Q92600 (RCD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cell differentiation protein RCD1 homolog
Short name=Rcd-1

Alternative name(s):
CCR4-NOT transcription complex subunit 9

Gene names

Name:	RQCD1
Synonyms:	CNOT9, RCD1

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	299 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Involved in down-regulation of MYB- and JUN-dependent transcription. May play a role in cell differentiation By similarity. Can bind oligonucleotides, such as poly-G, poly-C or poly-T (in vitro), but the physiological relevance of this is not certain. Does not bind poly-A. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA, expect ESR1-mediated transcription that is not only slightly increased, if at all. Ref.5 Ref.8
Subunit structure	Homodimer. Component of the CCR4-NOT complex; distinct complexes seem to exist that differ in the participation of probably mutually exclusive catalytic subunits. Interacts with MYB, ATF2, RARA, RARB, RARG, RXRA, RXRB and RXRG. Identified in a complex with ATF2 bound to target DNA By similarity. Interacts with NANOS2 By similarity. Directly interacts with ZNF335. Ref.5 Ref.7 Ref.8
Subcellular location	Nucleus By similarity. Cytoplasm › P-body By similarity. Note: NANOS2 promotes its localization to P-body By similarity.
Tissue specificity	Detected in spleen, thymus, prostate, testis, ovary and intestine. Ref.1
Sequence similarities	Belongs to the RCD1 family.
Sequence caution	The sequence AAH07102.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	RNA-mediated gene silencing Transcription Transcription regulation Translation regulation
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Polymorphism
Molecular function	Activator Repressor
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	cytokine-mediated signaling pathway Inferred from electronic annotation. Source: Compara negative regulation of intracellular estrogen receptor signaling pathway Inferred from mutant phenotype PubMed 16778766. Source: UniProtKB nuclear-transcribed mRNA poly(A) tail shortening Traceable author statement. Source: Reactome positive regulation of ligand-dependent nuclear receptor transcription coactivator activity Inferred from direct assay Ref.5. Source: UniProtKB regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW sex differentiation Traceable author statement Ref.1. Source: ProtInc transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	CCR4-NOT complex Inferred from direct assay PubMed 19558367. Source: UniProtKB cytoplasmic mRNA processing body Inferred from sequence or structural similarity. Source: UniProtKB cytosol Traceable author statement. Source: Reactome nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 299

299

Cell differentiation protein RCD1 homolog

PRO_0000327224

Amino acid modifications

Modified residue

1

1

N-acetylmethionine Ref.4

Natural variations

Natural variant

143

1

I → T. Ref.3
Corresponds to variant rs17856204 [ dbSNP | Ensembl ].

VAR_042429

Experimental info

Mutagenesis

227

1

R → E: Loss of DNA binding. Ref.8

Sequence conflict

245 – 280

36

AREAL…LAQLV → FSDLTFCWSSFQR in AAH07102. Ref.3

Secondary structure

1

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299

Helix Strand Turn

Details...

Helix

20 – 28

9

Turn

32 – 34

3

Helix

35 – 45

11

Turn

46 – 48

3

Helix

52 – 58

7

Helix

62 – 72

11

Helix

73 – 77

5

Turn

78 – 80

3

Helix

84 – 102

19

Turn

104 – 106

3

Helix

107 – 112

6

Helix

115 – 118

4

Helix

120 – 124

5

Helix

130 – 146

17

Helix

147 – 149

3

Helix

152 – 160

9

Helix

163 – 173

11

Helix

176 – 191

16

Helix

193 – 199

7

Helix

203 – 219

17

Turn

220 – 222

3

Helix

226 – 239

14

Helix

243 – 252

10

Helix

255 – 257

3

Helix

263 – 266

4

Helix

270 – 282

13

Sequences

	Sequence		Length	Mass (Da)
	Q92600 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: CFA0E108F5E9D8F2	FASTA	299	33,631
	10 20 30 40 50 60 MHSLATAAPV PTTLAQVDRE KIYQWINELS SPETRENALL ELSKKRESVP DLAPMLWHSF 70 80 90 100 110 120 GTIAALLQEI VNIYPSINPP TLTAHQSNRV CNALALLQCV ASHPETRSAF LAAHIPLFLY 130 140 150 160 170 180 PFLHTVSKTR PFEYLRLTSL GVIGALVKTD EQEVINFLLT TEIIPLCLRI MESGSELSKT 190 200 210 220 230 240 VATFILQKIL LDDTGLAYIC QTYERFSHVA MILGKMVLQL SKEPSARLLK HVVRCYLRLS 250 260 270 280 290 DNPRAREALR QCLPDQLKDT TFAQVLKDDT TTKRWLAQLV KNLQEGQVTD PRGIPLPPQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Novel factor highly conserved among eukaryotes controls sexual development in fission yeast." Okazaki N., Okazaki K., Watanabe Y., Kato-Hayashi M., Yamamoto M., Okayama H. Mol. Cell. Biol. 18:887-895(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY. Tissue: Foreskin.
[2]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases 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], VARIANT THR-143. Tissue: Brain.
[4]	Bienvenut W.V., Lempens A., Norman J.C. Submitted (OCT-2009) to UniProtKB Cited for: PROTEIN SEQUENCE OF 1-21; 36-44; 180-188 AND 275-292, ACETYLATION AT MET-1, MASS SPECTROMETRY. Tissue: Ovarian carcinoma.
[5]	"Components of the CCR4-NOT complex function as nuclear hormone receptor coactivators via association with the NRC-interacting Factor NIF-1." Garapaty S., Mahajan M.A., Samuels H.H. J. Biol. Chem. 283:6806-6816(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH ZNF335.
[6]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]	"C2ORF29/CNOT11 and CNOT10 form a new module of the CCR4-NOT complex." Mauxion F., Preve B., Seraphin B. RNA Biol. 10:0-0(2012) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE CCR4-NOT COMPLEX.
[8]	"Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties." Garces R.G., Gillon W., Pai E.F. Protein Sci. 16:176-188(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 18-285, DOMAIN, SUBUNIT, FUNCTION, MUTAGENESIS OF ARG-227.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D87957 Genomic DNA. Translation: BAA13508.1.
CH471063 Genomic DNA. Translation: EAW70625.1.
BC007102 mRNA. Translation: AAH07102.2. Different initiation.
BC137455 mRNA. Translation: AAI37456.1.
BC137456 mRNA. Translation: AAI37457.1.

IPI

IPI00023101.

RefSeq

NP_001258564.1. NM_001271635.1.
NP_005435.1. NM_005444.2.

UniGene

Hs.148767.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2FV2	X-ray	2.20	A/B/C/D	18-285	[»]

ProteinModelPortal

Q92600.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-46840N.

IntAct

Q92600. 5 interactions.

MINT

MINT-1162783.

STRING

9606.ENSP00000273064.

PTM databases

PhosphoSite

Q92600.

Polymorphism databases

DMDM

74716599.

Proteomic databases

PaxDb

Q92600.

PRIDE

Q92600.

Protocols and materials databases

DNASU

9125.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000273064; ENSP00000273064; ENSG00000144580.
ENST00000542068; ENSP00000443687; ENSG00000144580.

GeneID

9125.

KEGG

hsa:9125.

UCSC

uc010zkh.2. human.

Organism-specific databases

CTD

9125.

GeneCards

GC02P219433.

HGNC

HGNC:10445. RQCD1.

HPA

HPA046622.

MIM

612054. gene.

neXtProt

NX_Q92600.

PharmGKB

PA34859.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5209.

HOGENOM

HOG000192069.

HOVERGEN

HBG056785.

InParanoid

Q92600.

KO

K12606.

OrthoDB

EOG4W9J4C.

PhylomeDB

Q92600.

Enzyme and pathway databases

Reactome

REACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

Q92600.

Bgee

Q92600.

CleanEx

HS_RQCD1.

Genevestigator

Q92600.

Family and domain databases

Gene3D

1.25.10.10. 1 hit.

InterPro

IPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR007216. Rcd1.
[Graphical view]

PANTHER

PTHR12262. PTHR12262. 1 hit.

Pfam

PF04078. Rcd1. 1 hit.
[Graphical view]

SUPFAM

SSF48371. ARM-type_fold. 1 hit.

ProtoNet

Search...

Other

ChiTaRS

RQCD1. human.

EvolutionaryTrace

Q92600.

GenomeRNAi

9125.

NextBio

34205.

SOURCE

Search...

Entry information

Entry name

RCD1_HUMAN

Accession

Primary (citable) accession number: Q92600
Secondary accession number(s): B2RPI0, Q96IX4

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 8, 2008
Last sequence update:	February 1, 1997
Last modified:	May 29, 2013
This is version 105 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.