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Protein

Stromal cell-derived factor 2-like protein

Gene

SDF2

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

Functioni

Involved in the endoplasmic reticulum (ER) protein quality control and unfolded protein response. May be involved in the quality control of glycoproteins. Forms a complex in the ER with ERDJ3B and MED37A/BIP1 which is required for the proper accumulation and function of the surface-exposed leucine-rich repeat receptor kinases EFR involved in pathogen-associated molecular pattern (PAMP) triggered immunity.2 Publications

GO - Biological processi

  • cell wall mannoprotein biosynthetic process Source: GO_Central
  • chain elongation of O-linked mannose residue Source: GO_Central
  • defense response to bacterium Source: TAIR
  • defense response to fungus Source: TAIR
  • multicellular organism development Source: GO_Central
  • pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response Source: TAIR
  • regulation of endoplasmic reticulum unfolded protein response Source: GO_Central
Complete GO annotation...

Keywords - Biological processi

Plant defense

Names & Taxonomyi

Protein namesi
Recommended name:
Stromal cell-derived factor 2-like protein
Short name:
AtSDF2
Short name:
SDF2-like protein
Gene namesi
Name:SDF2
Ordered Locus Names:At2g25110
ORF Names:F13D4.70
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G25110.

Subcellular locationi

GO - Cellular componenti

  • endoplasmic reticulum Source: TAIR
  • membrane Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum

Pathology & Biotechi

Disruption phenotypei

No visible phenotype under normal growth conditions, but mutant plants are insensitive to seedling growth inhibition in response to the pathogen-associated molecular pattern (PAMP) elf18 and show increased susceptibility to phytopathogenic bacteria.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi64 – 641G → D in sdf2-3; decreased response to the PAMP elf18. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2121Sequence analysisAdd
BLAST
Chaini22 – 218197Stromal cell-derived factor 2-like proteinPRO_0000031959Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi214 – 2141N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ93ZE8.
PRIDEiQ93ZE8.

Expressioni

Inductioni

By tunicamycin.1 Publication

Gene expression databases

GenevisibleiQ93ZE8. AT.

Interactioni

Subunit structurei

Interacts with ERDJ3B.1 Publication

Protein-protein interaction databases

BioGridi2401. 1 interaction.
IntActiQ93ZE8. 1 interaction.
MINTiMINT-7950181.
STRINGi3702.AT2G25110.1.

Structurei

Secondary structure

1
218
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi42 – 476Combined sources
Turni48 – 503Combined sources
Beta strandi53 – 608Combined sources
Beta strandi68 – 736Combined sources
Helixi79 – 813Combined sources
Beta strandi83 – 864Combined sources
Beta strandi104 – 1096Combined sources
Turni110 – 1123Combined sources
Beta strandi115 – 1228Combined sources
Turni124 – 1263Combined sources
Beta strandi128 – 1347Combined sources
Helixi142 – 1443Combined sources
Beta strandi146 – 1538Combined sources
Beta strandi162 – 1676Combined sources
Turni168 – 1703Combined sources
Beta strandi173 – 1808Combined sources
Beta strandi183 – 1853Combined sources
Beta strandi189 – 1968Combined sources
Helixi199 – 2013Combined sources
Beta strandi203 – 2097Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3MALX-ray1.95A/B24-218[»]
ProteinModelPortaliQ93ZE8.
SMRiQ93ZE8. Positions 35-215.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini34 – 8855MIR 1PROSITE-ProRule annotationAdd
BLAST
Domaini96 – 15156MIR 2PROSITE-ProRule annotationAdd
BLAST
Domaini154 – 20855MIR 3PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 3 MIR domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal

Phylogenomic databases

eggNOGiKOG3358. Eukaryota.
ENOG410ZBU3. LUCA.
HOGENOMiHOG000236354.
InParanoidiQ93ZE8.
OMAiMAQPSQN.
PhylomeDBiQ93ZE8.

Family and domain databases

InterProiIPR027005. GlyclTrfase_39-like.
IPR016093. MIR_motif.
[Graphical view]
PANTHERiPTHR10050. PTHR10050. 1 hit.
PfamiPF02815. MIR. 1 hit.
[Graphical view]
SMARTiSM00472. MIR. 3 hits.
[Graphical view]
SUPFAMiSSF82109. SSF82109. 1 hit.
PROSITEiPS50919. MIR. 3 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q93ZE8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALGFFCLAI FLYLSLDPDS GYTSASAAAS GKEGVEITYG SAIKLMHEKT
60 70 80 90 100
KFRLHSHDVP YGSGSGQQSV TGFPGVVDSN SYWIVKPVPG TTEKQGDAVK
110 120 130 140 150
SGATIRLQHM KTRKWLHSHL HASPISGNLE VSCFGDDTNS DTGDHWKLII
160 170 180 190 200
EGSGKTWKQD QRVRLQHIDT SGYLHSHDKK YQRIAGGQQE VCGIREKKAD
210
NIWLAAEGVY LPLNESSK
Length:218
Mass (Da):23,935
Last modified:December 1, 2001 - v1
Checksum:i575F683AC0C3BC87
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti203 – 2031W → C in AAM65625 (Ref. 4) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002685 Genomic DNA. Translation: AEC07659.1.
AY057588 mRNA. Translation: AAL14383.1.
AY143822 mRNA. Translation: AAN28761.1.
AY088079 mRNA. Translation: AAM65625.1.
PIRiD84644.
RefSeqiNP_565585.1. NM_128068.2.
UniGeneiAt.14653.

Genome annotation databases

EnsemblPlantsiAT2G25110.1; AT2G25110.1; AT2G25110.
GeneIDi817049.
GrameneiAT2G25110.1; AT2G25110.1; AT2G25110.
KEGGiath:AT2G25110.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002685 Genomic DNA. Translation: AEC07659.1.
AY057588 mRNA. Translation: AAL14383.1.
AY143822 mRNA. Translation: AAN28761.1.
AY088079 mRNA. Translation: AAM65625.1.
PIRiD84644.
RefSeqiNP_565585.1. NM_128068.2.
UniGeneiAt.14653.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3MALX-ray1.95A/B24-218[»]
ProteinModelPortaliQ93ZE8.
SMRiQ93ZE8. Positions 35-215.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi2401. 1 interaction.
IntActiQ93ZE8. 1 interaction.
MINTiMINT-7950181.
STRINGi3702.AT2G25110.1.

Proteomic databases

PaxDbiQ93ZE8.
PRIDEiQ93ZE8.

Protocols and materials databases

DNASUi817049.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G25110.1; AT2G25110.1; AT2G25110.
GeneIDi817049.
GrameneiAT2G25110.1; AT2G25110.1; AT2G25110.
KEGGiath:AT2G25110.

Organism-specific databases

TAIRiAT2G25110.

Phylogenomic databases

eggNOGiKOG3358. Eukaryota.
ENOG410ZBU3. LUCA.
HOGENOMiHOG000236354.
InParanoidiQ93ZE8.
OMAiMAQPSQN.
PhylomeDBiQ93ZE8.

Miscellaneous databases

PROiQ93ZE8.

Gene expression databases

GenevisibleiQ93ZE8. AT.

Family and domain databases

InterProiIPR027005. GlyclTrfase_39-like.
IPR016093. MIR_motif.
[Graphical view]
PANTHERiPTHR10050. PTHR10050. 1 hit.
PfamiPF02815. MIR. 1 hit.
[Graphical view]
SMARTiSM00472. MIR. 3 hits.
[Graphical view]
SUPFAMiSSF82109. SSF82109. 1 hit.
PROSITEiPS50919. MIR. 3 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "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.
  4. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  5. Cited for: FUNCTION, INTERACTION WITH ERDJ3B, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLY-64.
  6. "Arabidopsis stromal-derived Factor2 (SDF2) is a crucial target of the unfolded protein response in the endoplasmic reticulum."
    Schott A., Ravaud S., Keller S., Radzimanowski J., Viotti C., Hillmer S., Sinning I., Strahl S.
    J. Biol. Chem. 285:18113-18121(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 24-218, FUNCTION, INDUCTION.

Entry informationi

Entry nameiSDF2_ARATH
AccessioniPrimary (citable) accession number: Q93ZE8
Secondary accession number(s): O81720, Q9SEZ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 19, 2002
Last sequence update: December 1, 2001
Last modified: May 11, 2016
This is version 101 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.