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Protein

Intermediate filament protein ifb-1

Gene

ifb-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Cytoplasmic intermediate filaments provide mechanical strength to cells. Essential protein, involved in attachment structures in epidermal cells that connect muscles to the external cuticle. Required in morphogenesis and epidermal integrity. Probable component of embryonic epidermal attachment structures. Functions in larval muscle attachment independently of ifa-2.3 Publications

GO - Molecular functioni

Complete GO annotation...

Enzyme and pathway databases

ReactomeiREACT_287964. Unblocking of NMDA receptor, glutamate binding and activation.
REACT_304705. CREB phosphorylation through the activation of CaMKII.

Names & Taxonomyi

Protein namesi
Recommended name:
Intermediate filament protein ifb-1
Alternative name(s):
Cel IF B1
Intermediate filament protein B1
Short name:
IF-B1
Gene namesi
Name:ifb-1
ORF Names:F10C1.2
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
ProteomesiUP000001940 Componenti: Chromosome II

Organism-specific databases

WormBaseiF10C1.2a; CE02618; WBGene00002053; ifb-1.
F10C1.2b; CE02619; WBGene00002053; ifb-1.

Subcellular locationi

GO - Cellular componenti

  • apical plasma membrane Source: WormBase
  • cytoplasm Source: UniProtKB-SubCell
  • intermediate filament Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Intermediate filament

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 589589Intermediate filament protein ifb-1PRO_0000063838Add
BLAST

Proteomic databases

PaxDbiQ19289.
PRIDEiQ19289.

2D gel databases

World-2DPAGE0020:Q19289.

Expressioni

Tissue specificityi

Expressed in epidermal cells. Expressed in amphid sensory neurons, the excretory cells, the vulva, the uterus, the rectum and some neurons of the tail. Isoform a and isoform b display a similar pattern of expression. Isoform a is predominant in pharyngeal tonofilaments.2 Publications

Interactioni

Subunit structurei

Forms some heteropolymeric filaments with ifa-1, ifa-2, ifa-3 and probably ifa-4.

Binary interactionsi

WithEntry#Exp.IntActNotes
T04C9.1Q8MPT25EBI-316236,EBI-2315635
Y56A3A.7A7DTF54EBI-316236,EBI-2413939

Protein-protein interaction databases

BioGridi39317. 6 interactions.
DIPiDIP-26309N.
IntActiQ19289. 9 interactions.
MINTiMINT-1053724.
STRINGi6239.F10C1.2b.

Structurei

3D structure databases

ProteinModelPortaliQ19289.
SMRiQ19289. Positions 473-583.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini467 – 584118LTDAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 8477HeadAdd
BLAST
Regioni85 – 433349RodAdd
BLAST
Regioni85 – 11632Coil 1AAdd
BLAST
Regioni117 – 13014Linker 1Add
BLAST
Regioni131 – 268138Coil 1BAdd
BLAST
Regioni269 – 28517Linker 12Add
BLAST
Regioni286 – 433148Coil 2Add
BLAST
Regioni434 – 588155TailAdd
BLAST

Sequence similaritiesi

Belongs to the intermediate filament family.Curated
Contains 1 LTD domain.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiNOG315022.
GeneTreeiENSGT00760000118905.
HOGENOMiHOG000017007.
InParanoidiQ19289.
KOiK18585.
OMAiGENTWGI.
OrthoDBiEOG7FV3Q8.
PhylomeDBiQ19289.

Family and domain databases

Gene3Di2.60.40.1260. 1 hit.
InterProiIPR001664. IF.
IPR016451. Intermed_filament_ifa/ifb.
IPR018039. Intermediate_filament_CS.
IPR001322. Lamin_tail_dom.
[Graphical view]
PANTHERiPTHR23239. PTHR23239. 1 hit.
PfamiPF00038. Filament. 1 hit.
PF00932. LTD. 1 hit.
[Graphical view]
PIRSFiPIRSF005546. Intermed_filamnt_Ifb-2. 1 hit.
SUPFAMiSSF74853. SSF74853. 1 hit.
PROSITEiPS00226. IF. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform a (identifier: Q19289-1) [UniParc]FASTAAdd to basket

Also known as: B1b, IFB-1B

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
MSSHKESSEY EMQYRSTIQP RTAVRSQSRQ SGNYVSGGNG AGSGGRVLKM
60 70 80 90 100
VTEMGSATVG GISPALSANA AKSFLEATDK EKKTLQGLND RLGNYIDRVK
110 120 130 140 150
KLEEQNRKLV ADLDELRGKW GKDTSEIKIK YSESLSTARK DIDDAARRKA
160 170 180 190 200
EVDVKVARHR DDLAEYRSRY EDIQQRRESD REKISQWTNA IADAQSEVEM
210 220 230 240 250
LRARFKQLTD EEKRVTADNS RIWEELQKAR SDLDDETIGR IDFQNQVQTL
260 270 280 290 300
MEELEFLRRV HEQEVKELQA LLAQAPADTR EFFKNELALA IRDIKDEYDI
310 320 330 340 350
IAKQGKQDME SWYKLKVSEV QGSANRANME STYQRDEVKR MRDNIGDLRG
360 370 380 390 400
KLGDLENKNS LLEKEVQNLN YQLTDDQRQY EAALNDRDAT LRRMREECQT
410 420 430 440 450
LVAELQALLD TKQMLDAEIA IYRKMLEGEE TRVGLTQMVE QAVKTHSLQQ
460 470 480 490 500
QENTDSTRSV RGEVSTKTTF QRSAKGNVTI SECDPNGKFI KLENSHRNKD
510 520 530 540 550
ENVGEHKIRR KLDGRREIVY SIPANVVIKP GKNLTIYARD QGGINNPPES
560 570 580
LVFDGENTWG IGANVVTSLV NKDGEERATH TQKTIQSGQ
Length:589
Mass (Da):67,149
Last modified:November 1, 1996 - v1
Checksum:iC4B6231224ED9AB0
GO
Isoform b (identifier: Q19289-2) [UniParc]FASTAAdd to basket

Also known as: B1a IFB-1A

The sequence of this isoform differs from the canonical sequence as follows:
     1-42: MSSHKESSEYEMQYRSTIQPRTAVRSQSRQSGNYVSGGNGAG → MEAESAPQAPM

Show »
Length:558
Mass (Da):63,700
Checksum:iA25DFFAE9DAD7AAF
GO

Sequence cautioni

The sequence CAA50178.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 4242MSSHK…GNGAG → MEAESAPQAPM in isoform b. CuratedVSP_010147Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X70830 Genomic DNA. Translation: CAA50178.1. Sequence problems.
FO080600 Genomic DNA. Translation: CCD65029.1.
FO080600 Genomic DNA. Translation: CCD65030.1.
PIRiD88163.
T16018. S46326.
RefSeqiNP_495136.1. NM_062735.4. [Q19289-1]
NP_495137.1. NM_062736.3. [Q19289-2]
UniGeneiCel.7922.

Genome annotation databases

EnsemblMetazoaiF10C1.2b; F10C1.2b; WBGene00002053. [Q19289-1]
GeneIDi173976.
KEGGicel:CELE_F10C1.2.
UCSCiF10C1.2b. c. elegans. [Q19289-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X70830 Genomic DNA. Translation: CAA50178.1. Sequence problems.
FO080600 Genomic DNA. Translation: CCD65029.1.
FO080600 Genomic DNA. Translation: CCD65030.1.
PIRiD88163.
T16018. S46326.
RefSeqiNP_495136.1. NM_062735.4. [Q19289-1]
NP_495137.1. NM_062736.3. [Q19289-2]
UniGeneiCel.7922.

3D structure databases

ProteinModelPortaliQ19289.
SMRiQ19289. Positions 473-583.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi39317. 6 interactions.
DIPiDIP-26309N.
IntActiQ19289. 9 interactions.
MINTiMINT-1053724.
STRINGi6239.F10C1.2b.

2D gel databases

World-2DPAGE0020:Q19289.

Proteomic databases

PaxDbiQ19289.
PRIDEiQ19289.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiF10C1.2b; F10C1.2b; WBGene00002053. [Q19289-1]
GeneIDi173976.
KEGGicel:CELE_F10C1.2.
UCSCiF10C1.2b. c. elegans. [Q19289-1]

Organism-specific databases

CTDi173976.
WormBaseiF10C1.2a; CE02618; WBGene00002053; ifb-1.
F10C1.2b; CE02619; WBGene00002053; ifb-1.

Phylogenomic databases

eggNOGiNOG315022.
GeneTreeiENSGT00760000118905.
HOGENOMiHOG000017007.
InParanoidiQ19289.
KOiK18585.
OMAiGENTWGI.
OrthoDBiEOG7FV3Q8.
PhylomeDBiQ19289.

Enzyme and pathway databases

ReactomeiREACT_287964. Unblocking of NMDA receptor, glutamate binding and activation.
REACT_304705. CREB phosphorylation through the activation of CaMKII.

Miscellaneous databases

NextBioi881937.
PROiQ19289.

Family and domain databases

Gene3Di2.60.40.1260. 1 hit.
InterProiIPR001664. IF.
IPR016451. Intermed_filament_ifa/ifb.
IPR018039. Intermediate_filament_CS.
IPR001322. Lamin_tail_dom.
[Graphical view]
PANTHERiPTHR23239. PTHR23239. 1 hit.
PfamiPF00038. Filament. 1 hit.
PF00932. LTD. 1 hit.
[Graphical view]
PIRSFiPIRSF005546. Intermed_filamnt_Ifb-2. 1 hit.
SUPFAMiSSF74853. SSF74853. 1 hit.
PROSITEiPS00226. IF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Eight genes and alternative RNA processing pathways generate an unexpectedly large diversity of cytoplasmic intermediate filament proteins in the nematode Caenorhabditis elegans."
    Dodemont H., Riemer D., Ledger T.N., Weber K.
    EMBO J. 13:2625-2638(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM B).
    Strain: Bristol N2.
  2. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING.
    Strain: Bristol N2.
  3. "Essential roles for four cytoplasmic intermediate filament proteins in Caenorhabditis elegans development."
    Karabinos A., Schmidt H., Harborth J., Schnabel R., Weber K.
    Proc. Natl. Acad. Sci. U.S.A. 98:7863-7868(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY.
  4. "In vivo and in vitro evidence that the four essential intermediate filament (IF) proteins A1, A2, A3 and B1 of the nematode Caenorhabditis elegans form an obligate heteropolymeric IF system."
    Karabinos A., Schulze E., Schuenemann J., Parry D.A.D., Weber K.
    J. Mol. Biol. 333:307-319(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH IFA-1; IFA-2; IFA-3 AND IFA-4.
  5. "Intermediate filaments are required for C. elegans epidermal elongation."
    Woo W.-M., Goncharov A., Jin Y., Chisholm A.D.
    Dev. Biol. 267:216-229(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.

Entry informationi

Entry nameiIFB1_CAEEL
AccessioniPrimary (citable) accession number: Q19289
Secondary accession number(s): Q19290, Q21063
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: November 1, 1996
Last modified: July 22, 2015
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.