7R4H: AP-1 complex subunit beta-1

phospho-STING binding to adaptor protein complex-1. Determined by electron microscopy at 2.34 Å resolution. Released 14 Sept 2022.

Method: Electron microscopy
Resolution: 2.34 Å
Organisms: Homo sapiens, Mus musculus
Chains: 7
Atoms: 16,485
Mol. weight: 240.37 kDa
Ligands: GTP, MG
Released: 14 Sept 2022

Explore 7R4H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R4H contains 111 α-helices and 52 β-strands across 6 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 B: 39 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-22	7
α-helix	27-42	16
α-helix	48-50	3
α-helix	51-55	5
α-helix	63-75	13
α-helix	88-93	6
α-helix	100-111	12
α-helix	123-129	7
α-helix	135-151	17
α-helix	153-159	7
α-helix	161-167	7
α-helix	174-190	17
α-helix	201-211	11
α-helix	216-226	11
α-helix	234-244	11
α-helix	245-249	5
β-strand	250	1	1
α-helix	253-266	14
α-helix	276-290	15
α-helix	291-293	3
α-helix	296-312	17
α-helix	322-324	3
α-helix	332-344	13
α-helix	351-361	11
α-helix	367-383	17
α-helix	385-387	3
α-helix	388-399	12
α-helix	404-420	17
α-helix	429-432	4
α-helix	442-454	13
α-helix	462-466	5
α-helix	470-475	6
α-helix	479-494	16
α-helix	500-511	12
α-helix	517-532	16
α-helix	534-541	8
α-helix	555-556	2
α-helix	557-564	8
β-strand	569	1	2
α-helix	570-574	5
α-helix	578-580	3

Chain C: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	3
α-helix	30-38	9
α-helix	46-48	3
β-strand	51-58	8	3
β-strand	61-68	8	3
α-helix	75-77	3
β-strand	87-92	6	3
α-helix	97-110	14
β-strand	120-125	6	3
α-helix	138-143	6
α-helix	145-147	3
α-helix	166-175	10

Chain G: 39 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	20-39	20
α-helix	46-59	14
α-helix	64-66	3
α-helix	67-74	8
α-helix	79-92	14
α-helix	100-103	4
α-helix	104-111	8
α-helix	116-129	14
α-helix	134-137	4
α-helix	139-145	7
α-helix	151-167	17
α-helix	173-175	3
α-helix	177-179	3
α-helix	188-204	17
α-helix	212-215	4
α-helix	216-227	12
β-strand	236-237	2	4
β-strand	240-241	2	4
α-helix	243-255	13
α-helix	262-277	16
α-helix	283-298	16
α-helix	303-317	15
α-helix	322-334	13
α-helix	340-343	4
α-helix	344-346	3
α-helix	347-354	8
α-helix	359-371	13
α-helix	378-390	13
α-helix	397-410	14
α-helix	415-428	14
α-helix	430-432	3
α-helix	435-437	3
α-helix	438-447	10
α-helix	453-465	13
α-helix	470-487	18
α-helix	504-514	11
α-helix	522-536	15
α-helix	544-549	6
α-helix	557-572	16
α-helix	577-580	4

Chain H: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	5
α-helix	30-38	9
β-strand	51-57	7	5
β-strand	62-68	7	5
α-helix	75-81	7
β-strand	87-93	7	5
α-helix	100-110	11
β-strand	120-126	7	5
α-helix	134-135	2
α-helix	136-143	8
α-helix	145-147	3
β-strand	153-157	5	5
β-strand	159	1	6
β-strand	164	1	6
α-helix	166-175	10

Chain M: 14 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	7
β-strand	15-20	6	7
α-helix	29-32	4
α-helix	33-42	10
β-strand	49-52	4	7
β-strand	55-61	7	7
β-strand	66-71	6	7
β-strand	76	1	2
α-helix	77-94	18
α-helix	101-105	5
α-helix	107-117	11
β-strand	118-119	2	8
β-strand	122-123	2	8
α-helix	128-131	4
α-helix	148-150	3
α-helix	151-153	3
β-strand	170-183	14	1
β-strand	189-203	15	1
β-strand	209-214	6	9
β-strand	216	1	10
α-helix	217-223	7
β-strand	231	1	10
β-strand	235-238	4	1
β-strand	242	1	9
α-helix	244-250	7
β-strand	253-255	3	9
α-helix	257-258	2
β-strand	260-270	11	1
α-helix	274-275	2
β-strand	277-286	10	11
β-strand	290-299	10	11
β-strand	306-315	10	1
β-strand	321-327	7	11
β-strand	331-335	5	1
β-strand	340-349	10	1
β-strand	353-361	9	11
α-helix	366-367	2
α-helix	374-375	2
β-strand	376-377	2	1
β-strand	381-383	3	1
β-strand	392-398	7	9
β-strand	406-420	15	1

Chain S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	12
β-strand	14-19	6	12
α-helix	25-40	16
β-strand	49-51	3	12
β-strand	56-61	6	12
β-strand	66-71	6	12
α-helix	77-95	19
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	13
β-strand	122-123	2	13
α-helix	129-141	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-1 complex subunit beta-1	B	protein	584	Homo sapiens	Q10567 (AlphaFold model)
ADP-ribosylation factor 1	C, H	protein	165	Homo sapiens	P84077 (AlphaFold model)
AP-1 complex subunit gamma-1	G	protein	595	Mus musculus	P22892 (AlphaFold model)
Stimulator of interferon genes protein	L	protein	9	Homo sapiens	Q86WV6 (AlphaFold model)
AP-1 complex subunit mu-1	M	protein	423	Mus musculus	P35585
AP-1 complex subunit sigma-3	S	protein	154	Homo sapiens	Q96PC3

Sequence of entity 1 (B), FASTA

>7R4H_1 AP-1 complex subunit beta-1 (chains B)
MTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANA
VAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQY
VALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELRE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRK
YPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQV
QLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEV
VLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEG

Sequence of entity 2 (C, H), FASTA

>7R4H_2 ADP-ribosylation factor 1 (chains C, H)
EMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGLDKIRP
LWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNA
AEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Sequence of entity 3 (G), FASTA

>7R4H_3 AP-1 complex subunit gamma-1 (chains G)
MPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLG
YPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQG
LALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATK
NLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGI
SDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIK
SESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVS
IKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHID
TIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCI
GEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCT
VNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGP

Sequence of entity 4 (L), FASTA

>7R4H_4 Stimulator of interferon genes protein (chains L)
QEPELLISG

Sequence of entity 5 (M), FASTA

>7R4H_5 AP-1 complex subunit mu-1 (chains M)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 6 (S), FASTA

>7R4H_6 AP-1 complex subunit sigma-3 (chains S)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQEVSTVCQTMGER

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Clathrin-associated AP-1 controls termination of STING signalling. Liu, Y., Xu, P., Rivara, S. et al. Nature (2022) 610:761-767. DOI 10.1038/s41586-022-05354-0 · PubMed

Other PDB entries of the same protein (UniProt Q10567 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
4HMY 7.0 Å, Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by…
8D4E 9.2 Å, Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r)…
8D4C 9.3 Å, beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I…
8D9W 9.3 Å, beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes
8D9V 9.4 Å, gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes
7UX3 9.6 Å, Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow…

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