6OWT: SIVsmm Nef and SMM tetherin

Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex. Determined by electron microscopy at 3.8 Å resolution. Released 25 Sept 2019.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Rattus norvegicus, Mus musculus, Cercocebus atys
Chains: 6
Atoms: 11,649
Mol. weight: 267.96 kDa
Released: 25 Sept 2019

Explore 6OWT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OWT contains 98 α-helices and 29 β-strands across 5 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: 43 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-43	12
α-helix	52-67	16
α-helix	77-80	4
α-helix	81-84	4
α-helix	88-100	13
α-helix	107-121	15
α-helix	125-138	14
α-helix	141-146	6
α-helix	150-155	6
α-helix	162-178	17
α-helix	189-193	5
α-helix	194-197	4
α-helix	202-214	13
α-helix	220-222	3
α-helix	223-237	15
β-strand	248	1	1
β-strand	253	1	1
α-helix	255-266	12
α-helix	269-271	3
α-helix	274-292	19
α-helix	294-295	2
α-helix	300-320	21
α-helix	324-337	14
α-helix	343-351	9
α-helix	354-357	4
α-helix	363-366	4
α-helix	367-369	3
α-helix	370-378	9
α-helix	383-396	14
α-helix	402-413	12
α-helix	421-434	14
α-helix	439-451	13
α-helix	459-471	13
α-helix	476-486	11
α-helix	494-507	14
α-helix	509-511	3
α-helix	515-517	3
α-helix	519-530	12
α-helix	535-551	17
α-helix	556-564	9
α-helix	566-569	4
α-helix	574-586	13
α-helix	592-598	7
α-helix	601-606	6
α-helix	611-619	9

Chain B: 40 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	2
β-strand	16	1	2
α-helix	18-23	6
α-helix	27-43	17
α-helix	48-50	3
α-helix	51-54	4
α-helix	63-75	13
α-helix	81-84	4
α-helix	88-92	5
α-helix	100-110	11
α-helix	118-121	4
α-helix	123-127	5
α-helix	135-148	14
α-helix	158-169	12
α-helix	174-187	14
α-helix	200-212	13
α-helix	218-227	10
α-helix	235-244	10
α-helix	254-265	12
α-helix	275-290	16
α-helix	296-312	17
α-helix	322-324	3
α-helix	332-344	13
α-helix	351-360	10
α-helix	361-363	3
α-helix	367-383	17
α-helix	385-387	3
α-helix	388-399	12
α-helix	404-420	17
α-helix	429-435	7
α-helix	442-453	12
α-helix	462-471	10
α-helix	479-482	4
α-helix	491-494	4
α-helix	500-503	4
α-helix	505-511	7
α-helix	517-530	14
α-helix	534-540	7
α-helix	546-549	4
α-helix	557-565	9
β-strand	569	1	3
α-helix	570-574	5
α-helix	578-580	3

Chain M: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	4
β-strand	14-16	3	4
α-helix	26-32	7
α-helix	33-37	5
β-strand	47-49	3	4
β-strand	54-59	6	4
β-strand	64-69	6	4
β-strand	74	1	3
α-helix	75-93	19
α-helix	98-103	6
α-helix	105-115	11
β-strand	117	1	5
β-strand	120	1	5

Chain N: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	113-126	14
β-strand	133	1	6
α-helix	136-149	14
β-strand	159	1	7
β-strand	166	1	6
β-strand	168	1	7
β-strand	175-179	5	6
β-strand	180-181	2	2
β-strand	211-215	5	6
α-helix	217-220	4
α-helix	225-228	4

Chain S: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	14-19	6	8
α-helix	25-39	15
β-strand	49-50	2	8
β-strand	55	1	9
β-strand	57-62	6	8
β-strand	65-71	7	8
β-strand	72	1	9
α-helix	77-94	18
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	10
β-strand	122-123	2	10
α-helix	129-137	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit alpha	A	protein	939	Rattus norvegicus	P18484 (AlphaFold model)
AP-2 complex subunit beta	B	protein	591	Rattus norvegicus	P62944 (AlphaFold model)
Adaptor protein complex AP-2, mu1	M	protein	141	Mus musculus	P84091 (AlphaFold model)
Tetherin,Protein Nef	N, T	protein	275	Cercocebus atys, Simian immunodeficiency virus	C3VHQ5 (AlphaFold model), Q4JGV0
AP-2 complex subunit sigma	S	protein	142	Rattus norvegicus	P62744

Sequence of entity 1 (A), FASTA

>6OWT_1 AP-2 complex subunit alpha (chains A)
MPAVSKGEGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKGPSTVTDLEETKRERSIDVNGGPEPVPASTSAASTPSPSA
DLLGLGAVPPAPTGPPPTSGGGLLVDVFSDSASAVAPLAPGSEDNFARFVCKNNGVLFEN
QLLQIGLKSEFRQNLGRMFIFYGNKTSTQFLNFTPTLICADDLQTNLNLQTKPVDPTVDG
GAQVQQVVNIECISDFTEAPVLNIQFRYGGTFQNVSVKLPITLNKFFQPTEMASQDFFQR
WKQLSNPQQEVQNIFKAKHPMDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQ
IGCLLRLEPNLQAQMYRLTLRTSKDTVSQRLCELLSEQF

Sequence of entity 2 (B), FASTA

>6OWT_2 AP-2 complex subunit beta (chains B)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

Sequence of entity 3 (M), FASTA

>6OWT_3 Adaptor protein complex AP-2, mu1 (chains M)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQ

Sequence of entity 4 (N, T), FASTA

>6OWT_4 Tetherin,Protein Nef (chains N, T)
ILYDYSRMPMGDIWKEDGDKRSKGSDEASEGSGMGGVTSKKQSKRRQGLRERLLQARGET
DGYSRSRGELGKGWNLPSAEGQGYSEEQFMNTPWRNPAREGEKLKYRQQNMDDVDDDDDE
LVGVAVHPKVPLRAMSYKLAIDMSHFIKEKGGLEGIYYSDRRHRILDIYLEKEEGIIPDW
QNYTSGPGVRYPLFFGWLWKLVPVNVSDEAQEDETHCLVHPAQTSQWDDPWGEVLAWKFD
PKLAYTYEAFIRYPEEFGNDSGLSKEEVKRRLTAR

Sequence of entity 5 (S), FASTA

>6OWT_5 AP-2 complex subunit sigma (chains S)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHCVSELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Primary citation

Structural Basis for Tetherin Antagonism as a Barrier to Zoonotic Lentiviral Transmission. Buffalo, C.Z., Sturzel, C.M., Heusinger, E. et al. Cell Host Microbe (2019) 26:359-368.e8. DOI 10.1016/j.chom.2019.08.002 · PubMed

Other PDB entries of the same protein (UniProt P18484 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QH5 2.56 Å, AP2 clathrin adaptor mu2T156-phosphorylated core in closed conformation
2VGL 2.6 Å, AP2 clathrin adaptor core
4UQI 2.79 Å, AP2 controls clathrin polymerization with a membrane-activated switch
7OHO 2.88 Å, Crystal structure of AP2 FCHO2 chimera
4NEE 2.88 Å, crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef
6URI 3.0 Å, HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex
2XA7 3.1 Å, AP2 clathrin adaptor core in active complex with cargo peptides
7OG1 3.25 Å, AP2 clathrin adaptor core in complex with cargo peptide and FCHO2
6QH7 3.4 Å, AP2 clathrin adaptor mu2T156-phosphorylated core with two cargo peptides in open+…
6YAE 3.9 Å, AP2 core in physiological buffer
7Z5C 4.16 Å, Chimera of AP2 with FCHO2 linker domain as a fusion on Cmu2 subunit
6QH6 5.0 Å, AP2 clathrin adaptor core with two cargo peptides in open+ conformation

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