6D83: Bone marrow stromal antigen 2,Protein Nef

Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer monomeric subunit. Determined by electron microscopy at 4.27 Å resolution. Released 8 Aug 2018.

Method: Electron microscopy
Resolution: 4.27 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1, Mus musculus
Chains: 8
Atoms: 16,588
Mol. weight: 306.76 kDa
Ligands: GTP, MG
Released: 8 Aug 2018

Explore 6D83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D83 contains 111 α-helices and 59 β-strands across 7 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 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	51-54	4
α-helix	56-58	3
α-helix	66-75	10
α-helix	84-87	4
α-helix	88-94	7
α-helix	100-112	13
α-helix	123-130	8
α-helix	135-151	17
α-helix	153-158	6
α-helix	161-167	7
α-helix	174-190	17
α-helix	201-209	9
α-helix	218-221	4
α-helix	235-244	10
α-helix	245-249	5
β-strand	250	1	1
α-helix	255-266	12
α-helix	276-290	15
α-helix	291-293	3
α-helix	296-312	17
α-helix	322-324	3
α-helix	332-345	14
α-helix	351-359	9
α-helix	367-383	17
α-helix	388-399	12
α-helix	404-420	17
α-helix	429-432	4
α-helix	442-454	13
α-helix	462-466	5
α-helix	473-475	3
α-helix	479-494	16
α-helix	500-508	9
α-helix	509-513	5
α-helix	517-532	16
α-helix	537-540	4
α-helix	545-549	5
α-helix	554-556	3
α-helix	557-564	8
β-strand	569	1	2
α-helix	570-572	3

Chain C: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	3
β-strand	23	1	4
α-helix	30-38	9
β-strand	51-58	8	3
β-strand	61-68	8	3
α-helix	75-78	4
β-strand	90-93	4	4
α-helix	97-110	14
α-helix	119-121	3
β-strand	123-126	4	4
α-helix	138-143	6
α-helix	145-147	3
β-strand	155-158	4	4
α-helix	166-177	12

Chain G: 38 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	20-38	19
α-helix	46-59	14
α-helix	68-74	7
α-helix	79-92	14
α-helix	95-97	3
α-helix	100-102	3
α-helix	103-110	8
α-helix	116-129	14
α-helix	132-142	11
α-helix	144-146	3
α-helix	151-167	17
α-helix	169-171	3
α-helix	188-204	17
α-helix	206-212	7
α-helix	216-227	12
β-strand	236-237	2	5
β-strand	240-241	2	5
α-helix	243-254	12
α-helix	262-266	5
α-helix	268-274	7
α-helix	283-298	16
α-helix	303-316	14
α-helix	322-334	13
α-helix	340-343	4
α-helix	344-346	3
α-helix	347-352	6
α-helix	353-355	3
α-helix	359-372	14
α-helix	378-390	13
α-helix	397-410	14
α-helix	415-428	14
α-helix	438-447	10
α-helix	453-463	11
α-helix	470-487	18
α-helix	504-514	11
α-helix	522-536	15
α-helix	544-550	7
α-helix	557-572	16
α-helix	582-586	5

Chain H: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18-24	7	6
α-helix	30-38	9
β-strand	51-57	7	6
β-strand	62-68	7	6
α-helix	75-81	7
β-strand	87-92	6	6
α-helix	97-99	3
α-helix	100-110	11
β-strand	120-125	6	6
α-helix	136-143	8
α-helix	145-147	3
β-strand	153	1	6
β-strand	156-157	2	6
β-strand	159	1	7
β-strand	164	1	7
α-helix	166-177	12

Chain M: 12 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	8
β-strand	15-20	6	8
α-helix	27-32	6
α-helix	33-41	9
β-strand	49-52	4	8
β-strand	55-61	7	8
β-strand	66-71	6	8
β-strand	76	1	2
α-helix	77-94	18
α-helix	100-103	4
α-helix	107-116	10
β-strand	118-119	2	9
β-strand	122-123	2	9
α-helix	128-132	5
α-helix	148-150	3
α-helix	151-153	3
β-strand	170-183	14	1
β-strand	189-202	14	1
β-strand	209-214	6	10
β-strand	216	1	11
α-helix	217-223	7
β-strand	231	1	11
β-strand	236-238	3	1
β-strand	242	1	10
α-helix	244-250	7
β-strand	253-255	3	10
β-strand	260-270	11	1
α-helix	274-275	2
β-strand	277-280	4	12
β-strand	283	1	12
β-strand	286	1	13
β-strand	290	1	13
β-strand	292-299	8	12
β-strand	306-315	10	1
β-strand	321-326	6	12
β-strand	331-335	5	1
β-strand	340-349	10	1
β-strand	353-361	9	12
α-helix	374-375	2
β-strand	376-377	2	1
β-strand	381-383	3	1
β-strand	392-398	7	10
β-strand	406-420	15	1

Chain S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	14
β-strand	14-19	6	14
α-helix	25-40	16
β-strand	49-51	3	14
β-strand	55-61	7	14
β-strand	66-72	7	14
α-helix	78-95	18
α-helix	100-105	6
α-helix	107-115	9
β-strand	118-119	2	15
β-strand	122-123	2	15
α-helix	130-141	12

Chain T: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9-10	2	1
α-helix	11-12	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bone marrow stromal antigen 2,Protein Nef	L, T	protein	264	Homo sapiens, Human immunodeficiency virus 1	Q10589 (AlphaFold model), Q90VU7
AP-1 complex subunit beta-1	B	protein	586	Homo sapiens	Q10567 (AlphaFold model)
ADP-ribosylation factor 1	C, H	protein	193	Homo sapiens	P84077 (AlphaFold model)
AP-1 complex subunit gamma-1	G	protein	601	Mus musculus	P22892
AP-1 complex subunit mu-1	M	protein	423	Mus musculus	P35585
AP-1 complex subunit sigma-3	S	protein	154	Homo sapiens	Q96PC3

Sequence of entity 1 (L, T), FASTA

>6D83_1 Bone marrow stromal antigen 2,Protein Nef (chains L, T)
MSYYHHHHHHDYDIPTTENLYFQGAMGSASTSYDYCRVPMEDGDKRCKGSDEASEGSGMG
GKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQE
EEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFP
DWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSAAHPVSLHGMDDPEREVLE
WRFDSRLAFHHVARELHPEYFKNC

Sequence of entity 2 (B), FASTA

>6D83_2 AP-1 complex subunit beta-1 (chains B)
GSMTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCM
QTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKI
TEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVA
NAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQ
SICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPEL
QYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAEL
REYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIF
RKYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKST
QVQLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAK
EVVLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEG

Sequence of entity 3 (C, H), FASTA

>6D83_3 ADP-ribosylation factor 1 (chains C, H)
MSYYHHHHHHDYDIPTTENLYFQGAMGSEMRILMVGLDAAGKTTILYKLKLGEIVTTIPT
IGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELM
RMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYE
GLDWLSNQLRNQK

Sequence of entity 4 (G), FASTA

>6D83_4 AP-1 complex subunit gamma-1 (chains G)
MPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLG
YPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQG
LALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATK
NLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGI
SDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIK
SESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVS
IKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHID
TIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCI
GEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCT
VNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGPENLYF
Q

Sequence of entity 5 (M), FASTA

>6D83_5 AP-1 complex subunit mu-1 (chains M)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 6 (S), FASTA

>6D83_6 AP-1 complex subunit sigma-3 (chains S)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQEVSTVCQTMGER

Ligands and cofactors

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

Primary citation

HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation. Morris, K.L., Buffalo, C.Z., Sturzel, C.M. et al. Cell (2018) 174:659-671.e14. DOI 10.1016/j.cell.2018.07.004 · PubMed

Other PDB entries of the same protein (UniProt Q10589 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Q9A 2.1 Å, MHC Class I A02 Allele presenting LLLGIGILVL, in complex with Mel5 TCR
3MQ7 2.28 Å, Crystal Structure of Ectodomain Mutant of BST-2/Tetherin/CD317
3NWH 2.6 Å, Crystal structure of BST2/Tetherin
2X7A 2.77 Å, Structural basis of HIV-1 tethering to membranes by the Bst2-tetherin ectodomain
3MQ9 2.8 Å, Crystal Structure of Ectodomain Mutant of BST-2/Tetherin/CD317 Fused to MBP
3MQC 2.8 Å, Crystal Structure of Ectodomain of BST-2/Tetherin/CD317 (P21)
4P6Z 3.0 Å, Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic…
3MQB 3.2 Å, Crystal Structure of Ectodomain of BST-2/Tetherin/CD317 (C2)
2XG7 3.45 Å, Crystal Structure of BST2-Tetherin Ectodomain expressed in HEK293T cells
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
6D84 6.72 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer

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