1W63: AP1 clathrin adaptor core

AP1 clathrin adaptor core. Determined by X-ray diffraction at 4.0 Å resolution. Released 21 Sept 2004.

Method: X-ray diffraction
Resolution: 4.0 Å
Organisms: MUS MUSCULUS, RATTUS NORVEGICUS
Chains: 24
Atoms: 81,744
Mol. weight: 1218.98 kDa
Released: 21 Sept 2004

Explore 1W63 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1W63 contains 498 α-helices and 210 β-strands across 24 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.

Chains A, C, E, G, I and K: 36 helices, 0 β-strands

Element	Residues	Length
α-helix	7-14	8
α-helix	20-38	19
α-helix	46-58	13
α-helix	64-66	3
α-helix	67-75	9
α-helix	79-92	14
α-helix	97-111	15
α-helix	117-129	13
α-helix	132-147	16
α-helix	151-167	17
α-helix	169-178	10
α-helix	188-201	14
α-helix	205-213	9
α-helix	216-228	13
α-helix	243-256	14
α-helix	261-265	5
α-helix	268-276	9
α-helix	284-298	15
α-helix	303-317	15
α-helix	325-343	19
α-helix	344-346	3
α-helix	347-352	6
α-helix	353-355	3
α-helix	359-372	14
α-helix	379-391	13
α-helix	394-409	16
α-helix	415-428	14
α-helix	430-432	3
α-helix	437-447	11
α-helix	452-465	14
α-helix	471-487	17
α-helix	502-514	13
α-helix	520-534	15
α-helix	541-551	11
α-helix	557-571	15
α-helix	576-581	6

Chains B, F and J: 37 helices, 0 β-strands

Element	Residues	Length
α-helix	14-23	10
α-helix	27-42	16
α-helix	51-55	5
α-helix	63-79	17
α-helix	81-85	5
α-helix	88-95	8
α-helix	100-111	12
α-helix	117-131	15
α-helix	135-150	16
α-helix	158-160	3
α-helix	161-171	11
α-helix	176-188	13
α-helix	203-211	9
α-helix	216-226	11
α-helix	234-249	16
α-helix	254-266	13
α-helix	277-292	16
α-helix	296-312	17
α-helix	314-316	3
α-helix	332-344	13
α-helix	348-363	16
α-helix	367-383	17
α-helix	385-387	3
α-helix	388-399	12
α-helix	404-420	17
α-helix	428-433	6
α-helix	442-454	13
α-helix	455-457	3
α-helix	462-469	8
α-helix	478-492	15
α-helix	500-512	13
α-helix	517-532	16
α-helix	534-541	8
α-helix	543-545	3
α-helix	557-564	8
α-helix	571-574	4
α-helix	578-581	4

Chains D, H and L: 37 helices, 0 β-strands

Element	Residues	Length
α-helix	14-23	10
α-helix	27-42	16
α-helix	51-55	5
α-helix	63-79	17
α-helix	81-85	5
α-helix	88-95	8
α-helix	100-111	12
α-helix	117-131	15
α-helix	135-150	16
α-helix	158-160	3
α-helix	161-171	11
α-helix	176-188	13
α-helix	203-211	9
α-helix	216-226	11
α-helix	234-249	16
α-helix	254-266	13
α-helix	277-292	16
α-helix	296-312	17
α-helix	314-316	3
α-helix	332-344	13
α-helix	348-363	16
α-helix	367-383	17
α-helix	385-387	3
α-helix	388-399	12
α-helix	404-420	17
α-helix	428-433	6
α-helix	442-454	13
α-helix	455-457	3
α-helix	462-471	10
α-helix	478-492	15
α-helix	500-512	13
α-helix	517-532	16
α-helix	534-541	8
α-helix	543-545	3
α-helix	557-564	8
α-helix	571-574	4
α-helix	578-581	4

Chains M, N, O, P, R and V: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
β-strand	14-15	2	1
β-strand	19	1	1
α-helix	30-42	13
β-strand	49-52	4	1
β-strand	55-62	8	1
β-strand	65-71	7	1
α-helix	78-94	17
α-helix	100-117	18
β-strand	170-184	15	2
β-strand	188-203	16	2
α-helix	208	1
β-strand	209-214	6	3
β-strand	233-238	6	2
β-strand	242-244	3	3
β-strand	252-255	4	3
β-strand	260-270	11	2
β-strand	280-286	7	4
β-strand	290-298	9	4
β-strand	306-308	3	5
β-strand	311-315	5	2
β-strand	324-327	4	4
β-strand	331-335	5	2
α-helix	337-339	3
β-strand	340-344	5	2
β-strand	347-349	3	5
β-strand	353-361	9	4
α-helix	374-375	2
β-strand	376-379	4	2
β-strand	380	1	6
β-strand	392-398	7	3
β-strand	406-414	9	2
β-strand	415	1	6
β-strand	418-420	3	2

Chains Q, S, T, U, W and X: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	25
β-strand	14-19	6	25
α-helix	25-40	16
β-strand	49-52	4	25
β-strand	55-62	8	25
β-strand	65-71	7	25
α-helix	77-95	19
α-helix	100-115	16
β-strand	118-119	2	26
β-strand	122-123	2	26
α-helix	128-146	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adapter-related protein complex 1 gamma 1 subunit	A, C, E, G, I, K	protein	618	MUS MUSCULUS	P22892 (AlphaFold model)
Adapter-related protein complex 1 beta 1 subunit	B, D, F, H, J, L	protein	584	RATTUS NORVEGICUS	P52303 (AlphaFold model)
Adaptor-related protein complex 1, mu 1 subunit	M, N, O, P, R, V	protein	423	MUS MUSCULUS	P35585 (AlphaFold model)
Adapter-related protein complex 1 sigma 1A subunit	Q, S, T, U, W, X	protein	158	MUS MUSCULUS	P61967 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>1W63_1 ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT (chains A, C, E, G, I, K)
GAGMSMPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLY
MHMLGYPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHST
QFVQGLALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMF
LPATKNLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEH
DVSGISDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLT
IMDIKSESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLK
DLDVSIKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSK
RWHIDTIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQV
AAWCIGEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLST
RFTCTVNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGP
SEIVQTNGETEPAPLETK

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>1W63_2 ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT (chains B, D, F, H, J, L)
MTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDTLKDLISDSNPMVVANR
VAALSEIAESHPSSNLLDLKAQSINKLLTALNECTEWAQIFILDCLGNYMPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYATLLKKLAPPLVTLLSAEPEPQY
VPLRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRK
YPNKYESVIATLCENLDSDDEPEARAAMIWIVGEYAERSDNADELLESFLDGFHDESTQV
QLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEV
VLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPNAFVEG

Sequence of entity 3 (M, N, O, P, R, V), FASTA

>1W63_3 ADAPTOR-RELATED PROTEIN COMPLEX 1, MU 1 SUBUNIT (chains M, N, O, P, R, V)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEFITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQAIPWVRYITQNGDYQL
RTQ

Sequence of entity 4 (Q, S, T, U, W, X), FASTA

>1W63_4 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1A SUBUNIT (chains Q, S, T, U, W, X)
MMRFMLLFSRQGKLRLQKWYLATSDKERKKMVRELMQVVLARKPKMCSFLEWRDLKVVYK
RYASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLMG
GDVQDTSKKSVLKAIEQADLLQEEDESPRSVLEEMGLA

Primary citation

Crystal Structure of the Clathrin Adaptor Protein 1 Core. Heldwein, E., Macia, E., Wang, J. et al. Proc Natl Acad Sci U S A (2004) 101:14108. DOI 10.1073/PNAS.0406102101 · PubMed

Other PDB entries of the same protein (UniProt P22892 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZY7 1.09 Å, Crystal structure of computationally redesigned gamma-adaptin appendage domain forming a…
2A7B 1.65 Å, On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- The…
1GYV 1.71 Å, Gamma-adaptin appendage domain from clathrin adaptor AP1, L762E mutant
1GYU 1.81 Å, Gamma-adaptin appendage domain from clathrin adaptor AP1
7R4H 2.34 Å, phospho-STING binding to adaptor protein complex-1
1GYW 2.4 Å, Gamma-adaptin appendage domain from clathrin adaptor AP1 A753D mutant
4P6Z 3.0 Å, Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic…
6CM9 3.73 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit
6DFF 3.9 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer
6D83 4.27 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant…
6D84 6.72 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer
6CRI 6.8 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer

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