8D9S: ADP ribosylation factor 1

AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1. Determined by electron microscopy at 20.0 Å resolution. Released 9 Nov 2022.

Method: Electron microscopy
Resolution: 20.0 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1, Mus musculus
Chains: 60
Atoms: 58,602
Mol. weight: 2142.96 kDa
Ligands: MG, GTP
Released: 9 Nov 2022

Explore 8D9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D9S contains 774 α-helices and 474 β-strands across 54 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 0, 1, 2, y, Y and z: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	345-346	2	53
β-strand	347	1	40
α-helix	352-354	3

Chains 3, 4, 5, 6, 7, a, b, c, C, d, H, J, K, O, P, Q, X and Z: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	19	1	98
β-strand	22-24	3	98
α-helix	30-38	9
β-strand	51-58	8	98
β-strand	61-68	8	98
α-helix	78-82	5
β-strand	89-93	5	98
α-helix	97-111	15
α-helix	120-121	2
β-strand	122-126	5	98
α-helix	138-143	6
α-helix	145-147	3
β-strand	154-157	4	98
α-helix	166-177	12

Chains A, B, D, E, F and I: 41 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-22	8
α-helix	27-43	17
α-helix	48-50	3
α-helix	51-56	6
α-helix	63-75	13
α-helix	82-87	6
α-helix	88-94	7
α-helix	100-112	13
α-helix	116-121	6
α-helix	123-130	8
α-helix	135-151	17
α-helix	153-159	7
α-helix	161-169	9
α-helix	174-190	17
α-helix	201-211	11
α-helix	216-228	13
α-helix	234-244	11
α-helix	245-249	5
β-strand	250	1	76
α-helix	253-267	15
α-helix	275-292	18
α-helix	296-310	15
α-helix	326-327	2
α-helix	332-344	13
α-helix	351-361	11
α-helix	367-383	17
α-helix	385-387	3
α-helix	388-400	13
α-helix	404-420	17
α-helix	429-433	5
α-helix	442-454	13
α-helix	462-469	8
α-helix	473-476	4
α-helix	478-494	17
α-helix	500-511	12
α-helix	517-532	16
α-helix	534-540	7
α-helix	550-552	3
α-helix	555-556	2
α-helix	557-565	9
β-strand	569	1	78
α-helix	570-574	5
α-helix	578-580	3

Chains G, R, T, U, V and W: 35 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-16	10
α-helix	20-39	20
α-helix	46-59	14
α-helix	68-74	7
α-helix	79-92	14
α-helix	103-111	9
α-helix	116-128	13
α-helix	132-146	15
α-helix	151-167	17
α-helix	169-175	7
α-helix	188-204	17
α-helix	207-213	7
α-helix	216-228	13
β-strand	236-237	2	30
β-strand	240-241	2	30
α-helix	243-255	13
α-helix	261-277	17
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	394-411	18
α-helix	415-429	15
α-helix	430-432	3
α-helix	437-447	11
α-helix	453-465	13
α-helix	470-487	18
α-helix	504-514	11
α-helix	522-536	15
α-helix	544-551	8
α-helix	557-572	16
α-helix	578-580	3
α-helix	582-585	4

Chains j, k, l, m, M and n: 13 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	87
β-strand	17-20	4	87
α-helix	29-43	15
β-strand	49	1	87
β-strand	52	1	88
β-strand	55	1	88
β-strand	56-58	3	87
β-strand	61	1	89
β-strand	66	1	89
β-strand	67-71	5	87
β-strand	76	1	78
α-helix	77-94	18
α-helix	100-103	4
α-helix	107-117	11
β-strand	118-119	2	90
β-strand	122-123	2	90
α-helix	128-134	7
α-helix	148-150	3
α-helix	151-154	4
β-strand	170-183	14	76
β-strand	189-203	15	76
β-strand	209-214	6	91
β-strand	216	1	92
α-helix	217-223	7
β-strand	231	1	92
β-strand	235-238	4	76
β-strand	242	1	91
α-helix	244-250	7
β-strand	253-255	3	91
α-helix	256-258	3
β-strand	260-270	11	76
α-helix	274-275	2
β-strand	277-280	4	93
β-strand	283	1	93
β-strand	290-299	10	93
β-strand	306-314	9	76
β-strand	321-327	7	93
β-strand	331-335	5	76
β-strand	340-349	10	76
β-strand	353-361	9	93
α-helix	366-367	2
α-helix	374-375	2
β-strand	376-378	3	76
β-strand	381-383	3	76
β-strand	385	1	69
β-strand	392-398	7	91
β-strand	408-415	8	76
β-strand	419-420	2	76

Chains N, o, p, q, r and s: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-22	16
β-strand	69	1	17
β-strand	76	1	18
β-strand	77-78	2	19
α-helix	79-80	2
α-helix	81-94	14
α-helix	100	1
β-strand	101-102	2	20
α-helix	104-118	15
β-strand	120-121	2	19
β-strand	127	1	21
α-helix	128-129	2
α-helix	133	1
β-strand	134	1	20
α-helix	135	1
β-strand	136	1	21
β-strand	143-147	5	20
β-strand	181-185	5	20
α-helix	187-191	5
α-helix	194-198	5

Chains S, t, u, v, w and x: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	55
β-strand	14-19	6	55
α-helix	25-40	16
β-strand	49-52	4	55
β-strand	55-59	5	55
β-strand	65-71	7	55
α-helix	77-95	19
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	56
β-strand	122-123	2	56
α-helix	129-141	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP ribosylation factor 1	3, 4, 5, 6, 7, C, H, J, K, O, P, Q, X, Z, a, b, c, d	protein	181	Homo sapiens	P84077 (AlphaFold model)
Protein Nef	L, N, e, f, g, h, i, o, p, q, r, s	protein	213	Human immunodeficiency virus 1	Q90VU7
HLA class I histocompatibility antigen, A alpha chain	0, 1, 2, Y, y, z	protein	44	Homo sapiens	P04439 (AlphaFold model)
AP-1 complex subunit beta-1	A, B, D, E, F, I	protein	949	Homo sapiens	Q10567 (AlphaFold model)
AP-1 complex subunit gamma-1	G, R, T, U, V, W	protein	601	Mus musculus	P22892
AP-1 complex subunit mu-1	M, j, k, l, m, n	protein	423	Mus musculus	P35585
AP-1 complex subunit sigma-3	S, t, u, v, w, x	protein	154	Homo sapiens	Q96PC3

Sequence of entity 1 (3, 4, 5, 6, 7, C, H, J, K, O, P, Q, X, Z, a, b, c, d), FASTA

>8D9S_1 ADP ribosylation factor 1 (chains 3, 4, 5, 6, 7, C, H, J, K, O, P, Q, X, Z, a, b, c, d)
XGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKN
ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAV
LLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQ
K

Sequence of entity 2 (L, N, e, f, g, h, i, o, p, q, r, s), FASTA

>8D9S_2 Protein Nef (chains L, N, e, f, g, h, i, o, p, q, r, s)
XGGKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEA
QEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGY
FPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREV
LEWRFDSRLAFHHVARELHPEYFKNCGHHHHHH

Sequence of entity 3 (0, 1, 2, Y, y, z), FASTA

>8D9S_3 HLA class I histocompatibility antigen, A alpha chain (chains 0, 1, 2, Y, y, z)
GAMGSCRKSSDRKGGSYSQAAGSDSAQSSDVSLTAAKVHHHHHH

Sequence of entity 4 (A, B, D, E, F, I), FASTA

>8D9S_4 AP-1 complex subunit beta-1 (chains A, B, D, E, F, I)
MTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANA
VAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQY
VALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELRE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRK
YPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQV
QLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEV
VLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEGGRGVVHKSLPPRTASS
ESAESPETAPTGAPPGEQPDVIPAQGDLLGDLLNLDLGPPVSGPPLATSSVQMGAVDLLG
GGLDSLMGDEPEGIGGTNFVAPPTAAVPANLGAPIGSGLSDLFDLTSGVGTLSGSYVAPK
AVWLPAMKAKGLEISGTFTRQVGSISMDLQLTNKALQVMTDFAIQFNRNSFGLAPAAPLQ
VHAPLSPNQTVEISLPLSTVGSVMKMEPLNNLQVAVKNNIDVFYFSTLYPLHILFVEDGK
MDRQMFLATWKDIPNENEAQFQIRDCPLNAEAASSKLQSSNIFTVAKRNVEGQDMLYQSL
KLTNGIWVLAELRIQPGNPSCTDLELSLKCRAPEVSQHVYQAYETILKN

Sequence of entity 5 (G, R, T, U, V, W), FASTA

>8D9S_5 AP-1 complex subunit gamma-1 (chains G, R, T, U, V, W)
MPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLG
YPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQG
LALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATK
NLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGI
SDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIK
SESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVS
IKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHID
TIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCI
GEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCT
VNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGPENLYF
Q

Sequence of entity 6 (M, j, k, l, m, n), FASTA

>8D9S_6 AP-1 complex subunit mu-1 (chains M, j, k, l, m, n)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 7 (S, t, u, v, w, x), FASTA

>8D9S_7 AP-1 complex subunit sigma-3 (chains S, t, u, v, w, x)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQEVSTVSQTMGER

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	18
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	18

Primary citation

Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. Hooy, R.M., Iwamoto, Y., Tudorica, D.A. et al. Sci Adv (2022) 8:eadd3914-eadd3914. DOI 10.1126/sciadv.add3914 · PubMed

Other PDB entries of the same protein (UniProt P84077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SDW 1.75 Å, Crystal structure of the non-myristoylated mutant [L8K]Arf1 in complex with a GDP analogue
1HUR 2.0 Å, Human ADP-ribosylation factor 1 complexed with GDP, full length non-myristoylated
7R4H 2.34 Å, phospho-STING binding to adaptor protein complex-1
6FAE 2.35 Å, The Sec7 domain of IQSEC2 (Brag1) in complex with the small GTPase Arf1
1RE0 2.4 Å, Structure of ARF1-GDP bound to Sec7 domain complexed with Brefeldin A
9QLO 2.47 Å, NMT1-NAC bound human RNC with full length ARF1 - State 1
9QLQ 2.57 Å, NMT1-NAC bound human RNC with full length ARF1 - alternative State
7DN8 2.61 Å, Crystal structure of Salmonella effector SopF in complex with ARF1
9QLP 2.75 Å, NMT1-NAC bound human RNC with full length ARF1 - State 2
3O47 2.8 Å, Crystal structure of ARFGAP1-ARF1 fusion protein
7DN9 3.29 Å, Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1
6CM9 3.73 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit

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