6YAI: Clathrin with bound beta2 appendage of AP2

Clathrin with bound beta2 appendage of AP2. Determined by electron microscopy at 9.2 Å resolution. Released 29 Jul 2020.

Method
Electron microscopy
Resolution
9.2 Å
Organisms
Sus scrofa, Homo sapiens
Chains
14
Atoms
35,282
Mol. weight
1811.58 kDa
Released
29 Jul 2020

Explore 6YAI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YAI contains 285 α-helices and 49 β-strands across 14 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 29 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix1250-126314
α-helix1266-12727
α-helix1276-12783
α-helix1281-129212
α-helix1296-130611
α-helix1314-132714
α-helix1329-13368
α-helix1345-135511
α-helix1358-136811
α-helix1371-138010
α-helix1388-13947
α-helix1395-13973
α-helix1402-141312
α-helix1420-14256
α-helix1432-144211
α-helix1445-145511
α-helix1456-14583
α-helix1461-147414
α-helix1478-14869
α-helix1493-15008
α-helix1505-151713
α-helix1524-15318
α-helix1536-15438
α-helix1550-155910
α-helix1563-15653
α-helix1566-15727
α-helix1573-15764
α-helix1579-158810
α-helix1596-162328
Chain B: 36 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix812-82211
α-helix827-8326
α-helix836-8372
α-helix845-8528
α-helix855-8584
α-helix859-8679
α-helix873-88513
α-helix891-8955
α-helix902-9087
α-helix914-92411
α-helix927-9348
α-helix941-9499
α-helix953-9597
α-helix967-97711
α-helix986-99712
α-helix1005-10139
α-helix1024-103512
α-helix1039-10468
α-helix1052-106110
α-helix1066-10749
α-helix1078-108811
α-helix1092-10965
α-helix1097-11015
α-helix1105-111713
α-helix1121-113111
α-helix1137-11448
α-helix1152-116110
α-helix1167-117913
α-helix1183-11908
α-helix1201-12077
α-helix1214-12207
α-helix1226-12338
α-helix1238-124710
α-helix1250-126213
α-helix1268-12725
α-helix1273-12753
Chain C: 40 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix361-37313
α-helix377-3859
α-helix388-3903
α-helix395-4039
α-helix413-42412
α-helix429-43911
α-helix440-4445
α-helix445-4539
α-helix461-47010
α-helix472-4787
α-helix479-4835
α-helix487-4915
α-helix498-5069
α-helix512-52211
α-helix533-5364
α-helix546-55510
α-helix559-57012
α-helix578-59013
α-helix594-6029
α-helix604-6074
α-helix610-62011
α-helix623-63311
α-helix636-64510
α-helix651-6588
α-helix663-67210
α-helix677-68913
α-helix696-70510
α-helix710-7178
α-helix725-73713
α-helix744-7496
α-helix756-76510
α-helix774-7807
α-helix784-79411
α-helix799-8024
α-helix803-8075
α-helix809-8113
α-helix812-82110
α-helix827-8348
α-helix842-85211
α-helix859-8668
Chain D: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix102-16160
α-helix190-1934
α-helix194-1985
α-helix206-2094
α-helix214-2185
Chain E: 31 helices, 28 β-strands
ElementResiduesLengthSheet
β-strand7-1481
β-strand30-3122
β-strand39-4462
β-strand47-5372
β-strand61-6442
β-strand70-7343
β-strand79-8463
β-strand87-9263
β-strand100-10343
β-strand110-11344
β-strand118-12254
β-strand126-13164
β-strand139-14354
β-strand152-15875
β-strand164-173105
β-strand176-185105
β-strand190-19565
β-strand198-20476
β-strand213-222106
β-strand225-23286
α-helix235-2373
α-helix240-2434
β-strand248-25036
α-helix2511
α-helix254-2563
β-strand261-26777
β-strand272-27767
β-strand281-28667
β-strand292-29767
β-strand305-30951
β-strand314-31851
β-strand323-32971
α-helix335-3406
α-helix345-35511
α-helix361-37313
α-helix377-3859
α-helix388-3903
α-helix395-4039
α-helix413-42311
α-helix429-44113
α-helix445-4539
α-helix461-4688
α-helix472-48211
α-helix486-4916
α-helix498-5069
α-helix511-52010
α-helix532-5398
α-helix546-55510
α-helix559-57113
α-helix578-59114
α-helix593-6019
α-helix610-62011
α-helix623-63311
α-helix636-64510
α-helix650-65910
α-helix664-67512
α-helix680-6889
α-helix695-70410
α-helix708-72013
Chain F: 8 helices, 19 β-strands
ElementResiduesLengthSheet
α-helix709-7113
β-strand712-71548
α-helix717-7193
β-strand723-732108
β-strand735-744108
β-strand75019
β-strand754-757410
β-strand760111
β-strand765-76628
β-strand77619
β-strand781-78998
β-strand794111
β-strand802-808710
β-strand813-819710
α-helix822-8254
β-strand826112
α-helix834-84310
α-helix846-8483
β-strand850-854513
α-helix861-8699
β-strand874-881813
β-strand884-892913
β-strand893112
β-strand898-905813
β-strand912-918713
α-helix921-9233
α-helix924-93512
Chain H: 18 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix639-6446
α-helix648-6569
α-helix663-67210
α-helix677-68913
α-helix696-7038
α-helix708-7169
α-helix725-73713
α-helix745-7506
α-helix756-76510
α-helix774-7807
α-helix784-79411
α-helix799-8024
α-helix803-8075
α-helix812-82110
α-helix826-8349
α-helix836-8372
α-helix842-85110
α-helix859-86810
Chain I: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix147-16014
α-helix190-1989
α-helix217-2193

6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Clathrin heavy chainA, B, E, H, J, K, L, Mprotein1630Sus scrofaI3LGD4
AP-2 complex subunit betaFprotein233Homo sapiensP63010 (AlphaFold model)
Clathrin heavy chainCprotein1630Sus scrofaI3LGD4
Clathrin light chainD, I, N, Oprotein229Sus scrofaA0A287BFZ5 (AlphaFold model)
Sequence of entity 1 (A, B, E, H, J, K, L, M), FASTA
>6YAI_1 Clathrin heavy chain (chains A, B, E, H, J, K, L, M)
MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSN
PIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVA
LVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGA
MQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGN
QPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISG
ETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGA
EELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRRFQSVPAQPGQTSPLLQYFGI
LLDQGQLNKYESLELCRPVLQQGRKQLLEKWLKEDKLECSEELGDLVKSVDPTLALSVYL
RANVPNKVIQCFAETGQVQKIVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDE
EPLADITQIVDVFMEYNLIQQCTAFLLDALKNNRPSEGPLQTRLLEMNLMHAPQVADAIL
GNQMFTHYDRAHIAQLCEKAGLLQRALEHFTDLYDIKRAVVHTHLLNPEWLVNYFGSLSV
EDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIELFESFKSFEGLFYFLGSIVN
FSQDPDVHFKYIQAACKTGQIKEVERICRESNCYDPERVKNFLKEAKLTDQLPLIIVCDR
FDFVHDLVLYLYRNNLQKYIEIYVQKVNPSRLPVVIGGLLDVDCSEDVIKNLILVVRGQF
STDELVAEVEKRNRLKLLLPWLEARIHEGCEEPATHNALAKIYIDSNNNPERFLRENPYY
DSRVVGKYCEKRDPHLACVAYERGQCDLELINVCNENSLFKSLSRYLVRRKDPELWGSVL
LESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSE
HRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIANIAISNELFEEAFAIFRKFDVNTS
AVQVLIEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIKADDPSSYMEV
VQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQ
VGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFAC
VDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTEL
AILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMN
HPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHTRAVNYFS
KVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLE
KHELIEFRRIAAYLFKGNNRWKQSVELCKKDSLYKDAMQYASESKDTELAEELLQWFLQE
EKRECFGACLFTCYDLLRPDVVLETAWRHNIMDFAMPYFIQVMKEYLTKVDKLDASESLR
KEEEQATETQ
Sequence of entity 2 (F), FASTA
>6YAI_2 AP-2 complex subunit beta (chains F)
GGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGV
IPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNV
LFVEDGKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQ
DMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN
Sequence of entity 3 (C), FASTA
>6YAI_3 Clathrin heavy chain (chains C)
MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSN
PIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVA
LVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGA
MQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGN
QPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISG
ETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGA
EELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRRFQSVPAQPGQTSPLLQYFGI
LLDQGQLNKYESLELCRPVLQQGRKQLLEKWLKEDKLECSEELGDLVKSVDPTLALSVYL
RANVPNKVIQCFAETGQVQKIVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDE
EPLADITQIVDVFMEYNLIQQCTAFLLDALKNNRPSEGPLQTRLLEMNLMHAPQVADAIL
GNQMFTHYDRAHIAQLCEKAGLLQRALEHFTDLYDIKRAVVHTHLLNPEWLVNYFGSLSV
EDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIELFESFKSFEGLFYFLGSIVN
FSQDPDVHFKYIQAACKTGQIKEVERICRESNCYDPERVKNFLKEAKLTDQLPLIIVCDR
FDFVHDLVLYLYRNNLQKYIEIYVQKVNPSRLPVVIGGLLDVDCSEDVIKNLILVVRGQF
STDELVAEVEKRNRLKLLLPWLEARIHEGCTEPATHNALAKIYIDSNNNPERFLRENPYY
DSRVVGKYCEKRDPHLACVAYERGQCDLELINVCNENSLFKSLSRYLVRRKDPELWGSVL
LESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSE
HRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIANIAISNELFEEAFAIFRKFDVNTS
AVQVLIEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIKADDPSSYMEV
VQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQ
VGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFAC
VDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTEL
AILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMN
HPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHTRAVNYFS
KVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLE
KHELIEFRRIAAYLFKGNNRWKQSVELCKKDSLYKDAMQYASESKDTELAEELLQWFLQE
EKRECFGACLFTCYDLLRPDVVLETAWRHNIMDFAMPYFIQVMKEYLTKVDKLDASESLR
KEEEQATETQ
Sequence of entity 4 (D, I, N, O), FASTA
>6YAI_4 Clathrin light chain (chains D, I, N, O)
MADDFGFFSSSESGAPEVAEEDPAAAFLAQQESEIAGIENDEGFGAPAGSQAALAQPGPA
SGAGPEDMGTTVNGDVFQDANGPADGYAAIAQADRLTQEPESIRKWREEQRKRLQELDAA
SKVTEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPDADIIGYVASEEAFV
KESKEETPGTEWEKVAQLCDFNPKSSKQCKDVSRLRSVLMSLKQTPLSR

Primary citation

Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles. Kovtun, O., Dickson, V.K., Kelly, B.T. et al. Sci Adv (2020) 6:eaba8381-eaba8381. DOI 10.1126/sciadv.aba8381 · PubMed

Other PDB entries of the same protein (UniProt I3LGD4), best resolution first:

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