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Protein

FACT complex subunit SSRP1

Gene

SSRP1

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

Functioni

Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II. Binds specifically to double-stranded DNA (Probable). Required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus (PubMed:16698901).1 Publication1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi561 – 63070HMG boxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • transcription factor activity, sequence-specific DNA binding Source: TAIR

GO - Biological processi

  • DNA repair Source: UniProtKB-KW
  • DNA replication Source: UniProtKB-KW
  • karyogamy Source: UniProtKB
  • polar nucleus fusion Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
  • vegetative to reproductive phase transition of meristem Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

DNA damage, DNA repair, DNA replication, Karyogamy, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-ATH-674695. RNA Polymerase II Pre-transcription Events.

Names & Taxonomyi

Protein namesi
Recommended name:
FACT complex subunit SSRP1
Alternative name(s):
Facilitates chromatin transcription complex subunit SSRP1
High mobility group B protein 8
Nucleosome/chromatin assembly factor group D 08
Short name:
Nucleosome/chromatin assembly factor group D 8
Protein NUCLEAR FUSION DEFECTIVE 81 Publication
Recombination signal sequence recognition protein 1
Gene namesi
Name:SSRP1
Synonyms:HMGB8, NFD81 Publication
Ordered Locus Names:At3g28730
ORF Names:T19N8.2
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G28730.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation1 Publication
  • Chromosome 1 Publication

  • Note: Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci.

GO - Cellular componenti

  • FACT complex Source: TAIR
  • nuclear euchromatin Source: TAIR
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Disruption phenotypei

Failure of fusion of the polar nuclei during megagametogenesis.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 646646FACT complex subunit SSRP1PRO_0000048610Add
BLAST

Proteomic databases

PaxDbiQ05153.
PRIDEiQ05153.

Expressioni

Tissue specificityi

Widely expressed. Present in embryos, shoots and roots, whereas it is not present in terminally differentiated cells such as mature trichoblasts or cells of the root cap (at protein level).1 Publication

Gene expression databases

GenevisibleiQ05153. AT.

Interactioni

Subunit structurei

Component of the FACT complex, a stable heterodimer of SPT16 and SSRP1.By similarity

Protein-protein interaction databases

BioGridi7834. 1 interaction.
STRINGi3702.AT3G28730.1.

Structurei

3D structure databases

ProteinModelPortaliQ05153.
SMRiQ05153. Positions 1-175, 207-440, 507-630.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi456 – 50651Asp-rich (acidic)Add
BLAST
Compositional biasi516 – 55742Lys-rich (basic)Add
BLAST

Sequence similaritiesi

Belongs to the SSRP1 family.Curated
Contains 1 HMG box DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0526. Eukaryota.
COG5165. LUCA.
COG5648. LUCA.
HOGENOMiHOG000241245.
InParanoidiQ05153.
KOiK09272.
OMAiEQNIIFK.
PhylomeDBiQ05153.

Family and domain databases

Gene3Di1.10.30.10. 1 hit.
2.30.29.30. 1 hit.
InterProiIPR013719. DUF1747.
IPR009071. HMG_box_dom.
IPR011993. PH_dom-like.
IPR000969. SSrcognition.
IPR024954. SSRP1_dom.
[Graphical view]
PfamiPF00505. HMG_box. 1 hit.
PF08512. Rtt106. 1 hit.
PF03531. SSrecog. 1 hit.
[Graphical view]
PRINTSiPR00887. SSRCOGNITION.
SMARTiSM00398. HMG. 1 hit.
SM01287. Rtt106. 1 hit.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 1 hit.
SSF50729. SSF50729. 1 hit.
PROSITEiPS50118. HMG_BOX_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q05153-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MADGHSFNNI SLSGRGGKNP GLLKINSGGI QWKKQGGGKA VEVDRSDIVS
60 70 80 90 100
VSWTKVTKSN QLGVKTKDGL YYKFVGFRDQ DVPSLSSFFQ SSYGKTPDEK
110 120 130 140 150
QLSVSGRNWG EVDLHGNTLT FLVGSKQAFE VSLADVSQTQ LQGKNDVTLE
160 170 180 190 200
FHVDDTAGAN EKDSLMEISF HIPNSNTQFV GDENRPPSQV FNDTIVAMAD
210 220 230 240 250
VSPGVEDAVV TFESIAILTP RGRYNVELHL SFLRLQGQAN DFKIQYSSVV
260 270 280 290 300
RLFLLPKSNQ PHTFVVISLD PPIRKGQTMY PHIVMQFETD TVVESELSIS
310 320 330 340 350
DELMNTKFKD KLERSYKGLI HEVFTTVLRW LSGAKITKPG KFRSSQDGFA
360 370 380 390 400
VKSSLKAEDG VLYPLEKGFF FLPKPPTLIL HDEIDYVEFE RHAAGGANMH
410 420 430 440 450
YFDLLIRLKT DHEHLFRNIQ RNEYHNLYTF ISSKGLKIMN LGGAGTADGV
460 470 480 490 500
AAVLGDNDDD DAVDPHLTRI RNQAADESDE EDEDFVMGED DDGGSPTDDS
510 520 530 540 550
GGDDSDASEG GVGEIKEKSI KKEPKKEASS SKGLPPKRKT VAADEGSSKR
560 570 580 590 600
KKPKKKKDPN APKRAMSGFM FFSQMERDNI KKEHPGIAFG EVGKVLGDKW
610 620 630 640
RQMSADDKEP YEAKAQVDKQ RYKDEISDYK NPQPMNVDSG NDSDSN
Length:646
Mass (Da):71,646
Last modified:December 6, 2002 - v2
Checksum:iDC45C2C13E2FCA0B
GO
Isoform 2 (identifier: Q05153-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     240-268: NDFKIQYSSVVRLFLLPKSNQPHTFVVIS → MTLKSSTVALSVCSCFQSQTNHTRLLLSL
     269-646: Missing.

Show »
Length:268
Mass (Da):29,182
Checksum:i4946DB6BB57DBC42
GO

Sequence cautioni

The sequence BAA02719.1 differs from that shown. Reason: Frameshift at positions 151, 164, 600 and 616. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti6 – 72SF → FL in BAA02719 (PubMed:1480495).Curated
Sequence conflicti237 – 2371G → E in BAA02719 (PubMed:1480495).Curated
Sequence conflicti644 – 6441D → N in BAD94127 (Ref. 6) Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei240 – 26829NDFKI…FVVIS → MTLKSSTVALSVCSCFQSQT NHTRLLLSL in isoform 2. 1 PublicationVSP_039931Add
BLAST
Alternative sequencei269 – 646378Missing in isoform 2. 1 PublicationVSP_039932Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13491 mRNA. Translation: BAA02719.1. Frameshift.
AP002057 Genomic DNA. Translation: BAB03170.1.
CP002686 Genomic DNA. Translation: AEE77484.1.
BT002507 mRNA. Translation: AAO00867.1.
AK318679 mRNA. Translation: BAH56794.1.
AK221855 mRNA. Translation: BAD94127.1.
PIRiS35511.
RefSeqiNP_189515.1. NM_113794.3. [Q05153-1]
UniGeneiAt.21931.
At.48716.

Genome annotation databases

EnsemblPlantsiAT3G28730.1; AT3G28730.1; AT3G28730. [Q05153-1]
GeneIDi822505.
KEGGiath:AT3G28730.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13491 mRNA. Translation: BAA02719.1. Frameshift.
AP002057 Genomic DNA. Translation: BAB03170.1.
CP002686 Genomic DNA. Translation: AEE77484.1.
BT002507 mRNA. Translation: AAO00867.1.
AK318679 mRNA. Translation: BAH56794.1.
AK221855 mRNA. Translation: BAD94127.1.
PIRiS35511.
RefSeqiNP_189515.1. NM_113794.3. [Q05153-1]
UniGeneiAt.21931.
At.48716.

3D structure databases

ProteinModelPortaliQ05153.
SMRiQ05153. Positions 1-175, 207-440, 507-630.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi7834. 1 interaction.
STRINGi3702.AT3G28730.1.

Proteomic databases

PaxDbiQ05153.
PRIDEiQ05153.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G28730.1; AT3G28730.1; AT3G28730. [Q05153-1]
GeneIDi822505.
KEGGiath:AT3G28730.

Organism-specific databases

TAIRiAT3G28730.

Phylogenomic databases

eggNOGiKOG0526. Eukaryota.
COG5165. LUCA.
COG5648. LUCA.
HOGENOMiHOG000241245.
InParanoidiQ05153.
KOiK09272.
OMAiEQNIIFK.
PhylomeDBiQ05153.

Enzyme and pathway databases

ReactomeiR-ATH-674695. RNA Polymerase II Pre-transcription Events.

Miscellaneous databases

PROiQ05153.

Gene expression databases

GenevisibleiQ05153. AT.

Family and domain databases

Gene3Di1.10.30.10. 1 hit.
2.30.29.30. 1 hit.
InterProiIPR013719. DUF1747.
IPR009071. HMG_box_dom.
IPR011993. PH_dom-like.
IPR000969. SSrcognition.
IPR024954. SSRP1_dom.
[Graphical view]
PfamiPF00505. HMG_box. 1 hit.
PF08512. Rtt106. 1 hit.
PF03531. SSrecog. 1 hit.
[Graphical view]
PRINTSiPR00887. SSRCOGNITION.
SMARTiSM00398. HMG. 1 hit.
SM01287. Rtt106. 1 hit.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 1 hit.
SSF50729. SSF50729. 1 hit.
PROSITEiPS50118. HMG_BOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A novel Arabidopsis DNA binding protein contains the conserved motif of HMG-box proteins."
    Yamaguchi-Shinozaki K., Shinozaki K.
    Nucleic Acids Res. 20:6737-6737(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones."
    Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.
    DNA Res. 7:217-221(2000) [PubMed] [Europe PMC] [Abstract]
    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] (ISOFORM 1).
    Strain: cv. Columbia.
  5. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
    Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
    DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: cv. Columbia.
    Tissue: Rosette leaf.
  6. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 438-646 (ISOFORM 1).
    Strain: cv. Columbia.
  7. "The chromatin remodelling complex FACT associates with actively transcribed regions of the Arabidopsis genome."
    Duroux M., Houben A., Ruzicka K., Friml J., Grasser K.D.
    Plant J. 40:660-671(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  8. "NUCLEAR FUSION DEFECTIVE1 encodes the Arabidopsis RPL21M protein and is required for karyogamy during female gametophyte development and fertilization."
    Portereiko M.F., Sandaklie-Nikolova L., Lloyd A., Dever C.A., Otsuga D., Drews G.N.
    Plant Physiol. 141:957-965(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    Strain: cv. Columbia.

Entry informationi

Entry nameiSSRP1_ARATH
AccessioniPrimary (citable) accession number: Q05153
Secondary accession number(s): C0Z265, Q56X23, Q9LHA2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: December 6, 2002
Last modified: May 11, 2016
This is version 130 of the entry and version 2 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.