CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-010773
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Clathrin heavy chain 1 
Protein Synonyms/Alias
 Clathrin heavy chain on chromosome 17; CLH-17 
Gene Name
 CLTC 
Gene Synonyms/Alias
 CLH17; CLTCL2; KIAA0034 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
78AIMNPASKVIALKAGubiquitination[1]
86VIALKAGKTLQIFNIubiquitination[1]
96QIFNIEMKSKMKAHTubiquitination[1]
163YRTDAKQKWLLLTGIubiquitination[2, 3]
189QLYSVDRKVSQPIEGubiquitination[4]
227VRGQAGGKLHIIEVGubiquitination[4]
246GNQPFPKKAVDVFFPubiquitination[1]
367AEELFARKFNALFAQubiquitination[1, 2, 3, 4, 5, 6, 7]
389KVAANAPKGILRTPDubiquitination[4, 5, 6]
429LDQGQLNKYESLELCacetylation[8]
450GRKQLLEKWLKEDKLubiquitination[2, 3]
453QLLEKWLKEDKLECSubiquitination[1, 9]
456EKWLKEDKLECSEELubiquitination[9]
507KIVLYAKKVGYTPDWubiquitination[1, 3, 5, 10]
619HIAQLCEKAGLLQRAubiquitination[1, 4, 5, 6, 7, 9, 11, 12, 13]
637FTDLYDIKRAVVHTHacetylation[14, 15]
637FTDLYDIKRAVVHTHubiquitination[1, 4]
742ACKTGQIKEVERICRubiquitination[1]
798LYRNNLQKYIEIYVQubiquitination[1, 2, 3, 5, 6]
806YIEIYVQKVNPSRLPubiquitination[1, 5, 6]
856VEKRNRLKLLLPWLEacetylation[14, 16]
856VEKRNRLKLLLPWLEubiquitination[4, 5, 7]
881ATHNALAKIYIDSNNubiquitination[4]
911VVGKYCEKRDPHLACubiquitination[5, 9]
941CNENSLFKSLSRYLVubiquitination[1, 2, 3, 4, 7, 12, 13]
1034LLILTAIKADRTRVMubiquitination[1, 3, 5]
1074EAFAIFRKFDVNTSAubiquitination[2, 3]
1118LAKAQLQKGMVKEAIubiquitination[4]
1130EAIDSYIKADDPSSYubiquitination[1]
1209GDRCYDEKMYDAAKLubiquitination[4]
1215EKMYDAAKLLYNNVSubiquitination[1, 2, 3, 4, 5]
1264CFACVDGKEFRLAQMubiquitination[4]
1347WSRVNIPKVLRAAEQubiquitination[1, 2, 3]
1392AWKEGQFKDIITKVAubiquitination[1]
1397QFKDIITKVANVELYubiquitination[1]
1441RAVNYFSKVKQLPLVacetylation[14]
1441RAVNYFSKVKQLPLVubiquitination[1, 2, 3, 4, 9]
1443VNYFSKVKQLPLVKPubiquitination[2, 3, 4, 5]
1449VKQLPLVKPYLRSVQubiquitination[1, 2, 3, 4, 5]
1461SVQNHNNKSVNESLNubiquitination[1]
1501SLAQRLEKHELIEFRacetylation[14]
1501SLAQRLEKHELIEFRubiquitination[1, 2, 3, 4, 5]
1522FKGNNRWKQSVELCKubiquitination[1, 4]
1535CKKDSLYKDAMQYASubiquitination[1, 5]
1609VMKEYLTKVDKLDASubiquitination[1, 2, 3, 4, 5]
1612EYLTKVDKLDASESLubiquitination[1]
Reference
 [1] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [2] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [3] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [4] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [5] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [6] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [7] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [8] Monoclonal antibody cocktail as an enrichment tool for acetylome analysis.
 Shaw PG, Chaerkady R, Zhang Z, Davidson NE, Pandey A.
 Anal Chem. 2011 May 15;83(10):3623-6. [PMID: 21466224]
 [9] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [10] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]
 [11] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [12] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [13] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [14] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [15] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [16] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773] 
Functional Description
 Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Two different adapter protein complexes link the clathrin lattice either to the plasma membrane or to the trans-Golgi network. 
Sequence Annotation
 REPEAT 537 683 CHCR 1.
 REPEAT 686 828 CHCR 2.
 REPEAT 833 972 CHCR 3.
 REPEAT 979 1124 CHCR 4.
 REPEAT 1128 1269 CHCR 5.
 REPEAT 1274 1420 CHCR 6.
 REPEAT 1423 1566 CHCR 7.
 REGION 2 479 Globular terminal domain.
 REGION 24 67 WD40-like repeat 1.
 REGION 68 107 WD40-like repeat 2.
 REGION 108 149 WD40-like repeat 3.
 REGION 150 195 WD40-like repeat 4.
 REGION 196 257 WD40-like repeat 5.
 REGION 258 301 WD40-like repeat 6.
 REGION 302 330 WD40-like repeat 7.
 REGION 449 465 Binding site for the uncoating ATPase,
 REGION 480 523 Flexible linker.
 REGION 524 1675 Heavy chain arm.
 REGION 524 634 Distal segment.
 REGION 639 1675 Proximal segment.
 REGION 1213 1522 Involved in binding clathrin light chain
 REGION 1550 1675 Trimerization (By similarity).
 MOD_RES 2 2 N-acetylalanine.
 MOD_RES 184 184 Phosphotyrosine (By similarity).
 MOD_RES 394 394 Phosphothreonine.
 MOD_RES 634 634 Phosphotyrosine.
 MOD_RES 856 856 N6-acetyllysine.
 MOD_RES 899 899 Phosphotyrosine (By similarity).
 MOD_RES 1206 1206 Phosphotyrosine (By similarity).
 MOD_RES 1441 1441 N6-acetyllysine.
 MOD_RES 1477 1477 Phosphotyrosine.
 MOD_RES 1487 1487 Phosphotyrosine (By similarity).
 MOD_RES 1494 1494 Phosphoserine.
 MOD_RES 1501 1501 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; Coated pit; Complete proteome; Cytoplasmic vesicle; Direct protein sequencing; Membrane; Phosphoprotein; Reference proteome; Repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1675 AA 
Protein Sequence
MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN 60
PIRRPISADS AIMNPASKVI ALKAGKTLQI FNIEMKSKMK AHTMTDDVTF WKWISLNTVA 120
LVTDNAVYHW SMEGESQPVK MFDRHSSLAG CQIINYRTDA KQKWLLLTGI SAQQNRVVGA 180
MQLYSVDRKV SQPIEGHAAS FAQFKMEGNA EESTLFCFAV RGQAGGKLHI IEVGTPPTGN 240
QPFPKKAVDV FFPPEAQNDF PVAMQISEKH DVVFLITKYG YIHLYDLETG TCIYMNRISG 300
ETIFVTAPHE ATAGIIGVNR KGQVLSVCVE EENIIPYITN VLQNPDLALR MAVRNNLAGA 360
EELFARKFNA LFAQGNYSEA AKVAANAPKG ILRTPDTIRR FQSVPAQPGQ TSPLLQYFGI 420
LLDQGQLNKY ESLELCRPVL QQGRKQLLEK WLKEDKLECS EELGDLVKSV DPTLALSVYL 480
RANVPNKVIQ CFAETGQVQK IVLYAKKVGY TPDWIFLLRN VMRISPDQGQ QFAQMLVQDE 540
EPLADITQIV DVFMEYNLIQ QCTAFLLDAL KNNRPSEGPL QTRLLEMNLM HAPQVADAIL 600
GNQMFTHYDR AHIAQLCEKA GLLQRALEHF TDLYDIKRAV VHTHLLNPEW LVNYFGSLSV 660
EDSLECLRAM LSANIRQNLQ ICVQVASKYH EQLSTQSLIE LFESFKSFEG LFYFLGSIVN 720
FSQDPDVHFK YIQAACKTGQ IKEVERICRE SNCYDPERVK NFLKEAKLTD QLPLIIVCDR 780
FDFVHDLVLY LYRNNLQKYI EIYVQKVNPS RLPVVIGGLL DVDCSEDVIK NLILVVRGQF 840
STDELVAEVE KRNRLKLLLP WLEARIHEGC EEPATHNALA KIYIDSNNNP ERFLRENPYY 900
DSRVVGKYCE KRDPHLACVA YERGQCDLEL INVCNENSLF KSLSRYLVRR KDPELWGSVL 960
LESNPYRRPL IDQVVQTALS ETQDPEEVSV TVKAFMTADL PNELIELLEK IVLDNSVFSE 1020
HRNLQNLLIL TAIKADRTRV MEYINRLDNY DAPDIANIAI SNELFEEAFA IFRKFDVNTS 1080
AVQVLIEHIG NLDRAYEFAE RCNEPAVWSQ LAKAQLQKGM VKEAIDSYIK ADDPSSYMEV 1140
VQAANTSGNW EELVKYLQMA RKKARESYVE TELIFALAKT NRLAELEEFI NGPNNAHIQQ 1200
VGDRCYDEKM YDAAKLLYNN VSNFGRLAST LVHLGEYQAA VDGARKANST RTWKEVCFAC 1260
VDGKEFRLAQ MCGLHIVVHA DELEELINYY QDRGYFEELI TMLEAALGLE RAHMGMFTEL 1320
AILYSKFKPQ KMREHLELFW SRVNIPKVLR AAEQAHLWAE LVFLYDKYEE YDNAIITMMN 1380
HPTDAWKEGQ FKDIITKVAN VELYYRAIQF YLEFKPLLLN DLLMVLSPRL DHTRAVNYFS 1440
KVKQLPLVKP YLRSVQNHNN KSVNESLNNL FITEEDYQAL RTSIDAYDNF DNISLAQRLE 1500
KHELIEFRRI AAYLFKGNNR WKQSVELCKK DSLYKDAMQY ASESKDTELA EELLQWFLQE 1560
EKRECFGACL FTCYDLLRPD VVLETAWRHN IMDFAMPYFI QVMKEYLTKV DKLDASESLR 1620
KEEEQATETQ PIVYGQPQLM LTAGPSVAVP PQAPFGYGYT APPYGQPQPG FGYSM 1675 
Gene Ontology
 GO:0030118; C:clathrin coat; NAS:UniProtKB.
 GO:0030132; C:clathrin coat of coated pit; IEA:InterPro.
 GO:0030130; C:clathrin coat of trans-Golgi network vesicle; IEA:InterPro.
 GO:0030669; C:clathrin-coated endocytic vesicle membrane; TAS:Reactome.
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0070062; C:extracellular vesicular exosome; IDA:UniProtKB.
 GO:0042470; C:melanosome; IEA:UniProtKB-SubCell.
 GO:0005739; C:mitochondrion; IEA:Compara.
 GO:0005819; C:spindle; IDA:UniProtKB.
 GO:0032588; C:trans-Golgi network membrane; TAS:Reactome.
 GO:0005198; F:structural molecule activity; NAS:UniProtKB.
 GO:0019886; P:antigen processing and presentation of exogenous peptide antigen via MHC class II; TAS:Reactome.
 GO:0016044; P:cellular membrane organization; TAS:Reactome.
 GO:0006886; P:intracellular protein transport; NAS:UniProtKB.
 GO:0007067; P:mitosis; IMP:UniProtKB.
 GO:0006892; P:post-Golgi vesicle-mediated transport; TAS:Reactome.
 GO:0031623; P:receptor internalization; IMP:BHF-UCL.
 GO:0033572; P:transferrin transport; IMP:BHF-UCL. 
Interpro
 IPR016024; ARM-type_fold.
 IPR000547; Clathrin_H-chain/VPS_repeat.
 IPR016025; Clathrin_H-chain_link/propller.
 IPR015348; Clathrin_H-chain_linker_core.
 IPR001473; Clathrin_H-chain_propeller_N.
 IPR022365; Clathrin_H-chain_propeller_rpt.
 IPR016341; Clathrin_heavy_chain.
 IPR011990; TPR-like_helical. 
Pfam
 PF00637; Clathrin
 PF09268; Clathrin-link
 PF01394; Clathrin_propel 
SMART
 SM00299; CLH 
PROSITE
 PS50236; CHCR 
PRINTS