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Available structures
PDBOrtholog search: PDBe RCSB
AliasesSMC1A, CDLS2, DXS423E, SB1.8, SMC1, SMC1L1, SMC1alpha, SMCB, structural maintenance of chromosomes 1A
External IDsOMIM: 300040 MGI: 1344345 HomoloGene: 4597 GeneCards: SMC1A
Gene location (Human)
X chromosome (human)
Chr.X chromosome (human)[1]
X chromosome (human)
Genomic location for SMC1A
Genomic location for SMC1A
BandXp11.22Start53,374,149 bp[1]
End53,422,728 bp[1]
RNA expression pattern
PBB GE SMC1A 201589 at fs.png

PBB GE SMC1A 217555 at fs.png
More reference expression data
RefSeq (mRNA)



RefSeq (protein)



Location (UCSC)Chr X: 53.37 – 53.42 MbChr X: 152.02 – 152.06 Mb
PubMed search[3][4]
View/Edit HumanView/Edit Mouse

Structural maintenance of chromosomes protein 1A is a protein that in humans is encoded by the SMC1A gene.[5][6] SMC1A gene (also called SMC1L1, SMC1alpha) belongs to the Structural Maintenance of Chromosome family. This gene encodes a protein that is a component of cohesin, a highly conserved complex in eukaryotes, which ensures correct chromosome segregation during mitosis and meiosis.[7]

Gene and protein structure[edit]

SMC1A gene is located on human Xp11.22–Xp11.21 chromosome, in a region that escapes X inactivation.[8][9] SMC1A has multiple transcripts and the full-length gene codes a protein of 1,233 amino acids. SMC1A protein has a modular structure organized in five domains: N-terminal, coiled-coil, hinge, coiled-coil and C-terminal domain. The N-terminal domain holds a nucleoside triphosphate (NTP) binding motif (Walker A box), and is responsible for binding ATP. The C-terminal contains the DNA binding domain DA box (Walker B box). SMC proteins are preserved not only in sequence but also in structure. In mammals, the coiled-coil domains of SMC1A and SMC3, which belongs to the SMC family, have an amino acid sequence variation of only around 0.1%.


SMC1A has been shown to interact with SMC3[10][11][12][13] and Ataxia telangiectasia mutated.[10] The hinge domain is responsible for SMC1A flexibility allowing homo- and hetero-dimerization, in particular with SMC3. The hinge domains of SMC1A-SMC3 heterodimer interact with each other while their head domains interact with RAD21, creating a closed ring-like structure. Finally, the cohesin complex is completed when the RAD21 subunit associates with SA1 or SA2 (also called STAG1 or STAG2) protein. Cohesin is also involved in meiotic chromosome segregation. Oocytes and spermatozoa express two different versions of cohesin complexes, containing either SMC1A or SMC1B (also called SMC1L2, SMC1beta). SMC1B is located on 22q13.31 human chromosome and codes a protein involved in sister chromatid cohesion, chromosome synapsis, and ensures telomere protection from rearrangement.[14][15][16][17][18] Although SMC1B is believed to be meiotic-specific, it has also been shown to be expressed in mitotic cells and is mutually exclusive with SMC1A.[19] SMC1A is also a component of the Recombination protein complex (RC-1) constituted by SMC1A, SMC3, a 5'-3' exonuclease, DNA polymerase ɛ and DNA ligase III. It is believed that RC-1 plays a role in the repair of double strand breaks and DNA deletion by recombination.[20][21][22][23] Finally, SMC1A interacts with RAE1 (RNA export factor 1), with Ataxia Telangiectasia Mutated (ATM) and the Ataxia Telangiectasia and Rad3 Related (ATR) (see both the “Function” and the “Genome instability and cancer” sections).


In addition to entrapping DNA to ensure proper chromosome segregation during the cell cycle, SMC1A, as a component of cohesin, contributes to facilitating inter-chromatid contacts mediating distant-element interactions and to creating chromosome domains called topologically associating domains (TADs). It has been proposed that cohesin promotes the interaction between enhancers and promoters for regulating gene transcription regulation.[24][25][26][27][28][29] The removal of cohesin triggers abnormal TAD topology because loops spanning multiple compartment intervals lead to mixing among loci in different compartments[30][31] As a consequence, loop loss causes gene expression dysregulation.[30] SMC1A also plays a role in spindle pole formation. In fact, in association with SMC3, it is recruited to mitotic spindle poles through interaction with RAE1. The dysregulation of SMC1A (both down- and up-regulation) causes aberrant multi-polar spindles, suggesting that cohesin would function to hold microtubules at the spindle pole.[32][33] Proper cohesion of sister chromatids is a prerequisite for the correct segregation of chromosomes during cell division. The cohesin multiprotein complex is required for sister chromatid cohesion. This complex is composed partly of two structural maintenance of chromosomes (SMC) proteins, SMC3 and either SMC1L2 or the protein encoded by this gene. Most of the cohesin complexes dissociate from the chromosomes before mitosis, although those complexes at the kinetochore remain. Therefore, the encoded protein is thought to be an important part of functional kinetochores. In addition, this protein interacts with BRCA1 and is phosphorylated by ATM, indicating a potential role for this protein in DNA repair. This gene, which belongs to the SMC gene family, is located in an area of the X-chromosome that escapes X inactivation.[6]

Human disorders[edit]

Pathogenic variants in SMC1A, missense and small in frame deletions, are associated with Cornelia de Lange syndrome (CdLS, MIM #122470, #300590, #610759, #614701, #300882). CdLS is a human rare disease characterized by dysmorphic features, pre- and post-natal growth delay, intellectual disability that is usually moderate to severe, synophrys, hirsutism, and alterations in hands and fingers. Additional CdLS signs can include hearing loss, heart defects, microcephaly, (i.e., an unusually small head) and problems with the digestive tract.[34][35] The frequency varies from 1:10 000 to 1:30 000 live births without differences between ethnic groups.[36] SMC1A variants, which maintain the frame of their encoded proteins, are associated with milder CdLS phenotypes with moderate neurocognitive disability and a paucity of major structural defects. The phenotype of SMC1A affected males is more severe than that of mutated females.[37][38][39] Since SMC1A escapes X inactivation, it has been hypothesized that the mechanism in affected females is the dominant-negative effect of the mutated protein. The binding of mutated cohesin to chromatin is stronger than that of normal cohesin and disturbs the recruitment of RNA polymerase II.[40][41] It has been postulated that these phenomena trigger gene expression dysregulation that is a molecular marker of CdLS cells harboring SMC1A pathogenic variants.[42][43][41] Instead, SMC1A truncation variants have been described in females characterized by a clinical phenotype different from CdLS, with pharmaco-resistant epilepsy and moderate to severe neurological impairment.[44][45][46][47][48][49][50]

Genome instability and cancer[edit]

SMC1A also takes part in DNA repair. The down-regulation of SMC1A causes genome instability, and CdLS cells carrying SMC1A variants display high level of chromosome aberrations.[51][52][40][53] Furthermore, SMC1A is phosphorylated on Ser957 and Ser966 residues by ATM and ATR threonine/serine kinases following DNA damage induced by chemical treatment or ionizing radiation. It has been hypothesized that the Breast cancer type 1 susceptibility (BRCA1) gene collaborates in phosphorylating SMC1A, which is required for activation of the S-phase checkpoint allowing blocking of the cell cycle and the repair of DNA.[54][55][52] SMC1A variants have been identified in blood, brain, bladder, and colon cancer.[56][57][58][59][60][61][62] SMC1A plays a pivotal role in colorectal tumorigenesis. Indeed, colorectal tissue acquires extra-copies of SMC1A during cancer development and its expression is significantly stronger in carcinomas than in normal mucosa and early adenoma.[62] Finally, the up-regulation of SMC1A is thought to be a predictor of poor prognosis in colorectal cancer.[63]

See also[edit]


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Further reading[edit]

  • Nakajima D, Okazaki N, Yamakawa H, Kikuno R, Ohara O, Nagase T (June 2002). "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones". DNA Research. 9 (3): 99–106. doi:10.1093/dnares/9.3.99. PMID 12168954.

External links[edit]