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Protein

Cold shock domain-containing protein 4

Gene

CSP4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Chaperone that binds to and unwinds RNA and both single-stranded DNA and double-stranded DNA (ssDNA and dsDNA DNA) (By similarity). Regulates the flowering transition and flower and seed development, particularly at late stages of embryo development, through regulation of gene expression (including MEA, FIS2, AP1, CAL, AG and SHP2).By similarity2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri136 – 15318CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri180 – 19718CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • embryo development ending in seed dormancy Source: TAIR
  • fruit development Source: TAIR
  • regulation of transcription, DNA-templated Source: InterPro
  • response to cold Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Chaperone

Keywords - Ligandi

DNA-binding, Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

ReactomeiR-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Cold shock domain-containing protein 4
Short name:
AtCSP4
Alternative name(s):
Glycine-rich protein 2b
Short name:
AtGRP2b
Gene namesi
Name:CSP4
Synonyms:GRP2B
Ordered Locus Names:At2g21060
ORF Names:F26H11.18
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G21060.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Nucleusnucleolus By similarity
  • Nucleus 1 Publication

GO - Cellular componenti

  • cytosol Source: TAIR
  • nucleolus Source: UniProtKB-SubCell
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 201200Cold shock domain-containing protein 4PRO_0000100354Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ38896.
PRIDEiQ38896.

PTM databases

iPTMnetiQ38896.

Expressioni

Tissue specificityi

Mostly expressed in shoot apices and siliques, and, to a lower extent, in roots, cotyledons, stems, shoots, leaves, floral buds and flowers. Present in shoot apical meristems and siliques (at protein level). Very low levels are observed in cv. Landsberg erecta compared to cv. Columbia (PubMed:19269998).2 Publications

Developmental stagei

Accumulates in floral buds, flowers, developing embryos during an early stage of silique development.1 Publication

Inductioni

Down-regulated during cold acclimation. Accumulation during silique development is AGL15-dependent.1 Publication

Gene expression databases

GenevisibleiQ38896. AT.

Interactioni

Protein-protein interaction databases

BioGridi1994. 2 interactions.
STRINGi3702.AT2G21060.1.

Structurei

3D structure databases

ProteinModelPortaliQ38896.
SMRiQ38896. Positions 14-79, 137-200.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 8168CSDAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi91 – 13444Gly-richAdd
BLAST
Compositional biasi154 – 17926Gly-richAdd
BLAST

Sequence similaritiesi

Belongs to the cold shock protein (CSP) family.Curated
Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
Contains 1 CSD (cold-shock) domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri136 – 15318CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri180 – 19718CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000186262.
InParanoidiQ38896.
OMAiYGFINRT.
PhylomeDBiQ38896.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
4.10.60.10. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
SM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF57756. SSF57756. 2 hits.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
PS50158. ZF_CCHC. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q38896-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGGGDVNMS GGDRRKGTVK WFDTQKGFGF ITPSDGGDDL FVHQSSIRSE
60 70 80 90 100
GFRSLAAEES VEFDVEVDNS GRPKAIEVSG PDGAPVQGNS GGGGSSGGRG
110 120 130 140 150
GFGGGGGRGG GRGGGSYGGG YGGRGSGGRG GGGGDNSCFK CGEPGHMARE
160 170 180 190 200
CSQGGGGYSG GGGGGRYGSG GGGGGGGGGL SCYSCGESGH FARDCTSGGA

R
Length:201
Mass (Da):19,077
Last modified:November 1, 1996 - v1
Checksum:i832411B7FD890E46
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U39072 mRNA. Translation: AAA91165.1.
AC006264 Genomic DNA. Translation: AAD29810.1.
CP002685 Genomic DNA. Translation: AEC07117.1.
AY057693 mRNA. Translation: AAL15323.1.
BT021142 mRNA. Translation: AAX22277.1.
PIRiF84596.
RefSeqiNP_179702.1. NM_127676.2.
UniGeneiAt.1680.

Genome annotation databases

EnsemblPlantsiAT2G21060.1; AT2G21060.1; AT2G21060.
GeneIDi816641.
GrameneiAT2G21060.1; AT2G21060.1; AT2G21060.
KEGGiath:AT2G21060.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U39072 mRNA. Translation: AAA91165.1.
AC006264 Genomic DNA. Translation: AAD29810.1.
CP002685 Genomic DNA. Translation: AEC07117.1.
AY057693 mRNA. Translation: AAL15323.1.
BT021142 mRNA. Translation: AAX22277.1.
PIRiF84596.
RefSeqiNP_179702.1. NM_127676.2.
UniGeneiAt.1680.

3D structure databases

ProteinModelPortaliQ38896.
SMRiQ38896. Positions 14-79, 137-200.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1994. 2 interactions.
STRINGi3702.AT2G21060.1.

PTM databases

iPTMnetiQ38896.

Proteomic databases

PaxDbiQ38896.
PRIDEiQ38896.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G21060.1; AT2G21060.1; AT2G21060.
GeneIDi816641.
GrameneiAT2G21060.1; AT2G21060.1; AT2G21060.
KEGGiath:AT2G21060.

Organism-specific databases

TAIRiAT2G21060.

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000186262.
InParanoidiQ38896.
OMAiYGFINRT.
PhylomeDBiQ38896.

Enzyme and pathway databases

ReactomeiR-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

PROiQ38896.

Gene expression databases

GenevisibleiQ38896. AT.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
4.10.60.10. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
SM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF57756. SSF57756. 2 hits.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
PS50158. ZF_CCHC. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Arabidopsis AtGRP2b, a glycine-rich protein containing multiple nucleic acid-binding motifs."
    van Nocker S., Vierstra R.D.
    Plant Gene Register PGR95-128
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Arabidopsis ORF clones."
    Cheuk R.F., Chen H., Kim C.J., Shinn P., Ecker J.R.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Conservation of the cold shock domain protein family in plants."
    Karlson D., Imai R.
    Plant Physiol. 131:12-15(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY COLD, GENE FAMILY.
  7. "Arabidopsis cold shock domain proteins: relationships to floral and silique development."
    Nakaminami K., Hill K., Perry S.E., Sentoku N., Long J.A., Karlson D.T.
    J. Exp. Bot. 60:1047-1062(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, GENE FAMILY, NOMENCLATURE.
    Strain: cv. Columbia and cv. Landsberg erecta.
  8. "Overexpression of AtCSP4 affects late stages of embryo development in Arabidopsis."
    Yang Y., Karlson D.T.
    J. Exp. Bot. 62:2079-2091(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    Strain: cv. Columbia.
  9. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiCSP4_ARATH
AccessioniPrimary (citable) accession number: Q38896
Secondary accession number(s): Q5BIT2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 2, 2001
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 131 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  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.