6CM9: PDB entry 6CM9

Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit. Determined by electron microscopy at 3.73 Å resolution. Released 8 Aug 2018.

Method: Electron microscopy
Resolution: 3.73 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1, Mus musculus
Chains: 9
Atoms: 17,683
Mol. weight: 336.89 kDa
Ligands: GTP, MG
Released: 8 Aug 2018

Explore 6CM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CM9 contains 114 α-helices and 82 β-strands across 8 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: 43 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	15-21	7
α-helix	27-40	14
α-helix	48-50	3
α-helix	51-54	4
α-helix	66-75	10
α-helix	83-85	3
α-helix	88-94	7
α-helix	100-110	11
α-helix	123-130	8
α-helix	135-151	17
α-helix	153-159	7
α-helix	162-166	5
α-helix	175-190	16
α-helix	201-208	8
α-helix	218-221	4
α-helix	235-244	10
α-helix	245-249	5
β-strand	250	1	2
α-helix	255-266	12
α-helix	276-281	6
α-helix	285-290	6
α-helix	291-293	3
α-helix	298-309	12
α-helix	317-319	3
α-helix	322-324	3
α-helix	332-344	13
α-helix	348-350	3
α-helix	351-358	8
α-helix	367-383	17
α-helix	388-399	12
α-helix	404-418	15
α-helix	429-432	4
α-helix	442-454	13
α-helix	462-465	4
α-helix	467-469	3
α-helix	473-475	3
α-helix	478-494	17
α-helix	500-510	11
α-helix	517-532	16
α-helix	537-540	4
α-helix	545-550	6
α-helix	555-556	2
α-helix	560-563	4
α-helix	570-573	4

Chain C: 5 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	76-78	3
β-strand	90-91	2	4
α-helix	97-110	14
β-strand	123-125	3	4
α-helix	138-143	6
β-strand	155-157	3	4
α-helix	166-177	12

Chain G: 36 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	20-39	20
α-helix	46-58	13
α-helix	68-74	7
α-helix	79-92	14
α-helix	100-103	4
α-helix	104-110	7
α-helix	118-129	12
α-helix	135-142	8
α-helix	151-167	17
α-helix	172-174	3
α-helix	188-204	17
α-helix	209-212	4
α-helix	216-228	13
β-strand	236-237	2	5
β-strand	240-241	2	5
α-helix	243-255	13
α-helix	262-266	5
α-helix	268-274	7
α-helix	283-298	16
α-helix	303-317	15
α-helix	322-334	13
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	416-428	13
α-helix	437-447	11
α-helix	453-463	11
α-helix	470-487	18
α-helix	504-514	11
α-helix	522-532	11
α-helix	544-550	7
α-helix	557-572	16
α-helix	578-580	3
α-helix	582-585	4

Chain H: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	6
β-strand	24	1	7
α-helix	30-37	8
β-strand	51-58	8	6
β-strand	61-68	8	6
α-helix	75-80	6
β-strand	87	1	8
β-strand	91-93	3	7
α-helix	100-110	11
β-strand	120	1	8
β-strand	124-126	3	7
α-helix	136-143	8
α-helix	145-147	3
β-strand	156	1	7
β-strand	159	1	9
β-strand	164	1	9
α-helix	166-175	10

Chain M: 14 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	10
β-strand	17-20	4	10
α-helix	27-32	6
α-helix	33-41	9
β-strand	49-52	4	10
β-strand	55-58	4	10
β-strand	61	1	11
β-strand	66	1	11
β-strand	69-71	3	10
α-helix	77-94	18
α-helix	100-103	4
α-helix	107-117	11
β-strand	118-119	2	12
β-strand	122-123	2	12
α-helix	128-131	4
α-helix	148-150	3
α-helix	151-154	4
β-strand	170-172	3	2
β-strand	175-176	2	2
β-strand	179-183	5	13
β-strand	189	1	13
β-strand	193-194	2	13
β-strand	197-203	7	2
β-strand	210-213	4	14
β-strand	216	1	15
α-helix	217-223	7
β-strand	231	1	15
β-strand	235-238	4	2
β-strand	242	1	14
α-helix	244-250	7
β-strand	253-255	3	14
β-strand	260-268	9	2
β-strand	269-270	2	13
α-helix	274-275	2
β-strand	277-280	4	16
β-strand	286	1	16
β-strand	290-299	10	16
β-strand	306-312	7	17
β-strand	313	1	13
β-strand	315	1	17
α-helix	316-317	2
β-strand	321-326	6	16
β-strand	332-335	4	17
β-strand	340-349	10	17
β-strand	353-361	9	16
α-helix	366-367	2
α-helix	374-375	2
β-strand	376-377	2	13
β-strand	381	1	17
β-strand	382-383	2	2
β-strand	385-386	2	18
β-strand	394-395	2	14
β-strand	406-408	3	2
β-strand	409	1	1
β-strand	411-413	3	2
β-strand	415-420	6	13

Chain N: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-22	8
β-strand	68-69	2	18
β-strand	77	1	23
α-helix	81-94	14
α-helix	100	1
β-strand	101-102	2	24
α-helix	104-118	15
β-strand	120	1	23
β-strand	127	1	25
β-strand	134	1	24
β-strand	136	1	25
β-strand	143-147	5	24
β-strand	181-185	5	24
α-helix	194-198	5

Chain S: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	19
β-strand	8	1	20
β-strand	14	1	20
β-strand	18-19	2	19
α-helix	25-39	15
β-strand	49-51	3	21
β-strand	56-58	3	21
β-strand	71	1	21
α-helix	78-95	18
α-helix	101-104	4
α-helix	107-115	9
β-strand	118-119	2	22
β-strand	122-123	2	22
α-helix	129-140	12

Chain T: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bone marrow stromal antigen 2, Protein Nef chimera	L, N, 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, N, T), FASTA

>6CM9_1 Bone marrow stromal antigen 2, Protein Nef chimera (chains L, N, T)
MSYYHHHHHHDYDIPTTENLYFQGAMGSASTSYDYCRVPMEDGDKRCKGSDEASEGSGMG
GKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQE
EEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFP
DWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLE
WRFDSRLAFHHVARELHPEYFKNC

Sequence of entity 2 (B), FASTA

>6CM9_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

>6CM9_3 ADP-ribosylation factor 1 (chains C, H)
MSYYHHHHHHDYDIPTTENLYFQGAMGSEMRILMVGLDAAGKTTILYKLKLGEIVTTIPT
IGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELM
RMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYE
GLDWLSNQLRNQK

Sequence of entity 4 (G), FASTA

>6CM9_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

>6CM9_5 AP-1 complex subunit mu-1 (chains M)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 6 (S), FASTA

>6CM9_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
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

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