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Protein

N-terminal EF-hand calcium-binding protein 3

Gene

NECAB3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Inhibits the interaction of APBA2 with beta-amyloid precursor protein (APP), and hence allows formation of beta-amyloid.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Calcium bindingi49 – 6012PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. calcium ion binding Source: InterPro

GO - Biological processi

  1. protein metabolic process Source: UniProtKB
  2. protein secretion Source: UniProtKB
  3. regulation of amyloid precursor protein biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Ligandi

Calcium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
N-terminal EF-hand calcium-binding protein 3
Alternative name(s):
Amyloid beta A4 protein-binding family A member 2-binding protein
Nek2-interacting protein 1
Neuronal calcium-binding protein 3
X11L-binding protein 51
Gene namesi
Name:NECAB3
Synonyms:APBA2BP, NIP1, SYTIP2, XB51
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15851. NECAB3.

Subcellular locationi

  1. Golgi apparatus 2 Publications

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. endoplasmic reticulum membrane Source: UniProtKB
  3. Golgi cis cisterna Source: UniProtKB
  4. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Golgi apparatus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA24871.

Polymorphism and mutation databases

BioMutaiNECAB3.
DMDMi41688800.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 396396N-terminal EF-hand calcium-binding protein 3PRO_0000073863Add
BLAST

Post-translational modificationi

Phosphorylated by NEK2.

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ96P71.
PRIDEiQ96P71.

PTM databases

PhosphoSiteiQ96P71.

Expressioni

Tissue specificityi

Strongly expressed in heart and skeletal muscle, moderately in brain and pancreas.2 Publications

Gene expression databases

BgeeiQ96P71.
CleanExiHS_NECAB3.
ExpressionAtlasiQ96P71. baseline and differential.
GenevestigatoriQ96P71.

Interactioni

Subunit structurei

Interacts with the N-terminal domain of APBA2. Interacts with NEK2.2 Publications

Protein-protein interaction databases

BioGridi122006. 5 interactions.
IntActiQ96P71. 1 interaction.

Structurei

3D structure databases

SMRiQ96P71. Positions 39-100.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini36 – 7136EF-handPROSITE-ProRule annotationAdd
BLAST
Domaini296 – 38590ABMAdd
BLAST

Sequence similaritiesi

Contains 1 ABM domain.Curated
Contains 1 EF-hand domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG70920.
GeneTreeiENSGT00390000009734.
HOVERGENiHBG050433.
InParanoidiQ96P71.
OMAiFFPASWW.
OrthoDBiEOG7BS49N.
PhylomeDBiQ96P71.
TreeFamiTF331029.

Family and domain databases

Gene3Di1.10.238.10. 1 hit.
InterProiIPR007138. ABM-like.
IPR011008. Dimeric_a/b-barrel.
IPR011992. EF-hand-dom_pair.
IPR018247. EF_Hand_1_Ca_BS.
IPR002048. EF_hand_dom.
[Graphical view]
PfamiPF03992. ABM. 1 hit.
PF13202. EF-hand_5. 1 hit.
[Graphical view]
SUPFAMiSSF54909. SSF54909. 1 hit.
PROSITEiPS51725. ABM. 1 hit.
PS00018. EF_HAND_1. 1 hit.
PS50222. EF_HAND_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist. Experimental confirmation may be lacking for some isoforms.

Isoform 2 (identifier: Q96P71-1) [UniParc]FASTAAdd to basket

Also known as: XB51-alpha

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
MACAGLLTVC LLRPPAPQPQ PQTPRHPQLA PDPGPAGHTL FQDVFRRADK
60 70 80 90 100
NDDGKLSFEE FQNYFADGVL SLGELQELFS GIDGHLTDNL ETEKLCDYFS
110 120 130 140 150
EHLGVYRPVL AALESLNRAV LAAMDATKLE YERASKVDQF VTRFLLRETV
160 170 180 190 200
SQLQALQSSL EGASDTLEAQ AHGWRSDAES VEAQSRLCGS RRAGRRALRS
210 220 230 240 250
VSRSSTWSPG SSDTGRSSEA EMQWRLQVNR LQELIDQLEC KVRAVGPGPH
260 270 280 290 300
KGGPSWYPPE PGPCWRPGPH SVPSQAPRLE PLREEDLAKG PDLHILMAQR
310 320 330 340 350
QVQVAEEGLQ DFHRALRCYV DFTGAQSHCL HVSAQKMLDG ASFTLYEFWQ
360 370 380 390
DEASWRRHQQ SPGSKAFQRI LIDHLRAPDT LTTVFFPASW WIMNNN
Length:396
Mass (Da):44,350
Last modified:February 28, 2003 - v2
Checksum:i9B24503AA629CB45
GO
Isoform 1 (identifier: Q96P71-2) [UniParc]FASTAAdd to basket

Also known as: XB51-beta

The sequence of this isoform differs from the canonical sequence as follows:
     242-275: Missing.

Show »
Length:362
Mass (Da):40,796
Checksum:i946EFAB4F5D97AC4
GO
Isoform 3 (identifier: Q96P71-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     176-203: SDAESVEAQSRLCGSRRAGRRALRSVSR → YVRVLSTCGASAQAPIVPPFQIPTVPAS
     204-396: Missing.

Note: May result from the retention of an intron in the cDNA.

Show »
Length:203
Mass (Da):22,251
Checksum:i5F7361BCCC745238
GO

Sequence cautioni

The sequence BAB14649.1 differs from that shown. Reason: Frameshift at position 56. Curated
The sequence BAB16413.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti383 – 3831T → I in AAG28415 (PubMed:12044471).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti254 – 2541P → L.
Corresponds to variant rs17124890 [ dbSNP | Ensembl ].
VAR_048643

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei176 – 20328SDAES…RSVSR → YVRVLSTCGASAQAPIVPPF QIPTVPAS in isoform 3. 1 PublicationVSP_000737Add
BLAST
Alternative sequencei204 – 396193Missing in isoform 3. 1 PublicationVSP_000738Add
BLAST
Alternative sequencei242 – 27534Missing in isoform 1. 4 PublicationsVSP_000739Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF193759 mRNA. Translation: AAG28415.1.
AF409141 mRNA. Translation: AAL01118.1.
AK023706 mRNA. Translation: BAB14649.1. Frameshift.
AK291895 mRNA. Translation: BAF84584.1.
AL121906 Genomic DNA. Translation: CAI22127.1.
AL121906 Genomic DNA. Translation: CAI22128.1.
AL121906 Genomic DNA. Translation: CAI22129.1.
CH471077 Genomic DNA. Translation: EAW76302.1.
CH471077 Genomic DNA. Translation: EAW76304.1.
BC047673 mRNA. Translation: AAH47673.1.
AB039947 mRNA. Translation: BAB16413.1. Different initiation.
CCDSiCCDS42866.1. [Q96P71-1]
CCDS42867.1. [Q96P71-2]
RefSeqiNP_112508.3. NM_031231.3. [Q96P71-2]
NP_112509.3. NM_031232.3. [Q96P71-1]
UniGeneiHs.516986.

Genome annotation databases

EnsembliENST00000246190; ENSP00000246190; ENSG00000125967. [Q96P71-1]
ENST00000375238; ENSP00000364386; ENSG00000125967. [Q96P71-2]
GeneIDi63941.
KEGGihsa:63941.
UCSCiuc002wzm.4. human. [Q96P71-2]
uc002wzn.4. human. [Q96P71-1]

Polymorphism and mutation databases

BioMutaiNECAB3.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF193759 mRNA. Translation: AAG28415.1.
AF409141 mRNA. Translation: AAL01118.1.
AK023706 mRNA. Translation: BAB14649.1. Frameshift.
AK291895 mRNA. Translation: BAF84584.1.
AL121906 Genomic DNA. Translation: CAI22127.1.
AL121906 Genomic DNA. Translation: CAI22128.1.
AL121906 Genomic DNA. Translation: CAI22129.1.
CH471077 Genomic DNA. Translation: EAW76302.1.
CH471077 Genomic DNA. Translation: EAW76304.1.
BC047673 mRNA. Translation: AAH47673.1.
AB039947 mRNA. Translation: BAB16413.1. Different initiation.
CCDSiCCDS42866.1. [Q96P71-1]
CCDS42867.1. [Q96P71-2]
RefSeqiNP_112508.3. NM_031231.3. [Q96P71-2]
NP_112509.3. NM_031232.3. [Q96P71-1]
UniGeneiHs.516986.

3D structure databases

SMRiQ96P71. Positions 39-100.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122006. 5 interactions.
IntActiQ96P71. 1 interaction.

PTM databases

PhosphoSiteiQ96P71.

Polymorphism and mutation databases

BioMutaiNECAB3.
DMDMi41688800.

Proteomic databases

PaxDbiQ96P71.
PRIDEiQ96P71.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000246190; ENSP00000246190; ENSG00000125967. [Q96P71-1]
ENST00000375238; ENSP00000364386; ENSG00000125967. [Q96P71-2]
GeneIDi63941.
KEGGihsa:63941.
UCSCiuc002wzm.4. human. [Q96P71-2]
uc002wzn.4. human. [Q96P71-1]

Organism-specific databases

CTDi63941.
GeneCardsiGC20M032244.
HGNCiHGNC:15851. NECAB3.
MIMi612478. gene.
neXtProtiNX_Q96P71.
PharmGKBiPA24871.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG70920.
GeneTreeiENSGT00390000009734.
HOVERGENiHBG050433.
InParanoidiQ96P71.
OMAiFFPASWW.
OrthoDBiEOG7BS49N.
PhylomeDBiQ96P71.
TreeFamiTF331029.

Miscellaneous databases

ChiTaRSiNECAB3. human.
GeneWikiiAPBA2BP.
GenomeRNAii63941.
NextBioi65710.
PROiQ96P71.
SOURCEiSearch...

Gene expression databases

BgeeiQ96P71.
CleanExiHS_NECAB3.
ExpressionAtlasiQ96P71. baseline and differential.
GenevestigatoriQ96P71.

Family and domain databases

Gene3Di1.10.238.10. 1 hit.
InterProiIPR007138. ABM-like.
IPR011008. Dimeric_a/b-barrel.
IPR011992. EF-hand-dom_pair.
IPR018247. EF_Hand_1_Ca_BS.
IPR002048. EF_hand_dom.
[Graphical view]
PfamiPF03992. ABM. 1 hit.
PF13202. EF-hand_5. 1 hit.
[Graphical view]
SUPFAMiSSF54909. SSF54909. 1 hit.
PROSITEiPS51725. ABM. 1 hit.
PS00018. EF_HAND_1. 1 hit.
PS50222. EF_HAND_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "NECABs: a family of neuronal Ca(2+)-binding proteins with an unusual domain structure and a restricted expression pattern."
    Sugita S., Ho A., Suedhof T.C.
    Neuroscience 112:51-63(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY.
  2. "NIP1/XB51/NECAB3 is a potential substrate of Nek2, suggesting specific roles of Nek2 in Golgi."
    Yoo J.C., Chang J.R., Kim S.H., Jang S.K., Wolgemuth D.J., Kim K., Rhee K.
    Exp. Cell Res. 292:393-402(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH NEK2, SUBCELLULAR LOCATION.
    Tissue: Liver.
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
    Tissue: Placenta and Skeletal muscle.
  4. "The DNA sequence and comparative analysis of human chromosome 20."
    Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E.
    , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
    Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  7. "Regulation of X11L-dependent amyloid precursor protein metabolism by XB51, a novel X11L-binding protein."
    Lee D.-S., Tomita S., Kirino Y., Suzuki T.
    J. Biol. Chem. 275:23134-23138(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 65-396 (ISOFORM 2), FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH APBA2.
    Tissue: Brain.

Entry informationi

Entry nameiNECA3_HUMAN
AccessioniPrimary (citable) accession number: Q96P71
Secondary accession number(s): A8K780
, E1P5N2, Q5JWF5, Q5JWF6, Q5JWF7, Q86VV1, Q9H433, Q9H8G8, Q9HBW7, Q9HCQ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 28, 2003
Last sequence update: February 28, 2003
Last modified: April 29, 2015
This is version 127 of the entry and version 2 of the sequence. [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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. 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.