8D4D: ADP-ribosylation factor 1

gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes. Determined by electron microscopy at 9.6 Å resolution. Released 14 Jun 2023.

Method: Electron microscopy
Resolution: 9.6 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1, Mus musculus
Chains: 18
Atoms: 18,028
Mol. weight: 669.13 kDa
Ligands: MG, GTP
Released: 14 Jun 2023

Explore 8D4D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D4D contains 242 α-helices and 136 β-strands across 16 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 and B: 40 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	116-119	4
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	216-226	11
α-helix	234-244	11
α-helix	245-249	5
β-strand	250	1	27
α-helix	253-266	14
α-helix	275-292	18
α-helix	296-310	15
α-helix	322-324	3
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	478-494	17
α-helix	500-511	12
α-helix	517-532	16
α-helix	534-540	7
α-helix	555-556	2
α-helix	557-565	9
β-strand	569	1	28
α-helix	570-573	4
α-helix	578-580	3

Chains C, D, F and H: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	19	1	1
β-strand	22	1	1
β-strand	23-24	2	2
α-helix	30-38	9
β-strand	51-58	8	1
β-strand	61-68	8	1
α-helix	75-80	6
β-strand	90-93	4	2
α-helix	97-111	15
β-strand	123-126	4	2
α-helix	138-143	6
α-helix	145-147	3
β-strand	155-157	3	2
α-helix	166-177	12

Chains E and G: 37 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	64-67	4
α-helix	68-74	7
α-helix	79-92	14
α-helix	95-97	3
α-helix	103-111	9
α-helix	116-128	13
α-helix	134-146	13
α-helix	151-167	17
α-helix	169-174	6
α-helix	188-204	17
α-helix	207-212	6
α-helix	216-228	13
β-strand	236-237	2	29
β-strand	240-241	2	29
α-helix	243-255	13
α-helix	261-266	6
α-helix	268-276	9
α-helix	283-297	15
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	397-411	15
α-helix	415-429	15
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 and M: 13 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	30
β-strand	17-20	4	30
α-helix	27-29	3
α-helix	30-43	14
β-strand	49-52	4	30
β-strand	55-61	7	30
β-strand	66-71	6	30
β-strand	76	1	28
α-helix	77-94	18
α-helix	100-103	4
α-helix	107-117	11
β-strand	118-119	2	31
β-strand	122-123	2	31
α-helix	128-131	4
α-helix	148-150	3
α-helix	151-154	4
β-strand	170-183	14	27
β-strand	189-203	15	27
β-strand	209-214	6	32
β-strand	216	1	33
α-helix	217-223	7
β-strand	231	1	33
β-strand	235-238	4	27
β-strand	242	1	32
α-helix	244-250	7
β-strand	253-255	3	32
β-strand	260-270	11	27
α-helix	274-275	2
β-strand	277-280	4	34
β-strand	283	1	34
β-strand	290-299	10	34
β-strand	306-314	9	27
β-strand	321-326	6	34
β-strand	331-335	5	27
β-strand	340-349	10	27
β-strand	353-361	9	34
α-helix	366-367	2
α-helix	374-375	2
β-strand	376-378	3	27
β-strand	381-383	3	27
β-strand	385	1	23
β-strand	392-398	7	32
β-strand	406-415	10	27
β-strand	419-420	2	27

Chains K and N: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-22	16
β-strand	69	1	23
β-strand	77	1	24
α-helix	78-80	3
α-helix	81-94	14
α-helix	100	1
β-strand	101	1	25
α-helix	102	1
α-helix	104-118	15
β-strand	120	1	24
β-strand	127	1	26
α-helix	133	1
β-strand	134	1	25
α-helix	135	1
β-strand	136	1	26
β-strand	143-147	5	25
β-strand	181-185	5	25
α-helix	187-190	4
α-helix	194-198	5
α-helix	200-203	4

Chains O and S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	35
β-strand	14-19	6	35
α-helix	25-40	16
β-strand	49-52	4	35
β-strand	55-59	5	35
β-strand	66-71	6	35
α-helix	77-95	19
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	36
β-strand	122-123	2	36
α-helix	129-140	12

Chains P and Y: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	345-346	2	27
α-helix	352-354	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor 1	C, D, F, H	protein	180	Homo sapiens	P84077 (AlphaFold model)
Protein Nef	I, K, L, N	protein	212	Human immunodeficiency virus 1	Q90VU7
HLA class I histocompatibility antigen, A alpha chain	P, Y	protein	39	Homo sapiens	P04439 (AlphaFold model)
AP-1 complex subunit beta-1	A, B	protein	949	Homo sapiens	Q10567 (AlphaFold model)
AP-1 complex subunit gamma-1	E, G	protein	601	Mus musculus	P22892
AP-1 complex subunit mu-1	J, M	protein	423	Mus musculus	P35585
AP-1 complex subunit sigma-3	O, S	protein	154	Homo sapiens	Q96PC3

Sequence of entity 1 (C, D, F, H), FASTA

>8D4D_1 ADP-ribosylation factor 1 (chains C, D, F, H)
GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNI
SFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVL
LVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Sequence of entity 2 (I, K, L, N), FASTA

>8D4D_2 Protein Nef (chains I, K, L, N)
GGKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQ
EEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYF
PDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVL
EWRFDSRLAFHHVARELHPEYFKNCGHHHHHH

Sequence of entity 3 (P, Y), FASTA

>8D4D_3 HLA class I histocompatibility antigen, A alpha chain (chains P, Y)
CRKSSDRKGGSYSQAAGSDSAQSSDVSLTAAKVHHHHHH

Sequence of entity 4 (A, B), FASTA

>8D4D_4 AP-1 complex subunit beta-1 (chains A, B)
MTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANA
VAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQY
VALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELRE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRK
YPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQV
QLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEV
VLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEGGRGVVHKSLPPRTASS
ESAESPETAPTGAPPGEQPDVIPAQGDLLGDLLNLDLGPPVSGPPLATSSVQMGAVDLLG
GGLDSLMGDEPEGIGGTNFVAPPTAAVPANLGAPIGSGLSDLFDLTSGVGTLSGSYVAPK
AVWLPAMKAKGLEISGTFTRQVGSISMDLQLTNKALQVMTDFAIQFNRNSFGLAPAAPLQ
VHAPLSPNQTVEISLPLSTVGSVMKMEPLNNLQVAVKNNIDVFYFSTLYPLHILFVEDGK
MDRQMFLATWKDIPNENEAQFQIRDCPLNAEAASSKLQSSNIFTVAKRNVEGQDMLYQSL
KLTNGIWVLAELRIQPGNPSCTDLELSLKCRAPEVSQHVYQAYETILKN

Sequence of entity 5 (E, G), FASTA

>8D4D_5 AP-1 complex subunit gamma-1 (chains E, G)
MPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLG
YPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQG
LALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATK
NLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGI
SDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIK
SESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVS
IKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHID
TIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCI
GEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCT
VNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGPENLYF
Q

Sequence of entity 6 (J, M), FASTA

>8D4D_6 AP-1 complex subunit mu-1 (chains J, M)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 7 (O, S), FASTA

>8D4D_7 AP-1 complex subunit sigma-3 (chains O, S)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQEVSTVSQTMGER

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	4

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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