8D9W: Protein Nef

beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes. Determined by electron microscopy at 9.3 Å resolution. Released 5 Jul 2023.

Method: Electron microscopy
Resolution: 9.3 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens, Mus musculus
Chains: 20
Atoms: 13,746
Mol. weight: 934.87 kDa
Ligands: GTP, MG
Released: 5 Jul 2023

Explore 8D9W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D9W contains 180 α-helices and 112 β-strands across 18 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: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	25
β-strand	18-20	3	25
β-strand	50-52	3	25
β-strand	55-61	7	25
β-strand	66-71	6	25
α-helix	77-94	18
α-helix	100-103	4
α-helix	107-117	11
β-strand	118-119	2	26
β-strand	122-123	2	26
α-helix	128-131	4
α-helix	148-150	3
α-helix	151-154	4
β-strand	170-183	14	24
β-strand	189-195	7	24
β-strand	197-203	7	24
β-strand	209-214	6	27
β-strand	216	1	28
α-helix	217-223	7
β-strand	231	1	28
β-strand	235-238	4	24
β-strand	242	1	27
α-helix	244-250	7
β-strand	253-255	3	27
β-strand	260-270	11	24
α-helix	274-275	2
β-strand	306-313	8	24
β-strand	331-334	4	24
β-strand	341-349	9	24
β-strand	377-378	2	24
β-strand	381-383	3	24
β-strand	385	1	20
β-strand	392-398	7	27
β-strand	406-415	10	24
β-strand	419	1	24

Chains A and D: 18 helices, 0 β-strands

Element	Residues	Length
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	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
α-helix	253-266	14

Chain B: 17 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	88-94	7
α-helix	100-112	13
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	5
α-helix	253-266	14
α-helix	275-291	17
α-helix	296-310	15
α-helix	322-324	3
α-helix	326-327	2
α-helix	332-344	13

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

Element	Residues	Length	Sheet
α-helix	7-22	16
β-strand	69	1	20
β-strand	77	1	21
α-helix	78-80	3
α-helix	81-94	14
α-helix	100	1
β-strand	101	1	22
α-helix	102	1
α-helix	104-118	15
β-strand	120	1	21
β-strand	127	1	23
α-helix	133	1
β-strand	134	1	22
α-helix	135	1
β-strand	136	1	23
β-strand	143-147	5	22
β-strand	181-185	5	22
α-helix	187-190	4
α-helix	194-198	5
α-helix	200-203	4

Chains e and f: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	13
β-strand	14-19	6	13
α-helix	25-40	16
β-strand	49-52	4	13
β-strand	55-58	4	13
β-strand	66-71	6	13
α-helix	77-95	19
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	14
β-strand	122-123	2	14

Chain E: 18 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	63-75	13
α-helix	88-94	7
α-helix	100-112	13
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	24
α-helix	253-266	14
α-helix	275-291	17
α-helix	296-310	15
α-helix	322-324	3
α-helix	326-327	2
α-helix	332-344	13

Chains F and I: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
β-strand	19-24	6	10
α-helix	30-38	9
β-strand	51-58	8	10
β-strand	61-68	8	10
α-helix	75-82	8
β-strand	89-93	5	10
α-helix	100-111	12
β-strand	123-126	4	10
α-helix	138-143	6
α-helix	145-147	3
β-strand	155-157	3	10
α-helix	166-177	12

Chains j and Y: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	350-351	2	24
α-helix	357-359	3

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein Nef	N, U, V, d	protein	213	Human immunodeficiency virus 1	Q90VU7
HLA class I histocompatibility antigen, A alpha chain	Y, j	protein	44	Homo sapiens	P04439 (AlphaFold model)
AP-1 complex subunit beta-1	A, B, D, E	protein	949	Homo sapiens	Q10567 (AlphaFold model)
AP-1 complex subunit mu-1	M, X, Z, a	protein	423	Mus musculus	P35585 (AlphaFold model)
ADP-ribosylation factor 1	F, I	protein	180	Homo sapiens	P84077
AP-1 complex subunit gamma-1	K, O	protein	601	Mus musculus	P22892
AP-1 complex subunit sigma-3	e, f	protein	154	Homo sapiens	Q96PC3

Sequence of entity 1 (N, U, V, d), FASTA

>8D9W_1 Protein Nef (chains N, U, V, d)
MGGKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEA
QEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGY
FPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREV
LEWRFDSRLAFHHVARELHPEYFKNCGHHHHHH

Sequence of entity 2 (Y, j), FASTA

>8D9W_2 HLA class I histocompatibility antigen, A alpha chain (chains Y, j)
GAMGSCRKSSDRKGGSYSQAAGSDSAQSSDVSLTAAKVHHHHHH

Sequence of entity 3 (A, B, D, E), FASTA

>8D9W_3 AP-1 complex subunit beta-1 (chains A, B, D, E)
MTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANA
VAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQY
VALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELRE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRK
YPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQV
QLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEV
VLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEGGRGVVHKSLPPRTASS
ESAESPETAPTGAPPGEQPDVIPAQGDLLGDLLNLDLGPPVSGPPLATSSVQMGAVDLLG
GGLDSLMGDEPEGIGGTNFVAPPTAAVPANLGAPIGSGLSDLFDLTSGVGTLSGSYVAPK
AVWLPAMKAKGLEISGTFTRQVGSISMDLQLTNKALQVMTDFAIQFNRNSFGLAPAAPLQ
VHAPLSPNQTVEISLPLSTVGSVMKMEPLNNLQVAVKNNIDVFYFSTLYPLHILFVEDGK
MDRQMFLATWKDIPNENEAQFQIRDCPLNAEAASSKLQSSNIFTVAKRNVEGQDMLYQSL
KLTNGIWVLAELRIQPGNPSCTDLELSLKCRAPEVSQHVYQAYETILKN

Sequence of entity 4 (M, X, Z, a), FASTA

>8D9W_4 AP-1 complex subunit mu-1 (chains M, X, Z, a)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 5 (F, I), FASTA

>8D9W_5 ADP-ribosylation factor 1 (chains F, I)
GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNI
SFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVL
LVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Sequence of entity 6 (K, O), FASTA

>8D9W_6 AP-1 complex subunit gamma-1 (chains K, O)
MPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLG
YPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQG
LALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATK
NLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGI
SDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIK
SESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVS
IKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHID
TIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCI
GEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCT
VNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGPENLYF
Q

Sequence of entity 7 (e, f), FASTA

>8D9W_7 AP-1 complex subunit sigma-3 (chains e, f)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQEVSTVSQTMGER

Ligands and cofactors

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

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. DOI 10.1126/sciadv.add3914 · PubMed

Other PDB entries of the same protein (UniProt Q90VU7), best resolution first:

4EN2 2.58 Å, HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1…
4EMZ 2.9 Å, HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1…
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
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…
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…
8D4D 9.6 Å, gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I…
8D4F 9.8 Å, beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I…

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