6D84: Bone marrow stromal antigen 2,Protein Nef

Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer. Determined by electron microscopy at 6.72 Å resolution. Released 8 Aug 2018.

Method: Electron microscopy
Resolution: 6.72 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1, Mus musculus
Chains: 16
Atoms: 33,176
Mol. weight: 613.52 kDa
Ligands: GTP, MG
Released: 8 Aug 2018

Explore 6D84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D84 contains 237 α-helices and 120 β-strands across 14 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 B and F: 44 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	63-75	13
α-helix	83-87	5
α-helix	88-94	7
α-helix	100-112	13
α-helix	124-130	7
α-helix	135-151	17
α-helix	153-159	7
α-helix	161-169	9
α-helix	174-190	17
α-helix	198-200	3
α-helix	201-209	9
α-helix	218-224	7
α-helix	225-227	3
α-helix	234-244	11
α-helix	245-249	5
β-strand	250	1	1
α-helix	253-266	14
α-helix	275-290	16
α-helix	291-293	3
α-helix	296-312	17
α-helix	322-324	3
α-helix	332-344	13
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	462-469	8
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	545-548	4
α-helix	554-556	3
α-helix	557-564	8
β-strand	569	1	2
α-helix	570-574	5
α-helix	578-580	3

Chain C: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	3
β-strand	23-24	2	4
α-helix	30-38	9
α-helix	46-48	3
β-strand	51-58	8	3
β-strand	61-68	8	3
α-helix	72-74	3
α-helix	76-78	3
β-strand	87	1	5
β-strand	90-93	4	4
α-helix	97-110	14
β-strand	120	1	5
β-strand	123-126	4	4
α-helix	138-143	6
α-helix	145-147	3
β-strand	155-157	3	4
α-helix	166-177	12

Chains G and K: 39 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	103-111	9
α-helix	116-129	14
α-helix	132-142	11
α-helix	151-167	17
α-helix	172-174	3
α-helix	188-204	17
α-helix	206-212	7
α-helix	216-227	12
β-strand	236-237	2	6
β-strand	240-241	2	6
α-helix	243-255	13
α-helix	262-266	5
α-helix	268-274	7
α-helix	283-298	16
α-helix	303-318	16
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	359-371	13
α-helix	378-390	13
α-helix	396-411	16
α-helix	415-428	14
α-helix	437-447	11
α-helix	453-463	11
α-helix	470-487	18
α-helix	504-514	11
α-helix	521-532	12
α-helix	544-550	7
α-helix	551-553	3
α-helix	557-571	15
α-helix	574-577	4
α-helix	582-586	5

Chain H: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-24	7	7
α-helix	30-38	9
β-strand	51-58	8	7
β-strand	61-68	8	7
α-helix	75-81	7
β-strand	87-93	7	7
α-helix	97-99	3
α-helix	100-111	12
β-strand	120-126	7	7
α-helix	136-143	8
α-helix	145-147	3
β-strand	153-157	5	7
β-strand	159	1	8
β-strand	164	1	8
α-helix	166-177	12

Chain I: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	19
β-strand	23-24	2	20
α-helix	30-38	9
α-helix	46-48	3
β-strand	51-58	8	19
β-strand	61-68	8	19
α-helix	75-78	4
β-strand	87	1	21
β-strand	90-93	4	20
α-helix	100-110	11
β-strand	120	1	21
β-strand	123-126	4	20
α-helix	138-143	6
α-helix	145-147	3
β-strand	155-157	3	20
α-helix	166-177	12

Chains M and P: 14 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	9
β-strand	15-20	6	9
α-helix	27-32	6
α-helix	33-41	9
β-strand	49-52	4	9
β-strand	55-61	7	9
β-strand	66-71	6	9
β-strand	76	1	2
α-helix	77-94	18
α-helix	100-103	4
α-helix	107-117	11
β-strand	118-119	2	10
β-strand	122-123	2	10
α-helix	128-132	5
α-helix	148-150	3
α-helix	151-154	4
β-strand	170-183	14	1
β-strand	189-203	15	1
β-strand	209-214	6	11
β-strand	216	1	12
α-helix	217-223	7
β-strand	231	1	12
β-strand	235-238	4	1
β-strand	242	1	11
α-helix	244-250	7
β-strand	253-255	3	11
α-helix	256-258	3
β-strand	260-270	11	1
α-helix	274-275	2
β-strand	277-283	7	13
β-strand	292-299	8	13
β-strand	306-312	7	14
β-strand	313	1	1
β-strand	315	1	14
β-strand	324-327	4	13
β-strand	331-335	5	14
β-strand	340-349	10	14
β-strand	353-359	7	13
α-helix	366-367	2
α-helix	374-375	2
β-strand	376-377	2	1
β-strand	381	1	14
β-strand	382-383	2	1
β-strand	392-398	7	11
β-strand	406-420	15	1

Chain N: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-24	7	23
α-helix	30-37	8
β-strand	51-57	7	23
β-strand	62-68	7	23
α-helix	75-80	6
β-strand	87-93	7	23
α-helix	97-99	3
α-helix	100-110	11
β-strand	120-126	7	23
α-helix	136-143	8
α-helix	145-147	3
β-strand	153-157	5	23
β-strand	159	1	24
β-strand	164	1	24
α-helix	166-175	10

Chains Q and S: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	31
β-strand	14-19	6	31
α-helix	25-40	16
β-strand	49-51	3	31
β-strand	55-61	7	31
β-strand	66-72	7	31
α-helix	78-91	14
α-helix	92-96	5
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	32
β-strand	122-123	2	32
α-helix	130-141	12

1 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
Bone marrow stromal antigen 2,Protein Nef	L, O, R, T	protein	264	Homo sapiens, Human immunodeficiency virus 1	Q10589 (AlphaFold model), Q90VU7
AP-1 complex subunit beta-1	B, F	protein	586	Homo sapiens	Q10567 (AlphaFold model)
ADP-ribosylation factor 1	C, H, I, N	protein	193	Homo sapiens	P84077 (AlphaFold model)
AP-1 complex subunit gamma-1	G, K	protein	601	Mus musculus	P22892
AP-1 complex subunit mu-1	M, P	protein	423	Mus musculus	P35585
AP-1 complex subunit sigma-3	Q, S	protein	154	Homo sapiens	Q96PC3

Sequence of entity 1 (L, O, R, T), FASTA

>6D84_1 Bone marrow stromal antigen 2,Protein Nef (chains L, O, R, T)
MSYYHHHHHHDYDIPTTENLYFQGAMGSASTSYDYCRVPMEDGDKRCKGSDEASEGSGMG
GKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQE
EEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFP
DWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSAAHPVSLHGMDDPEREVLE
WRFDSRLAFHHVARELHPEYFKNC

Sequence of entity 2 (B, F), FASTA

>6D84_2 AP-1 complex subunit beta-1 (chains B, F)
GSMTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCM
QTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKI
TEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVA
NAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQ
SICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPEL
QYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAEL
REYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIF
RKYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKST
QVQLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAK
EVVLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEG

Sequence of entity 3 (C, H, I, N), FASTA

>6D84_3 ADP-ribosylation factor 1 (chains C, H, I, N)
MSYYHHHHHHDYDIPTTENLYFQGAMGSEMRILMVGLDAAGKTTILYKLKLGEIVTTIPT
IGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELM
RMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYE
GLDWLSNQLRNQK

Sequence of entity 4 (G, K), FASTA

>6D84_4 AP-1 complex subunit gamma-1 (chains G, K)
MPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLG
YPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQG
LALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATK
NLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGI
SDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIK
SESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVS
IKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHID
TIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCI
GEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCT
VNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGPENLYF
Q

Sequence of entity 5 (M, P), FASTA

>6D84_5 AP-1 complex subunit mu-1 (chains M, P)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 6 (Q, S), FASTA

>6D84_6 AP-1 complex subunit sigma-3 (chains Q, S)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQEVSTVCQTMGER

Ligands and cofactors

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

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
6D83 4.27 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant…

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