4P6Z: AP-1 complex subunit gamma-1

Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic domain bound to the clathrin adaptor protein complex 1 (AP1) core. Determined by X-ray diffraction at 3.0 Å resolution. Released 21 May 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Mus musculus, Homo sapiens, Human immunodeficiency virus type 1 group M subtype B
Chains: 6
Atoms: 13,940
Mol. weight: 216.05 kDa
Released: 21 May 2014

Explore 4P6Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P6Z contains 105 α-helices and 41 β-strands across 6 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: 44 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	15-23	9
α-helix	27-42	16
α-helix	48-50	3
α-helix	51-55	5
α-helix	63-76	14
α-helix	83-87	5
α-helix	88-94	7
α-helix	100-110	11
α-helix	116-130	15
α-helix	135-151	17
α-helix	153-159	7
α-helix	161-168	8
α-helix	174-190	17
α-helix	201-213	13
α-helix	216-228	13
α-helix	234-244	11
α-helix	245-249	5
β-strand	250	1	8
α-helix	253-266	14
α-helix	267-269	3
α-helix	275-290	16
α-helix	291-293	3
α-helix	296-312	17
α-helix	321-324	4
α-helix	326-327	2
α-helix	332-345	14
α-helix	351-361	11
α-helix	367-383	17
α-helix	387-399	13
α-helix	404-420	17
α-helix	428-431	4
α-helix	432-434	3
α-helix	442-454	13
α-helix	462-467	6
α-helix	478-494	17
α-helix	500-507	8
α-helix	508-512	5
α-helix	517-532	16
α-helix	534-540	7
α-helix	543-548	6
α-helix	550-552	3
α-helix	555-556	2
α-helix	557-564	8
α-helix	570-574	5
α-helix	578-580	3

Chain G: 40 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	7-15	9
α-helix	20-39	20
α-helix	46-58	13
α-helix	64-66	3
α-helix	67-74	8
α-helix	79-92	14
α-helix	100-111	12
α-helix	116-129	14
α-helix	132-146	15
α-helix	151-167	17
α-helix	170-175	6
α-helix	176-179	4
α-helix	188-204	17
α-helix	206-212	7
α-helix	216-228	13
β-strand	236-237	2	1
β-strand	240-241	2	1
α-helix	243-255	13
α-helix	262-277	16
α-helix	283-298	16
α-helix	303-317	15
α-helix	322-334	13
α-helix	340-343	4
α-helix	347-352	6
α-helix	353-355	3
α-helix	359-370	12
α-helix	378-390	13
α-helix	394-410	17
α-helix	415-428	14
α-helix	430-432	3
α-helix	435-437	3
α-helix	438-446	9
α-helix	453-465	13
α-helix	470-482	13
α-helix	484-488	5
β-strand	493	1	2
β-strand	495	1	2
α-helix	503-514	12
α-helix	520-536	17
α-helix	541-550	10
α-helix	551-553	3
α-helix	557-572	16
α-helix	576-580	5

Chain M: 13 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	6
β-strand	15-20	6	6
α-helix	27-32	6
α-helix	33-43	11
β-strand	49-52	4	6
β-strand	55-62	8	6
β-strand	65-71	7	6
α-helix	77-94	18
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	7
β-strand	122-123	2	7
α-helix	128-131	4
α-helix	151-154	4
β-strand	170-183	14	8
β-strand	189-203	15	8
β-strand	209-214	6	9
β-strand	216	1	10
α-helix	217-221	5
β-strand	231	1	10
β-strand	235-238	4	8
β-strand	242	1	9
α-helix	244-250	7
β-strand	253-255	3	9
α-helix	257-258	2
β-strand	260-270	11	8
β-strand	277-286	10	11
β-strand	290-299	10	11
β-strand	306-315	10	8
β-strand	321-327	7	11
β-strand	331-335	5	8
α-helix	336-338	3
β-strand	340-349	10	8
β-strand	353-361	9	11
α-helix	366-367	2
α-helix	374-375	2
β-strand	376-383	8	8
β-strand	392-398	7	9
β-strand	406-420	15	8

Chain S: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	3
β-strand	14-19	6	3
α-helix	25-40	16
β-strand	49-52	4	3
β-strand	55-62	8	3
β-strand	65-71	7	3
α-helix	77-91	15
α-helix	92-96	5
β-strand	99	1	4
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	5
β-strand	122-123	2	5
α-helix	128-146	19

Chain T: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	9-10	2	8

Chain V: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	60-62	3
β-strand	65	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-1 complex subunit gamma-1	G	protein	627	Mus musculus	P22892 (AlphaFold model)
AP-1 complex subunit sigma-1A	S	protein	158	Homo sapiens	P61966 (AlphaFold model)
AP-1 complex subunit mu-1	M	protein	423	Mus musculus	P35585 (AlphaFold model)
AP-1 complex subunit beta-1	B	protein	600	Homo sapiens	Q10567 (AlphaFold model)
Protein Vpu	V	protein	63	Human immunodeficiency virus type 1 group M subtype B	P19554
Bone marrow stromal antigen 2	T	protein	25	Homo sapiens	Q10589

Sequence of entity 1 (G), FASTA

>4P6Z_1 AP-1 complex subunit gamma-1 (chains G)
MGSSHHHHHHSQDPMPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYR
CRNVAKLLYMHMLGYPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNC
IKNDLNHSTQFVQGLALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIR
KVPELMEMFLPATKNLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNL
IMSGYSPEHDVSGISDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGN
AILYETVLTIMDIKSESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRH
RSTIVDCLKDLDVSIKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFL
AAEKYAPSKRWHIDTIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGD
YSQQPLVQVAAWCIGEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYA
LTAIMKLSTRFTCTVNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPV
MEKVTTNGPSEIVQTNGETEPAPLETK

Sequence of entity 2 (S), FASTA

>4P6Z_2 AP-1 complex subunit sigma-1A (chains S)
MMRFMLLFSRRGKLRLQKWYLATSDKERKKMVRELMQVVLARKPKMCSFLEWRDLKVVYK
RYASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLMG
GDVQDTSKKSVLKAIEQADLLQEEDESPRSVLEEMGLA

Sequence of entity 3 (M), FASTA

>4P6Z_3 AP-1 complex subunit mu-1 (chains M)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 4 (B), FASTA

>4P6Z_4 AP-1 complex subunit beta-1 (chains B)
MGSSHHHHHHSQDPNSMTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVG
KDVSALFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRA
LAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDT
LKDLISDSNPMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILD
CLANYMPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKL
APPLVTLLSAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIR
LASQANIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVN
YVVQEAIVVIKDIFRKYPNKYESVIAALCENLDSLDEPEARAAMIWIVGEYAERIDNADE
LLESFLEGFHDKSTQVQLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGY
IYWRLLSTDPVAAKEVVLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEG

Sequence of entity 5 (V), FASTA

>4P6Z_5 Protein Vpu (chains V)
GSDEASEGSGEYRKILRQRKIDRLIDRITERAEDSGNESEGDQEELSALVERGHLAPWDV
DDL

Sequence of entity 6 (T), FASTA

>4P6Z_6 Bone marrow stromal antigen 2 (chains T)
AGFSMASTSYDYCRVPMEDGDKRCK

Primary citation

Structural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1. Jia, X., Weber, E., Tokarev, A. et al. Elife (2014) 3:e02362-e02362. DOI 10.7554/eLife.02362 · PubMed

Other PDB entries of the same protein (UniProt P22892 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZY7 1.09 Å, Crystal structure of computationally redesigned gamma-adaptin appendage domain forming a…
2A7B 1.65 Å, On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- The…
1GYV 1.71 Å, Gamma-adaptin appendage domain from clathrin adaptor AP1, L762E mutant
1GYU 1.81 Å, Gamma-adaptin appendage domain from clathrin adaptor AP1
7R4H 2.34 Å, phospho-STING binding to adaptor protein complex-1
1GYW 2.4 Å, Gamma-adaptin appendage domain from clathrin adaptor AP1 A753D mutant
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
1W63 4.0 Å, AP1 clathrin adaptor core
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
6CRI 6.8 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer

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