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Protein

LIM domain and actin-binding protein 1

Gene

LIMA1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Actin-binding protein involved in actin cytoskeleton regulation and dynamics. Increases the number and size of actin stress fibers and inhibits membrane ruffling. Inhibits actin filament depolymerization. Bundles actin filaments, delays filament nucleation and reduces formation of branched filaments (PubMed:12566430). Plays a role in cholesterol homeostasis. Influences plasma cholesterol levels through regulation of intestinal cholesterol absorption. May act as a scaffold protein by regulating NPC1L1 transportation, an essential protein for cholesterol absorption, to the plasma membrane by recruiting MYO5B to NPC1L1, and thus facilitates cholesterol uptake (By similarity).By similarity1 Publication

GO - Molecular functioni

  • actin filament binding Source: UniProtKB
  • actin monomer binding Source: UniProtKB
  • cadherin binding Source: BHF-UCL
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

Molecular functionActin-binding
Biological processCholesterol metabolism, Lipid metabolism, Steroid metabolism, Sterol metabolism
LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
LIM domain and actin-binding protein 1
Alternative name(s):
Epithelial protein lost in neoplasm
Gene namesi
Name:LIMA1Imported
Synonyms:EPLIN1 Publication, SREBP3
ORF Names:PP624
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

EuPathDBiHostDB:ENSG00000050405.13
HGNCiHGNC:24636 LIMA1
MIMi608364 gene
neXtProtiNX_Q9UHB6

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell junction, Cell membrane, Cytoplasm, Cytoskeleton, Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi51474
MIMi618079 phenotype
OpenTargetsiENSG00000050405
PharmGKBiPA143485527

Polymorphism and mutation databases

BioMutaiLIMA1
DMDMi20138067

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000757301 – 759LIM domain and actin-binding protein 1Add BLAST759

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei4PhosphoserineCombined sources1
Modified residuei15PhosphoserineCombined sources1
Modified residuei55PhosphoserineCombined sources1
Modified residuei132PhosphoserineCombined sources1
Modified residuei225PhosphoserineCombined sources1
Modified residuei229PhosphotyrosineCombined sources1
Modified residuei230PhosphoserineBy similarity1
Modified residuei242PhosphoserineBy similarity1
Modified residuei263PhosphoserineCombined sources1
Modified residuei343PhosphoserineCombined sources1
Modified residuei350PhosphoserineCombined sources1
Modified residuei362PhosphoserineCombined sources1
Modified residuei365PhosphoserineCombined sources1
Modified residuei369PhosphoserineCombined sources1
Modified residuei374PhosphoserineCombined sources1
Modified residuei439N6-succinyllysineBy similarity1
Modified residuei490PhosphoserineCombined sources1
Modified residuei601PhosphoserineCombined sources1
Modified residuei604PhosphoserineCombined sources1
Modified residuei609PhosphoserineCombined sources1
Modified residuei617PhosphoserineCombined sources1
Modified residuei686PhosphoserineCombined sources1
Modified residuei692PhosphoserineCombined sources1
Modified residuei698PhosphoserineCombined sources1
Modified residuei726PhosphoserineCombined sources1
Modified residuei741PhosphoserineBy similarity1
Isoform Alpha (identifier: Q9UHB6-2)
Modified residuei1N-acetylmethionineCombined sources1
Isoform 5 (identifier: Q9UHB6-5)
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei183PhosphoserineCombined sources1
Isoform 4 (identifier: Q9UHB6-4)
Modified residuei343PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylation of the C-terminal region by MAPK1/MAPK3 reduces its association with F-actin and contributes to actin filament reorganization and enhances cell motility.By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9UHB6
PaxDbiQ9UHB6
PeptideAtlasiQ9UHB6
PRIDEiQ9UHB6
ProteomicsDBi84296
84297 [Q9UHB6-2]
84298 [Q9UHB6-3]
84299 [Q9UHB6-4]

PTM databases

iPTMnetiQ9UHB6
PhosphoSitePlusiQ9UHB6

Expressioni

Tissue specificityi

Highly expressed in placenta, kidney, pancreas, prostate, ovary, spleen and heart. Also detected in lung, liver, brain, skeletal muscle, thymus, testis and intestine. Not detected in leukocytes. Isoform Beta expressed generally at very low levels. Isoform Alpha abundant in epithelial cells from mammary gland, prostate and in normal oral keratinocytes. Low levels in aortic endothelial cells and dermal fibroblasts. Not detectable in myocardium.1 Publication

Inductioni

Down-regulated in some cancer cell lines. Isoform Alpha is induced by serum. Isoform Beta is constitutively expressed.1 Publication

Gene expression databases

BgeeiENSG00000050405 Expressed in 230 organ(s), highest expression level in oocyte
ExpressionAtlasiQ9UHB6 baseline and differential
GenevisibleiQ9UHB6 HS

Organism-specific databases

HPAiHPA023871
HPA052645

Interactioni

Subunit structurei

Interacts with NPCL1; bridges NPC1L1 with MYO5B (PubMed:29880681). Interacts with MYO5B; bridges NPC1L1 with MYO5B (PubMed:29880681). Interacts with PXN; this complex stabilizes actin dynamics (PubMed:24694988). Interacts with F-actin and G-actin (PubMed:12566430).3 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi119559, 273 interactors
DIPiDIP-29633N
IntActiQ9UHB6, 184 interactors
MINTiQ9UHB6
STRINGi9606.ENSP00000378400

Structurei

Secondary structure

1759
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ9UHB6
SMRiQ9UHB6
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UHB6

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini388 – 448LIM zinc-bindingPROSITE-ProRule annotationAdd BLAST61

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni493 – 513Required for interaction with MYO5BBy similarityAdd BLAST21

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi164 – 166Required for interaction with NPC1L1By similarity3

Domaini

Contains at least 2 actin-binding domains, one on each side of the LIM domain. Both domains bind actin monomers and filaments. The C-terminal domain binds filaments more efficiently than the N-terminus.1 Publication

Keywords - Domaini

LIM domain

Phylogenomic databases

eggNOGiENOG410ITI7 Eukaryota
ENOG41102B0 LUCA
GeneTreeiENSGT00510000046839
HOGENOMiHOG000059621
HOVERGENiHBG051492
InParanoidiQ9UHB6
OMAiRETCVEC
OrthoDBiEOG091G0043
PhylomeDBiQ9UHB6
TreeFamiTF350273

Family and domain databases

InterProiView protein in InterPro
IPR028740 EPLIN
IPR001781 Znf_LIM
PANTHERiPTHR24206:SF50 PTHR24206:SF50, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 1 hit
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 1 hit
PS50023 LIM_DOMAIN_2, 1 hit

Sequences (5+)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative promoter usage and alternative splicing. AlignAdd to basket

This entry has 5 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

Isoform Beta (identifier: Q9UHB6-1) [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
MESSPFNRRQ WTSLSLRVTA KELSLVNKNK SSAIVEIFSK YQKAAEETNM
60 70 80 90 100
EKKRSNTENL SQHFRKGTLT VLKKKWENPG LGAESHTDSL RNSSTEIRHR
110 120 130 140 150
ADHPPAEVTS HAASGAKADQ EEQIHPRSRL RSPPEALVQG RYPHIKDGED
160 170 180 190 200
LKDHSTESKK MENCLGESRH EVEKSEISEN TDASGKIEKY NVPLNRLKMM
210 220 230 240 250
FEKGEPTQTK ILRAQSRSAS GRKISENSYS LDDLEIGPGQ LSSSTFDSEK
260 270 280 290 300
NESRRNLELP RLSETSIKDR MAKYQAAVSK QSSSTNYTNE LKASGGEIKI
310 320 330 340 350
HKMEQKENVP PGPEVCITHQ EGEKISANEN SLAVRSTPAE DDSRDSQVKS
360 370 380 390 400
EVQQPVHPKP LSPDSRASSL SESSPPKAMK KFQAPARETC VECQKTVYPM
410 420 430 440 450
ERLLANQQVF HISCFRCSYC NNKLSLGTYA SLHGRIYCKP HFNQLFKSKG
460 470 480 490 500
NYDEGFGHRP HKDLWASKNE NEEILERPAQ LANARETPHS PGVEDAPIAK
510 520 530 540 550
VGVLAASMEA KASSQQEKED KPAETKKLRI AWPPPTELGS SGSALEEGIK
560 570 580 590 600
MSKPKWPPED EISKPEVPED VDLDLKKLRR SSSLKERSRP FTVAASFQST
610 620 630 640 650
SVKSPKTVSP PIRKGWSMSE QSEESVGGRV AERKQVENAK ASKKNGNVGK
660 670 680 690 700
TTWQNKESKG ETGKRSKEGH SLEMENENLV ENGADSDEDD NSFLKQQSPQ
710 720 730 740 750
EPKSLNWSSF VDNTFAEEFT TQNQKSQDVE LWEGEVVKEL SVEEQIKRNR

YYDEDEDEE
Note: Produced by alternative promoter usage.
Length:759
Mass (Da):85,226
Last modified:May 1, 2000 - v1
Checksum:i996378AFD3B003D5
GO
Isoform Alpha (identifier: Q9UHB6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-160: Missing.

Note: Produced by alternative promoter usage.Combined sources
Show »
Length:599
Mass (Da):67,119
Checksum:iDE0AE1D7A916BE30
GO
Isoform 3 (identifier: Q9UHB6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-302: Missing.

Note: Produced by alternative splicing of isoform Beta.
Show »
Length:457
Mass (Da):51,219
Checksum:iDD730BA1D2FB8E2E
GO
Isoform 4 (identifier: Q9UHB6-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     344-344: R → PG

Note: Produced by alternative splicing.Combined sources
Show »
Length:760
Mass (Da):85,224
Checksum:i5FD64F6E2ECEFAE2
GO
Isoform 5 (identifier: Q9UHB6-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-160: Missing.
     344-344: R → PG

Note: No experimental confirmation available.Combined sources
Show »
Length:600
Mass (Da):67,117
Checksum:iDAE126F756B45C5F
GO

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F8VQE1F8VQE1_HUMAN
LIM domain and actin-binding protei...
LIMA1
598Annotation score:
F8VS07F8VS07_HUMAN
LIM domain and actin-binding protei...
LIMA1
456Annotation score:
F8VVQ7F8VVQ7_HUMAN
LIM domain and actin-binding protei...
LIMA1
111Annotation score:
F8VRN8F8VRN8_HUMAN
LIM domain and actin-binding protei...
LIMA1
388Annotation score:
F8VTU2F8VTU2_HUMAN
LIM domain and actin-binding protei...
LIMA1
130Annotation score:

Sequence cautioni

The sequence AAG17267 differs from that shown. Reason: Frameshift at positions 365 and 662.Curated
The sequence BAA91120 differs from that shown. Reason: Frameshift at position 697.Curated
The sequence BAD92749 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti381Missing in BAA90914 (PubMed:14702039).Curated1
Sequence conflicti381Missing in AAH01247 (PubMed:15489334).Curated1
Sequence conflicti415F → L in AAG17267 (PubMed:15498874).Curated1
Sequence conflicti463D → G in BAA90914 (PubMed:14702039).Curated1
Sequence conflicti491P → Q in AAF67491 (PubMed:10931946).Curated1
Sequence conflicti520 – 521DK → NR in AAF67491 (PubMed:10931946).Curated2

Polymorphismi

Genetic variations in LIMA1 influence low density lipoprotein cholesterol (LDL-C) variability and contribute to the low density lipoprotein cholesterol level quantitative trait locus 8 (LDLCQ8) [MIMi:618079].1 Publication

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_08086425L → I Polymorphism; associated with lower plasma levels of low-density lipoprotein cholesterol; reduces protein stability. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0031171 – 302Missing in isoform 3. 2 PublicationsAdd BLAST302
Alternative sequenceiVSP_0031161 – 160Missing in isoform Alpha and isoform 5. 2 PublicationsAdd BLAST160
Alternative sequenceiVSP_040136344R → PG in isoform 4 and isoform 5. 2 Publications1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF198454 mRNA Translation: AAF23755.1
AF198455 mRNA Translation: AAF23756.1
AF157325 mRNA Translation: AAF67491.1
AL136911 mRNA Translation: CAB66845.1
AK000372 mRNA Translation: BAA91120.1 Frameshift.
AK000335 mRNA Translation: BAA91092.1
AK023649 mRNA Translation: BAB14625.1
AK000057 mRNA Translation: BAA90914.1
AK314447 mRNA Translation: BAG37056.1
AB209512 mRNA Translation: BAD92749.1 Different initiation.
CH471111 Genomic DNA Translation: EAW58135.1
BC001247 mRNA Translation: AAH01247.2
BC010664 mRNA Translation: AAH10664.1
BC110815 mRNA Translation: AAI10816.1
BC136763 mRNA Translation: AAI36764.1
AF218025 mRNA Translation: AAG17267.1 Frameshift.
CCDSiCCDS44877.1 [Q9UHB6-4]
CCDS55826.1 [Q9UHB6-5]
CCDS58230.1 [Q9UHB6-3]
CCDS8802.1 [Q9UHB6-1]
RefSeqiNP_001107018.1, NM_001113546.1 [Q9UHB6-4]
NP_001107019.1, NM_001113547.1 [Q9UHB6-5]
NP_001230704.1, NM_001243775.1 [Q9UHB6-3]
NP_057441.1, NM_016357.4 [Q9UHB6-1]
XP_011536757.1, XM_011538455.2 [Q9UHB6-4]
XP_016874919.1, XM_017019430.1 [Q9UHB6-3]
UniGeneiHs.525419

Genome annotation databases

EnsembliENST00000341247; ENSP00000340184; ENSG00000050405 [Q9UHB6-1]
ENST00000394943; ENSP00000378400; ENSG00000050405 [Q9UHB6-4]
ENST00000547825; ENSP00000448706; ENSG00000050405 [Q9UHB6-3]
ENST00000552783; ENSP00000448779; ENSG00000050405 [Q9UHB6-5]
ENST00000552823; ENSP00000450266; ENSG00000050405 [Q9UHB6-2]
GeneIDi51474
KEGGihsa:51474
UCSCiuc001rwg.5 human [Q9UHB6-1]

Keywords - Coding sequence diversityi

Alternative promoter usage, Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF198454 mRNA Translation: AAF23755.1
AF198455 mRNA Translation: AAF23756.1
AF157325 mRNA Translation: AAF67491.1
AL136911 mRNA Translation: CAB66845.1
AK000372 mRNA Translation: BAA91120.1 Frameshift.
AK000335 mRNA Translation: BAA91092.1
AK023649 mRNA Translation: BAB14625.1
AK000057 mRNA Translation: BAA90914.1
AK314447 mRNA Translation: BAG37056.1
AB209512 mRNA Translation: BAD92749.1 Different initiation.
CH471111 Genomic DNA Translation: EAW58135.1
BC001247 mRNA Translation: AAH01247.2
BC010664 mRNA Translation: AAH10664.1
BC110815 mRNA Translation: AAI10816.1
BC136763 mRNA Translation: AAI36764.1
AF218025 mRNA Translation: AAG17267.1 Frameshift.
CCDSiCCDS44877.1 [Q9UHB6-4]
CCDS55826.1 [Q9UHB6-5]
CCDS58230.1 [Q9UHB6-3]
CCDS8802.1 [Q9UHB6-1]
RefSeqiNP_001107018.1, NM_001113546.1 [Q9UHB6-4]
NP_001107019.1, NM_001113547.1 [Q9UHB6-5]
NP_001230704.1, NM_001243775.1 [Q9UHB6-3]
NP_057441.1, NM_016357.4 [Q9UHB6-1]
XP_011536757.1, XM_011538455.2 [Q9UHB6-4]
XP_016874919.1, XM_017019430.1 [Q9UHB6-3]
UniGeneiHs.525419

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2D8YNMR-A381-457[»]
ProteinModelPortaliQ9UHB6
SMRiQ9UHB6
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119559, 273 interactors
DIPiDIP-29633N
IntActiQ9UHB6, 184 interactors
MINTiQ9UHB6
STRINGi9606.ENSP00000378400

PTM databases

iPTMnetiQ9UHB6
PhosphoSitePlusiQ9UHB6

Polymorphism and mutation databases

BioMutaiLIMA1
DMDMi20138067

Proteomic databases

EPDiQ9UHB6
PaxDbiQ9UHB6
PeptideAtlasiQ9UHB6
PRIDEiQ9UHB6
ProteomicsDBi84296
84297 [Q9UHB6-2]
84298 [Q9UHB6-3]
84299 [Q9UHB6-4]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000341247; ENSP00000340184; ENSG00000050405 [Q9UHB6-1]
ENST00000394943; ENSP00000378400; ENSG00000050405 [Q9UHB6-4]
ENST00000547825; ENSP00000448706; ENSG00000050405 [Q9UHB6-3]
ENST00000552783; ENSP00000448779; ENSG00000050405 [Q9UHB6-5]
ENST00000552823; ENSP00000450266; ENSG00000050405 [Q9UHB6-2]
GeneIDi51474
KEGGihsa:51474
UCSCiuc001rwg.5 human [Q9UHB6-1]

Organism-specific databases

CTDi51474
DisGeNETi51474
EuPathDBiHostDB:ENSG00000050405.13
GeneCardsiLIMA1
H-InvDBiHIX0171649
HGNCiHGNC:24636 LIMA1
HPAiHPA023871
HPA052645
MIMi608364 gene
618079 phenotype
neXtProtiNX_Q9UHB6
OpenTargetsiENSG00000050405
PharmGKBiPA143485527
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410ITI7 Eukaryota
ENOG41102B0 LUCA
GeneTreeiENSGT00510000046839
HOGENOMiHOG000059621
HOVERGENiHBG051492
InParanoidiQ9UHB6
OMAiRETCVEC
OrthoDBiEOG091G0043
PhylomeDBiQ9UHB6
TreeFamiTF350273

Miscellaneous databases

ChiTaRSiLIMA1 human
EvolutionaryTraceiQ9UHB6
GeneWikiiLIMA1
GenomeRNAii51474
PROiPR:Q9UHB6
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000050405 Expressed in 230 organ(s), highest expression level in oocyte
ExpressionAtlasiQ9UHB6 baseline and differential
GenevisibleiQ9UHB6 HS

Family and domain databases

InterProiView protein in InterPro
IPR028740 EPLIN
IPR001781 Znf_LIM
PANTHERiPTHR24206:SF50 PTHR24206:SF50, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 1 hit
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 1 hit
PS50023 LIM_DOMAIN_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLIMA1_HUMAN
AccessioniPrimary (citable) accession number: Q9UHB6
Secondary accession number(s): B2RB09
, Q2TAN7, Q59FE8, Q9BVF2, Q9H8J1, Q9HBN5, Q9NX96, Q9NXC3, Q9NXU6, Q9P0H8, Q9UHB5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 5, 2002
Last sequence update: May 1, 2000
Last modified: November 7, 2018
This is version 180 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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