00000167705. Homo sapiens.

Family and domain databases

InterPro

IPR019143. JNK/Rab-associated_protein-1_N.
IPR021563. RILP.
[Graphical view]

Pfam

PF09744. Jnk-SapK_ap_N. 1 hit.
PF11461. RILP. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q96NA2.

GenomeRNAi

83547.

NextBio

72481.

SOURCE

Search...

Entry information

Entry name

RILP_HUMAN

Accession

Primary (citable) accession number: Q96NA2
Secondary accession number(s): B2RBQ8 , Q71RE6, Q9BSL3, Q9BYS3

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 8, 2005
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.