HumanLectome - Human Lectin Entry

NCBI Summary

This gene encodes a member of the calnexin family of molecular chaperones. The encoded protein is a calcium-binding, endoplasmic reticulum (ER)-associated protein that interacts transiently with newly synthesized N-linked glycoproteins, facilitating protein folding and assembly. It may also play a central role in the quality control of protein folding by retaining incorrectly folded protein subunits within the ER for degradation. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2018].

Protein

Protein (NP_001737)

Protein name

Calnexin

Synonym(s)

Calnexin (IP90) (Major histocompatibility complex class I antigen-binding protein p88) (p90)

HGNC gene name

CANX

HGNC name

calnexin

Protein_CD_name

Undefined

Lectin confidence

Curated

UniLectin class

calnexin-calreticulin like

Known lectin group

L-Type Lectins

Lectin fold

b-sandwich / ConA-like

Glycan specificity

Glc(a1-3)Man(a1-2)Man(a1-2)Man / glucosylated N-glycan

RefSeq accession

Gene ID

UniProt accession

Ensembl protein ID

UniRef cluster ID

LectomeXplore score

0.608

Reference

10.1074/jbc.270.9.4697

Other links

PFAM, InterPro

Protein sequence and protein families (fasta) (592 amino acids) Download

MEGKWLLCMLLVLGTAIVEAHDGHDDDVIDIEDDLDDVIEEVEDSKPDTTAPPSSPKVTYKAPVPTGEVYFADSFDRGTLSGWILSKAKKDDTDDEIAKYDGKWEVEEMKESKLPGDKGLVLMSRAKHHAISAKLNKPFLFDTKPLIVQYEVNFQNGIECGGAYVKLLSKTPELNLDQFHDKTPYTIMFGPDKCGEDYKLHFIFRHKNPKTGIYEEKHAKRPDADLKTYFTDKKTHLYTLILNPDNSFEILVDQSVVNSGNLLNDMTPPVNPSREIEDPEDRKPEDWDERPKIPDPEAVKPDDWDEDAPAKIPDEEATKPEGWLDDEPEYVPDPDAEKPEDWDEDMDGEWEAPQIANPRCESAPGCGVWQRPVIDNPNYKGKWKPPMIDNPSYQGIWKPRKIPNPDFFEDLEPFRMTPFSAIGLELWSMTSDIFFDNFIICADRRIVDDWANDGWGLKKAADGAAEPGVVGQMIEAAEERPWLWVVYILTVALPVFLVILFCCSGKKQTSGMEYKKTDAPQPDVKEEEEEKEEEKDKGDEEEEGEEKLEEKQKSDAEEDGGTVSQEEEDRKPKAEEDEILNRSPRNRKPRRE

No structure currently available in the PDB RCSB Databank.

Structural models

AlphaFold v2: AF-P27824-F1 Download

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

SWISS-MODEL structural models

SWISS-MODEL structural model

Modeller structural model (Homology modelling pipeline), Error: [0.3, 0.78] Å Download

The location of the lectin domain structural model is: 68-466
We infer [0.3, 0.78] Å as the interval of error of this structural model.
Template 1: 1JHN chain: A, P24643, NP_001003232.1, sequence identity: 94.0%, coverage: 97.7%, location in sequence: 61-458, (61-458 in PDB).
Template 2: 6ENY chain: G, P27797, NP_004334.1, sequence identity: 38.6%, coverage: 84.2%, location in sequence: 18-386, (18-386 in PDB).
Template 3: 3O0W chain: A, P14211, NP_031617.1, sequence identity: 38.1%, coverage: 84.2%, location in sequence: 18-362, (18-362 in PDB).
Show the alignment used for the construction of the structural model, Download.
Show the plot of DOPE energy score, Download.

Oligomerization and Known Interactions

Interacts with MAPK3/ERK1 (By similarity). Interacts with KCNH2 (PubMed:16361248). Associates with ribosomes (By similarity). Interacts with SGIP1; involved in negative regulation of endocytosis (By similarity). The palmitoylated form interacts with the ribosome-translocon complex component SSR1, promoting efficient folding of glycoproteins (PubMed:22314232). Interacts with SERPINA2P/SERPINA2 and with the S and Z variants of SERPINA1 (PubMed:23826168). Interacts with PPIB (PubMed:20801878). Interacts with ZNRF4 (PubMed:21205830). Interacts with SMIM22 (PubMed:29765154). Interacts with TMX2 (PubMed:31735293). Interacts with TMEM35A/NACHO (By similarity). Interacts with CHRNA7 (PubMed:32783947). Interacts with reticulophagy regulators RETREG2 and RETREG3 (PubMed:34338405). Interacts with DNM1L; may form part of a larger protein complex at the ER-mitochondrial interface during mitochondrial fission (PubMed:24196833). Interacts with ADAM7 (By similarity)

(Microbial infection) Interacts with HBV large envelope protein, isoform L

(Microbial infection) Interacts with HBV large envelope protein, isoform M; this association may be essential for isoform M proper secretion

Annotation

Ligand

Glycan ligands from structural data

No crystal structures of complexes with glycan ligand.

Expression

Human Protein Atlas

GeneCards

Functionality temporarily unavailable.

ProteomicsDB

References

NCBI References (10 PubMed Identifiers)

Circulating small extracellular vesicles increase after an acute bout of moderate-intensity exercise in pregnant compared to non-pregnant women. [34135428]

Ca2+ Regulates ERp57-Calnexin Complex Formation. [34064874]

The Role of Cardiolipin as a Scaffold Mitochondrial Phospholipid in Autophagosome Formation: In Vitro Evidence. [33562550]

Calnexin mediates the maturation of GPI-anchors through ER retention. [32967966]

ER-resident oxidoreductases are glycosylated and trafficked to the cell surface to promote matrix degradation by tumour cells. [33077910]

The integrin chains beta 1 and alpha 6 associate with the chaperone calnexin prior to integrin assembly. [8163531]

Human, mouse, and rat calnexin cDNA cloning: identification of potential calcium binding motifs and gene localization to human chromosome 5. [8136357]

The molecular chaperones HSP28, GRP78, endoplasmin, and calnexin exhibit strikingly different levels in quiescent keratinocytes as compared to their proliferating normal and transformed counterparts: cDNA cloning and expression of calnexin. [8055875]

Microsequences of 145 proteins recorded in the two-dimensional gel protein database of normal human epidermal keratinocytes. [1286667]

The major histocompatibility complex class I antigen-binding protein p88 is the product of the calnexin gene. [1326756]

UniProt Main References (30 PubMed Identifiers)

Interaction with newly synthesized and retained proteins in the endoplasmic reticulum suggests a chaperone function for human integral membrane protein IP90 (calnexin). [8486646]

Complete sequencing and characterization of 21,243 full-length human cDNAs. [14702039]

The DNA sequence and comparative analysis of human chromosome 5. [15372022]

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). [15489334]

Formation of intracellular particles by hepatitis B virus large surface protein. [9188622]

Role for calnexin and N-linked glycosylation in the assembly and secretion of hepatitis B virus middle envelope protein particles. [9420286]

Proteomic analysis of early melanosomes: identification of novel melanosomal proteins. [12643545]

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. [17081983]

Mechanisms of pharmacological rescue of trafficking-defective hERG mutant channels in human long QT syndrome. [16361248]

Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes. [17081065]

Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. [18691976]

A quantitative atlas of mitotic phosphorylation. [18669648]

Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography. [18318008]

Large-scale proteomics analysis of the human kinome. [19369195]

Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. [19690332]

Lysine acetylation targets protein complexes and co-regulates major cellular functions. [19608861]

Structural basis of cyclophilin B binding by the calnexin/calreticulin P-domain. [20801878]

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. [20068231]

Initial characterization of the human central proteome. [21269460]

A systematic search for endoplasmic reticulum (ER) membrane-associated RING finger proteins identifies Nixin/ZNRF4 as a regulator of calnexin stability and ER homeostasis. [21205830]

System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. [21406692]

Palmitoylated calnexin is a key component of the ribosome-translocon complex. [22314232]

Toward a comprehensive characterization of a human cancer cell phosphoproteome. [23186163]

SERPINA2 is a novel gene with a divergent function from SERPINA1. [23826168]

An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. [24275569]

N-terminome analysis of the human mitochondrial proteome. [25944712]

The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation. [29765154]

TMX2 Is a Crucial Regulator of Cellular Redox State, and Its Dysfunction Causes Severe Brain Developmental Abnormalities. [31735293]

NACHO Engages N-Glycosylation ER Chaperone Pathways for alpha7 Nicotinic Receptor Assembly. [32783947]

All isoforms of this gene containing a lectin domain

NP_001350927.1, NP_001350928.1, NP_001019820.1, NP_001350925.1, NP_001350926.1, NP_001737.1, XP_011532967.1, NP_001350923.1, NP_001350922.1, XP_011532966.1, NP_001350924.1, NP_001350929.1, NP_001350930.1

RNA

RNA (Transcript ID: NM_001746.4)

RNA RefSeq ID

NM_001746.4

RNA name

calnexin, transcript variant 1

Isoforms

All isoforms of CANX containing a lectin domain

RNA Ensembl ID

ENST00000247461.9

Coding region

140..1918 (or 179705682.. 179728644)

mRNA location

179698967.. 179731641

NCBI Matured mRNA sequence 4915 NTP Download

m⁷G-5')ppp(5'-AGCGGUGGCCGAGGCCUCUUGGUUCUGCGGCACGUGACGGUCGGGCCGCCUCCGCCUCUCUCUUUACUGCGGCGCGGGGCAAGGUGUGCGGGCGGGAAGGGGCACGGGCACCCCCGCGGUCCCCGGGAGGCUAGAGAUCAUGGAAGGGAAGUGGUUGCUGUGUAUGUUACUGGUGCUUGGAACUGCUAUUGUUGAGGCUCAUGAUGGACAUGAUGAUGAUGUGAUUGAUAUUGAGGAUGACCUUGACGAUGUCAUUGAAGAGGUAGAAGACUCAAAACCAGAUACCACUGCUCCUCCUUCAUCUCCCAAGGUUACUUACAAAGCUCCAGUUCCAACAGGGGAAGUAUAUUUUGCUGAUUCUUUUGACAGAGGAACUCUGUCAGGGUGGAUUUUAUCCAAAGCCAAGAAAGACGAUACCGAUGAUGAAAUUGCCAAAUAUGAUGGAAAGUGGGAGGUAGAGGAAAUGAAGGAGUCAAAGCUUCCAGGUGAUAAAGGACUUGUGUUGAUGUCUCGGGCCAAGCAUCAUGCCAUCUCUGCUAAACUGAACAAGCCCUUCCUGUUUGACACCAAGCCUCUCAUUGUUCAGUAUGAGGUUAAUUUCCAAAAUGGAAUAGAAUGUGGUGGUGCCUAUGUGAAACUGCUUUCUAAAACACCAGAACUCAACCUGGAUCAGUUCCAUGACAAGACCCCUUAUACGAUUAUGUUUGGUCCAGAUAAAUGUGGAGAGGACUAUAAACUGCACUUCAUCUUCCGACACAAAAACCCCAAAACGGGUAUCUAUGAAGAAAAACAUGCUAAGAGGCCAGAUGCAGAUCUGAAGACCUAUUUUACUGAUAAGAAAACACAUCUUUACACACUAAUCUUGAAUCCAGAUAAUAGUUUUGAAAUACUGGUUGACCAAUCUGUGGUGAAUAGUGGAAAUCUGCUCAAUGACAUGACUCCUCCUGUAAAUCCUUCACGUGAAAUUGAGGACCCAGAAGACCGGAAGCCCGAGGAUUGGGAUGAAAGACCAAAAAUCCCAGAUCCAGAAGCUGUCAAGCCAGAUGACUGGGAUGAAGAUGCCCCUGCUAAGAUUCCAGAUGAAGAGGCCACAAAACCCGAAGGCUGGUUAGAUGAUGAGCCUGAGUACGUACCUGAUCCAGACGCAGAGAAACCUGAGGAUUGGGAUGAAGACAUGGAUGGAGAAUGGGAGGCUCCUCAGAUUGCCAACCCUAGAUGUGAGUCAGCUCCUGGAUGUGGUGUCUGGCAGCGACCUGUGAUUGACAACCCCAAUUAUAAAGGCAAAUGGAAGCCUCCUAUGAUUGACAAUCCCAGUUACCAGGGAAUCUGGAAACCCAGGAAAAUACCAAAUCCAGAUUUCUUUGAAGAUCUGGAACCUUUCAGAAUGACUCCUUUUAGUGCUAUUGGUUUGGAGCUGUGGUCCAUGACCUCUGACAUUUUUUUUGACAACUUUAUCAUUUGUGCUGAUCGAAGAAUAGUUGAUGAUUGGGCCAAUGAUGGAUGGGGCCUGAAGAAAGCUGCUGAUGGGGCUGCUGAGCCAGGCGUUGUGGGGCAGAUGAUCGAGGCAGCUGAAGAGCGCCCGUGGCUGUGGGUAGUCUAUAUUCUAACUGUAGCCCUUCCUGUGUUCCUGGUUAUCCUCUUCUGCUGUUCUGGAAAGAAACAGACCAGUGGUAUGGAGUAUAAGAAAACUGAUGCACCUCAACCGGAUGUGAAGGAAGAGGAAGAAGAGAAGGAAGAGGAAAAGGACAAGGGAGAUGAGGAGGAGGAAGGAGAAGAGAAACUUGAAGAGAAACAGAAAAGUGAUGCUGAAGAAGAUGGUGGCACUGUCAGUCAAGAGGAGGAAGACAGAAAACCUAAAGCAGAGGAGGAUGAAAUUUUGAACAGAUCACCAAGAAACAGAAAGCCACGAAGAGAGUGAAACAAUCUUAAGAGCUUGAUCUGUGAUUUCUUCUCCCUCCUCCCCUGCAAGAGUGGUCCUAGGAGAGGACCUGGCACACCUUAGGUUGACAUUCAGAAAACUUCAAGACAUCACCAUCAGCAGGCUCCAGUUGAACACUAGUCUGUGUAACUUUAAACAUCUAGCAGUAAAUACUUGCAGUUGUGAUAUAAAGGACCCUGUUUCUGUAGAAAAGAAAACAUUUAACAUAAUGGUUGUGAAAUGUAACAUGAAGCAAACUAACUUUUUUUUUUUUAACAUCUUUGUUUUUAAAAUAGAAUGAUAGAACUUUGCCAGUCUUUAAGAUCUUGGCUUAAUUUAAUGUAUUAAUCUGUUUGUGCAAACAUAAUACCACCAUUUAAAAAUGUUAGGGAGAUGAGUUGCAGUUUUUAUAAUAGAUUUUUUUUAAAGUUUGGUAUUGUAAAACAUUCACACCUCUGUCCCUCAAAAUUGAUAAUUACGUUUAAAGUGCAGUCAUUUGUGGUUAGAAUCUUGUUUUGUUUGCUUCCAUUAUUGAGUUCCUCCUAAGGAAAUUGAGGAGAGGGACUGAAUAGAAGCCCAAAUUCAUAUAAAAGUUGCGUUUAAGUUGUAUUAAAAAUAGAUAUAUAAGAAAAAAUUCUUUCACUUGAUGUUUGUUAGACCAGAAAGUGUGUGUGUUCUGUAGCUCAGUUCCCAGACAGCUUUUUAGGUAGUGGAGGAGGUGGCUUCAUGUGGCACUUGGGCAUUUAUAUUCCACUUGGGAGGGUCAGGCUGUGGCCUUCUGGAGCAGGUGGCUUGUUAAGGAAUGCUAGCAGGGCAUGGCACGUGAGCUCCGGAAUAGAUGUCUUCAUCACUUCUUCCACUGUGUGUUGACACUGUUUUCCUUACCUAUUUCCUCAGAUCCCCAGCUUUCUCCUCUGCUAUGCAUUUUCUUCACAGUGCAGCUUGCAGUCCGUUGCUGAAAAUGAUUAUAAGCCCUGCAUAAUGUUAAGCUUUAUUGUGAUUACGUGUAUGUUUCUUCUUUCUUUUAAGCAGACCCAUACCUUUCCAGGGUCAAAGUACAGAAUAGAAUACAUUGAUACAAAGUACAGAAAAAUACUUUGAUUUUUAUCCAUUUCUUUUACUCUGUGUAAAGACUUGAGAAGUCUAAUUCACAGGCAAACCAAUACAGAAUUGACUGCAGUUGAACAGACUAGAAGUAUUUGUGGGAGGAGUGACAUGAAGCAUGAGUUAUCUGAUUUUUUUUGUAGCUGCUAUAUAUUUUAAGCCUUCAUUUGCAAUUCAUGUAACAGUUGUGUCAUAAAUUACACAAUAAAGCAGUCCUGUUCAAAUUUUUUUUUAACGUGGCUUGUAGAAUUUUUAAAAAAGUGAUCUUAGGUUUGUUUUUUCAUGCGGGAUGCAGAUGGGUGCUAUCAGAGCCUCUCCCACACCACUAUAGUGUAAUAAUGUUAUUAUUACUCUACACUGAAACGUAUUCAGAGUUAGAUAUUAUUUUAGCUUCAGUUGUUCUUUAGAGGCUUUCAAAUGUACCGAUGAUACUGUUUCUUGCACUGAAUAUAUAAACACUCCACAGUGUUUAUAUUGGGAAGAUAUUGGGAAGGAAAUAUAUUUGUAAAAGAUGAAGGCUGUAUCUAUUUUUUUUUCUUUUUAAAGUUUGUUCACUUAAAUUCUUUUGAGGAUGGGAUGUAUUUUUCUUGCUGUUCAGUGCUUUUUCCUUUUCAUCUGUUGUUCUGUGGUCACAGUGACCUUAGCUACAUAGCAGACUUUCCCAAAUGUAUUGAUUACAAAUAAACAGUUGUUACUUAGCAAGACCUGAAAAUAUGUCUGCAGGUUUCUCCUUGAAGCAAAUGUGUGGGAUCAUUGCAUUUCCAGAAAUCUGCCUCCUUCACCCUCCGUUGACAGUAUAUGUCAUGCCUCACUUUCUUCUAGCUGAGCUUUAAAUCAUUAGAGCUUAAAUUGUCAGAUCGUUCAUUGCCUUUCCAGGGUUAUUUAGUAAAGUUUGUUGAAAACAAAAACGCCUUUUCUUGGUUCUUUUUUCAGUUAUUUUGAAGGUCCAGCAUCCUGAUUAAAUGUCUGACACAUUAAUGAAUGACCAGCAGCAGCUUUCAGCUCUUAAAAAGACACUUAUAUUUUGAUUUUACAUGCUGGUUACCUGUUCCAUUGUUGUCAAAUGCCCACUCUCCAUCAGAUGUGUUCCUCCAUUUUCUUAUCCACAAAGUACUCCUCACUUUUCAAUUUGUCAUGUUACUAAAUGGUGUUACAUUAAAGCCCUGUGUUAAGUGUCUGCUUUUGACUGAAUUUCUUCAUAGUAACCUUCAGUGUGUGUGUGUGACUAUGUUCAAUUAGUGGGUUGAUCUUCGUAUAAUUGGCCACUAUGUGAGAGUUCACUACUAGGCAGAAACUAUUAUGGACAGUGAAAUAAUGACUUUUAUCUCACCACGUGAGUUUGAUGCAGUCUUUUCUGUCUAGCCCUUGCCUCUUCCUGCCCAUGUGAUUGCGGUGCAGUAGUUUCUGUUGUAUAAUAGUGUGGACAGCAGCUCAGAAAAGGAGGGAAUGCUACUGAUAAUUUGUAGAUAAUAUUCUUUAAGACUUAGGGGAACCAUUGAACUUUGAAAUUUUUAUUAGAAAAUUAUUUGUUCAGAAUCAGACUCCAUUAUUUUACAUAUACUUAAAUACUUUAGGGGUAUUUUUGAAAGUUAGCCCAGUUUUUUAUGUGCUAUUAAAUUUUUAGAUUACAUACUAAAGAAAAGUAUGUACACAGAAUGUAGUGCUCCUAGUUACUAUUUUUUCUAUUAAGAAAUAGUUUAGUUCUGGUGUAAAAUUUGUUUGAAUGCUAAAAAAAAAAAAGCAGGACUGCAUUAUGGCACUUUUGCCUUGGUGGCCCACUUUCUCCAUUUAAAACAUUAGGAUUUGUAUUUUUCUGCUGCGUUUGUAUGAAGACAUAUUUGAUUGUUGUUUUCUCUUGAUUUUAAAAUAAAACCUCAUGAGCCCUAGUAAAAA-3'- Poly-A tail

Coding region

mRNA-related data

DNA

DNA (Gene ID: 821)

HGNC Gene symbol

CANX

HGNC Gene name

calnexin

Chr. RefSeq ID

NC_000005.10

Chromosome N°

5 179705682.. 179728644

CDS location

179705682.. 179728644

DNA strand

strand +

CCDS ID

CCDS4447.1

Mouse ortholog gene

MGI:88261

Gene Variant

ClinVar, dbVar

DNA Ensembl ID

ENSG00000127022

HGNC other symbol

CNX, IP90, P90

UCSC ID

uc003mkl.4

GeneBank

INSDC: L18887

GeneCards

1473

MIM

114217

VEGA ID

OTTHUMG00000130910

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