Draft:CCDC200

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Draft:CCDC200
  • Comment: Of all the cited sources, only source 22 (Priyanka and Yenugu) appears to be secondary and significant, and it discusses CCDC proteins in general, not specifically this one. All other sources are databases (primary) and research articles mostly on other topics (primary and not significant). Furthermore, the level of detail in the article, plus the sourcing almost entirely to databases, suggests a degree of WP:OR. I think a general article on CCDC proteins might be more appropriate than individual articles about the individual proteins, but if significant secondary coverage of the individual proteins (not databases) that might make individual articles appropriate. WeirdNAnnoyed (talk) 21:37, 6 August 2025 (UTC)


Coiled-coil domain-containing protein 200 (CCDC200) is a human protein, also denoted as LINC00854 and TMEM106A-AS1, that has the highest expression in the kidneys.[1] The CCDC200 transcript variant 1 (NM_001363254) is a gene that has 727 base pairs (bp), is located on the minus strand of chromosome 17 (17q21.31), has 4 exons, and encodes a protein that is 168 amino acids long.[1] This protein has an isoelectric point of 9.3 and a molecular weight of ~19.4 kilodaltons (kDa).[2] It also contains an evolutionarily conserved coiled-coil region and is predicted to be localized in the nucleus.[3] While CCDC200 is a highly conserved protein with many orthologs, dating as far back as 319 million years ago (mya),  no human paralogs have been found yet for this protein.[1]

When CCDC200 was knocked out, an increase in viral infection as well as a change in host and pathogen interactions was observed, suggesting potential roles in immune response.[4]

Gene

Figure 1. The gene neighborhood of CCDC200 includes upstream (TMEM106A and NBR1) and downstream (RNU2-1) genes.[1]
Figure 2. Depicts chromosome 17 and provides a visual representation of where the CCDC200 gene is located (marked by a red band).

The human CCDC200 gene is located on chromosome 17, at position 17q21.31, on the minus strand and has 4 exons, spanning 4998 bp.[1] The gene neighborhood of CCDC200 includes upstream (TMEM106A and NBR1) and downstream (RNU2-1) genes.[1]

Transcript

The CCDC200 gene has one isoform and two splice variants that are different based on their coding potential.[1] Transcript variant 1 has 3 introns and encodes for the CCDC200 protein, while transcript variant 2 (NR_047479) is labeled as a non-coding RNA (see Figure 3).[1]

Tissue Expression

According to RNA sequencing data of total RNA from 20 different human tissues, biased expression in the kidneys was found with low expression located in the lungs, stomach, uterus, spleen, and thymus.[1] When comparing the highest tissue expression, in reads per kilobase million (or RPKM), for kidneys (3.28) and in skeletal muscle (0.049), there was a ~67-fold difference.[1]

Figure 3. Shows the two variants of CCDC200 that exist, one that encodes for the CCDC200 protein and one that is a non-coding RNA. This article primarily discusses isoform 1, which is located at the top of the figure.

Proteins

General Information:

The Human CCDC200 protein (NP_001350183.1) contains 168 amino acids with an isoelectric point of 9.3 and a molecular weight is 19.4 kDa.[3] This aligns with CCDC200’s distant mammalian orthologs (such as Mus musculus) that has an isoelectric point of 9.6 and a molecular weight of 19.4 kDa.[3] This protein is glutamine and proline-rich, which can play a role in characterizing proteins as intrinsically disordered proteins (IDPs) due to limiting the formation of alpha helices or beta sheets.[5] This protein is also phenylalanine and glycine-deficient, suggesting that this protein in unlikely a transmembrane protein.[5][6]

Species Accession Molecular Weight (kDa)[2] Isoelectric Point[2]
Homo Sapiens NP_001350183.1[7] 19.4 9.3
Mus musculus NP_001359474.1[8] 19.4 9.6
Bos taurus XP_024836665.1[9] 17.7 9.0

Table 1. CCDC200 Protein Characteristics Shown in Humans and Close Mammalian Orthologs

Primary

The human CCDC200 protein is predicted to have nuclear localization signals in their N-terminal and C-terminal regions.[10] The protein is also predicted to be sub-cellularly localized to the nucleus with a 52.2% chance and is further supported with similar results when compared to Mus musculus (56.5%).[11]

There is a coiled-coil region is predicted to be found from residues 16-50 and intrinsically disordered regions found at 23-168.[3] The protein is also predicted to have a polyampholyte region (31-52), an area of low complexity (70-82), proline-rich regions (83-94 & 104-117), and polar regions (124-138 & 145-168).[3]

Figure 4. The annotated primary structure of CCDC200 shows domains, disordered regions, motifs, and phosphorylation sites (using InterPro and DTU HealthTech). The boxes show domains, regions, and motifs spanning different amino acid residues: the coiled-coil region is in royal blue (16-50), the polyampholyte motif in purple (31-52), the low-complexity region in red (70-82), the proline-rich regions in teal (84-95 & 103-116), the polar regions are in green (124-138 & 145-168), and the disordered region is marked (23-168). The different phosphorylation sites with highest probabilities are marked at their respective locations.[12]

Post-Translational Modification

The human CCDC200 protein is predicted to contain various phosphorylation, ubiquitination, and sumoylation motifs.[13]

Secondary and Tertiary Protein Structure

Predicted secondary structures of human CCDC200 show that the N-terminal region is more disordered compared to the rest of the protein.[14][15]

Figure 5. Predicted tertiary structure of human CCDC200 (C-score -3.48 and cluster density of 0.0267) shows an alpha-helical structure (at N-terminus) with a disordered region located towards the C-terminal region. Confidence score (C-score) refers to how accurate the predicted model is on a scale from [-5,2]

Regulation

The proteins that interact with CCDC200 highly are known as TRIM17, C6orf15, ADGRF4, CNTNAP5, LETM2, TMEM89, BPIFA, and OR1N2. Proteins such as VSTM2B, CATSPER2, and CCDC42 interact with CCDC200 less in comparison to the aforementioned proteins.[16][17]

Sub-cellular Localization

CCDC200 Human protein is predicted to be localized in the nucleus (52.2%), mitochondria  (21.7%), cytoplasm (13%), cytoskeleton (8.7%), and in secretory vesicles (4.3%). There is a weak peripheral (30.6%), transmembrane (12.9%), and lipid anchor (11.8%) association, meaning that the protein is predicted to be localized primarily in the nucleus or cytoplasm. This could give more insight as to which function the CCDC200 protein might have.

Homology

Orthologs

Coiled-Coil Domain Containing protein 200 (CCDC200) is found in varying species of mammals such as primates, rodents, lagomorphs, and monotremes.[18]Since orthologs of the human CCDC200 protein have been found in platypus, which diverged from humans around 180 million years ago, and have also been found in reptile species (such as the brown anole which diverged 319 mya), due to the presence of this gene, we can conclude that the CCDC200 gene is at least 319 million years old.[19] Since this gene has been conserved across many different species for 320 million years, it suggests that it serves an important biological function.

The CCDC200 protein can be found in primata, rodentia, lagomorpha, carnivora, artiodactyla, monotremata, and reptilia, but was not found in aves or various fish clades.[18] However, it is worth noting that some aquatic mammalian species do have the CCDC200 protein, notably Phocoena sinus, Orcinus orca, and Kogia breviceps.[18]

Figure 6. Global sequence alignment comparing the CCDC200 protein in Homo sapiens and Mus musculus. There is a 39.9% sequence identity and 48.5% similarity between the human and mouse genes. Highly conserved areas are highlighted in blue (marked with -), while orange indicates similarity (marked with :).[20]
Figure 7. This multiple sequence alignment was created using amino acid sequences of Homo sapiens, Ornithorhynchus anatinus, and Anolis sagrei. The first 13 amino acids are conserved across the three different species; however, the remaining amino acids vary more significantly. The N-terminal region of the CCDC200 protein is more conserved, further supporting the MSA of close orthologs, suggesting that there is an evolutionary benefit to preserving this region. (*) denotes areas of high conservation while (-) shows gaps (insertions/deletions).[21]
Clades Sequence # Genus Species Common Name Family Date of Divergence (MYA) Accession Number[18] Sequence Length (AA) Sequence Identity (%) Sequence Similarity (%)
1 Homo sapiens Humans Hominidae 0 A0A1B0GVQ3.1 168.00 100.00 100.00
2 Pongo pygmaeus Bornean Orangutan Hominidae 15.2 XP_054313734.1 172.00 92.40 94.20
3 Papio anubis Olive Baboon Cercopithecidae 28.8 XP_009189005.2 181.00 66.00 70.10
Primates 4 Cebus imitator Panamanian White-Faced Capuchin Cebidae 43 XP_037587582.1 168.00 74.90 80.70
5 Nycticebus coucang Sunda Slow Loris Lorisidae 74 XP_053426744.1 154.00 56.00 63.40
Rodentia 6 Mus musculus Mice Muridae 87 XP_030102092.1 168.00 39.90 48.50
7 Arvicanthis niloticus African Grass Rat Muridae 87 XP_034360446.1 215.00 86.96 86.03
Lagomorpha 8 Ochotona curzoniae Pika Ochotonidae 87 XP_040857462.1 155.00 47.40 56.10
9 Suricata suricatta Meercat Herpestidae 94 XP_029782790.1 167.00 38.30 45.60
Carnivora 10 Panthera leo Lion Felidae 94 XP_042771316.1 182.00 44.60 52.90
11 Lutra lutra Eurasian River Otter Mustelidae 94 XP_047561971.1 215.00 30.80 36.80
12 Vicugna pacos Alpaca Camelidae 94 XP_072796168.1 168.00 44.10 51.00
13 Camelus dromedarius Arabian Camel Camelidae 94 XP_031324555.1 160.00 48.10 56.90
Artiodactyla 14 Bos taurus Cow Bovidae 94 XP_024836665.1 151.00 52.70 58.60
15 Budorcas taxicolor Takin Bovidae 94 XP_052514448.1 150.00 50.50 57.00
17 Kogia breviceps Pygymy Sperm Whale Kogiidae 94 XP_066876845.1 160.00 47.90 56.30
18 Phocoena sinus Vaquita Phocoenidae 94 XP_032471384.1 117.00 36.50 41.40
Monotremata 19 Ornithorhynchus anatinus Platypus Ornithorhynchidae 180.00 XP_028930563.1 114.00 25.00 32.70
Reptilia 20 Anolis sagrei Brown Anole Dactyloidae 319 XP_060639141.2 118.00 26.70 41.30

Table 2. Table of CCDC200 Orthologs

This figure shows 20 orthologs of the human CCDC200 protein. Orthologs in seven orders were analyzed: primata (56.00-94.4% sequence identity), rodentia (39.9-86.96%), lagomorphs (47.4%), carnivora (30.8-44.6%), artiodactyla (36.5-52.7%), monotremata (25.0%), and reptilia (26.7%). It is also important to note that , there were no orthologs present in avian or fish species.[19] [18][20]

The graph shows the molecular clock analysis for the CCDC200 protein which measures the mutation rate to determine rates of divergence. It plots fibrinogen alpha chain(FGA), cytochrome c, and CCDC200. FGA (blue) has the highest trendline of the three proteins, showing that it has a higher mutation rate. CCDC200 (yellow) has a more moderate trendline, suggesting that there is not much evolutionary pressure to have high conservation; however, cytochrome c (red) has the lowest, which shows that there is a higher need to have more conservation.[18]

Paralogs

There are no human paralogs have been found yet for this protein.[1]

Function

The CCDC family of proteins has been found to play a role in both physiological and pathological processes like hematopoiesis, embryogenesis, and have been implicated in the developments of some cancers.[22] Researchers have also identified highly conserved motif sequences in CCDC200 found within humans, even though there was considerable differentiation in non-human primates, suggesting that environmental pressures have selected for different traits.[23]

CCDC200 can be associated with immune function, cell communication, metabolic processes, and the nervous system due to its highly conserved motifs.[23] The gene’s potential role in immune function can suggest that the CCDC200 protein could have co-evolved with environmental pathogens.[23]

The knockout of CCDC200 was found to increase viral invasion and change host and pathogen interactions.[24] Gene knockout suggests that CCDC200 may play a role in contributing to the immune defense system by regulating the life cycle of viruses.[24]

References

  1. ^ a b c d e f g h i j k "CCDC200 coiled-coil domain containing 200 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-08-05.
  2. ^ a b c "Expasy - Compute pI/Mw tool". web.expasy.org. Retrieved 2025-08-05.
  3. ^ a b c d e "InterPro". www.ebi.ac.uk. Retrieved 2025-08-05.
  4. ^ Wen, Zhuofeng; Liang, Weixuan; Yang, Ziyang; Liu, Junjie; Yang, Jing; Xu, Runge; Lin, Keye; Pan, Jia; Chen, Zisheng (2025-03-16). "Genetic insights into idiopathic pulmonary fibrosis: a multi-omics approach to identify potential therapeutic targets". Journal of Translational Medicine. 23 (1): 337. doi:10.1186/s12967-025-06368-8. ISSN 1479-5876. PMC 11912729. PMID 40091050.
  5. ^ a b "SAPS Compositional Analysis". www.ebi.ac.uk. Retrieved 2025-08-05.
  6. ^ Cortese, Marc S.; Uversky, Vladimir N.; Dunker, A. Keith (2009). "Intrinsic disorder in scaffold proteins: getting more from less". Progress in Biophysics and Molecular Biology. 98 (1): 85–106. doi:10.1016/j.pbiomolbio.2008.05.007. ISSN 0079-6107. PMC 2671330. PMID 18619997.
  7. ^ "coiled-coil domain-containing protein 200 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-08-05.
  8. ^ "coiled-coil domain-containing protein 200 isoform 1 [Mus musculus] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-08-05.
  9. ^ "coiled-coil domain-containing protein 200 [Bos taurus] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2025-08-05.
  10. ^ "DeepLoc 2.0 - DTU Health Tech - Bioinformatic Services". services.healthtech.dtu.dk. Retrieved 2025-08-05.
  11. ^ "PSORT II Prediction". psort.hgc.jp. Retrieved 2025-08-05.
  12. ^ "Frontpage". www.healthtech.dtu.dk. Retrieved 2025-08-05.
  13. ^ "ELM - unknown". elm.eu.org. Retrieved 2025-08-05.
  14. ^ "JPred: A Protein Secondary Structure Prediction Server". www.compbio.dundee.ac.uk. Retrieved 2025-08-05.
  15. ^ "I-TASSER server for protein structure and function prediction". zhanggroup.org. Retrieved 2025-08-05.
  16. ^ "GeneMANIA". genemania.org. Retrieved 2025-08-05.
  17. ^ "STRING: functional protein association networks". string-db.org. Retrieved 2025-08-05.
  18. ^ a b c d e f "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2025-08-05.
  19. ^ a b "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2025-08-05.
  20. ^ a b "EMBOSS Needle". www.ebi.ac.uk. Retrieved 2025-08-05.
  21. ^ "Clustal Omega (Multiple Sequence Alignment (MSA))". www.ebi.ac.uk. Retrieved 2025-08-05.
  22. ^ Priyanka, Patra Priyadarshini; Yenugu, Suresh (2021). "Coiled-Coil Domain-Containing (CCDC) Proteins: Functional Roles in General and Male Reproductive Physiology". Reproductive Sciences (Thousand Oaks, Calif.). 28 (10): 2725–2734. doi:10.1007/s43032-021-00595-2. ISSN 1933-7205. PMID 33942254.
  23. ^ a b c Du, Duo; Zhong, Fan; Liu, Lei (2024-08-12). "Enhancing recognition and interpretation of functional phenotypic sequences through fine-tuning pre-trained genomic models". Journal of Translational Medicine. 22 (1): 756. doi:10.1186/s12967-024-05567-z. ISSN 1479-5876. PMC 11318145. PMID 39135093.
  24. ^ a b Wen, Zhuofeng; Liang, Weixuan; Yang, Ziyang; Liu, Junjie; Yang, Jing; Xu, Runge; Lin, Keye; Pan, Jia; Chen, Zisheng (2025-03-16). "Genetic insights into idiopathic pulmonary fibrosis: a multi-omics approach to identify potential therapeutic targets". Journal of Translational Medicine. 23 (1): 337. doi:10.1186/s12967-025-06368-8. ISSN 1479-5876. PMC 11912729. PMID 40091050.

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