8D9V: ADP ribosylation factor 1
gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes. Determined by electron microscopy at 9.4 Å resolution. Released 9 Nov 2022.
- Method
- Electron microscopy
- Resolution
- 9.4 Å
- Organisms
- Homo sapiens, Human immunodeficiency virus 1, Mus musculus
- Chains
- 18
- Atoms
- 18,028
- Mol. weight
- 671.02 kDa
- Ligands
- GTP, MG
- Released
- 9 Nov 2022
Explore 8D9V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8D9V contains 246 α-helices and 130 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: 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 | 82-86 | 5 | |
| 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 | 216-225 | 10 | |
| 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 | |
| α-helix | 348-350 | 3 | |
| 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 | 555-556 | 2 | |
| α-helix | 557-565 | 9 | |
| β-strand | 569 | 1 | 25 |
| α-helix | 570-573 | 4 | |
| α-helix | 578-580 | 3 | |
Chains C, D, F and H: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-13 | 9 | |
| β-strand | 19-24 | 6 | 1 |
| α-helix | 30-38 | 9 | |
| β-strand | 51-58 | 8 | 1 |
| β-strand | 61-68 | 8 | 1 |
| α-helix | 75-80 | 6 | |
| β-strand | 89-93 | 5 | 1 |
| α-helix | 97-110 | 14 | |
| β-strand | 123-126 | 4 | 1 |
| α-helix | 138-143 | 6 | |
| α-helix | 145-147 | 3 | |
| β-strand | 155-157 | 3 | 1 |
| α-helix | 166-177 | 12 | |
Chains E and G: 38 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 | 213-215 | 3 | |
| α-helix | 216-228 | 13 | |
| β-strand | 236-237 | 2 | 26 |
| β-strand | 240-241 | 2 | 26 |
| 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, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-8 | 4 | 27 |
| β-strand | 17-20 | 4 | 27 |
| α-helix | 27-32 | 6 | |
| α-helix | 33-42 | 10 | |
| β-strand | 49 | 1 | 27 |
| β-strand | 52 | 1 | 28 |
| β-strand | 55 | 1 | 28 |
| β-strand | 56-61 | 6 | 27 |
| β-strand | 66-71 | 6 | 27 |
| β-strand | 76 | 1 | 25 |
| α-helix | 77-94 | 18 | |
| α-helix | 100-103 | 4 | |
| α-helix | 107-117 | 11 | |
| β-strand | 118-119 | 2 | 29 |
| β-strand | 122-123 | 2 | 29 |
| α-helix | 128-131 | 4 | |
| α-helix | 148-150 | 3 | |
| α-helix | 151-154 | 4 | |
| β-strand | 170-183 | 14 | 24 |
| β-strand | 189-203 | 15 | 24 |
| β-strand | 209-214 | 6 | 30 |
| β-strand | 216 | 1 | 31 |
| α-helix | 217-223 | 7 | |
| β-strand | 231 | 1 | 31 |
| β-strand | 235-238 | 4 | 24 |
| β-strand | 242 | 1 | 30 |
| α-helix | 244-250 | 7 | |
| β-strand | 253-255 | 3 | 30 |
| β-strand | 260-270 | 11 | 24 |
| α-helix | 274-275 | 2 | |
| β-strand | 277-280 | 4 | 32 |
| β-strand | 283 | 1 | 32 |
| β-strand | 291-299 | 9 | 32 |
| β-strand | 306-314 | 9 | 24 |
| β-strand | 321-326 | 6 | 32 |
| β-strand | 331-335 | 5 | 24 |
| β-strand | 340-349 | 10 | 24 |
| β-strand | 353-361 | 9 | 32 |
| α-helix | 366-367 | 2 | |
| α-helix | 374-375 | 2 | |
| β-strand | 376-378 | 3 | 24 |
| β-strand | 381-383 | 3 | 24 |
| β-strand | 385 | 1 | 20 |
| β-strand | 392-398 | 7 | 30 |
| β-strand | 406-420 | 15 | 24 |
Chains K 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 O and S: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-8 | 7 | 33 |
| β-strand | 14-19 | 6 | 33 |
| α-helix | 25-40 | 16 | |
| β-strand | 50-52 | 3 | 33 |
| β-strand | 55-59 | 5 | 33 |
| β-strand | 66-71 | 6 | 33 |
| α-helix | 77-95 | 19 | |
| α-helix | 100-105 | 6 | |
| α-helix | 107-117 | 11 | |
| β-strand | 118-119 | 2 | 34 |
| β-strand | 122-123 | 2 | 34 |
| α-helix | 129-140 | 12 | |
Chains P and Y: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 350-351 | 2 | 24 |
| α-helix | 357-359 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| ADP ribosylation factor 1 | C, D, F, H | protein | 181 | Homo sapiens | A0A8C2UGL4 (AlphaFold model) |
| Protein Nef | I, K, L, N | protein | 213 | Human immunodeficiency virus 1 | Q90VU7 |
| HLA class I histocompatibility antigen, A alpha chain | P, Y | protein | 44 | 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
>8D9V_1 ADP ribosylation factor 1 (chains C, D, F, H)
MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKN
ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAV
LLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQ
K
Sequence of entity 2 (I, K, L, N), FASTA
>8D9V_2 Protein Nef (chains I, K, L, N)
MGGKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEA
QEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGY
FPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREV
LEWRFDSRLAFHHVARELHPEYFKNCGHHHHHH
Sequence of entity 3 (P, Y), FASTA
>8D9V_3 HLA class I histocompatibility antigen, A alpha chain (chains P, Y)
GAMGSCRKSSDRKGGSYSQAAGSDSAQSSDVSLTASKVHHHHHH
Sequence of entity 4 (A, B), FASTA
>8D9V_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
>8D9V_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
>8D9V_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
>8D9V_7 AP-1 complex subunit sigma-3 (chains O, S)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQEVSTVSQTMGER
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 4 |
| MG | Magnesium ion | Mg | 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 A0A8C2UGL4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8D9T 20.0 Å, AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes,…
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