4HMY: AP-1 complex subunit gamma-1

Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1. Determined by X-ray diffraction at 7.0 Å resolution. Released 6 Mar 2013.

Method: X-ray diffraction
Resolution: 7.0 Å
Organisms: Mus musculus, Homo sapiens
Chains: 5
Atoms: 14,743
Mol. weight: 221.75 kDa
Ligands: MG, GTP
Released: 6 Mar 2013

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

Secondary structure: helices and β-sheets

4HMY contains 97 α-helices and 52 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: 39 helices, 0 β-strands

Element	Residues	Length
α-helix	14-16	3
α-helix	23-33	11
α-helix	35-37	3
α-helix	49-58	10
α-helix	64-66	3
α-helix	71-74	4
α-helix	79-91	13
α-helix	101-110	10
α-helix	118-129	12
α-helix	140-147	8
α-helix	151-167	17
α-helix	172-175	4
α-helix	188-201	14
α-helix	205-213	9
α-helix	216-226	11
α-helix	243-256	14
α-helix	262-265	4
α-helix	268-276	9
α-helix	283-297	15
α-helix	303-317	15
α-helix	324-336	13
α-helix	340-343	4
α-helix	344-346	3
α-helix	347-353	7
α-helix	359-371	13
α-helix	375-377	3
α-helix	378-391	14
α-helix	394-410	17
α-helix	415-428	14
α-helix	437-447	11
α-helix	452-465	14
α-helix	471-482	12
α-helix	502-514	13
α-helix	520-532	13
α-helix	533-535	3
α-helix	541-550	10
α-helix	551-553	3
α-helix	557-570	14
α-helix	576-582	7

Chain B: 38 helices, 0 β-strands

Element	Residues	Length
α-helix	16-21	6
α-helix	28-42	15
α-helix	48-50	3
α-helix	51-58	8
α-helix	64-77	14
α-helix	81-84	4
α-helix	89-94	6
α-helix	100-110	11
α-helix	118-130	13
α-helix	135-149	15
α-helix	158-167	10
α-helix	174-187	14
α-helix	201-212	12
α-helix	216-226	11
α-helix	234-244	11
α-helix	254-265	12
α-helix	276-282	7
α-helix	285-290	6
α-helix	291-293	3
α-helix	296-312	17
α-helix	326-327	2
α-helix	332-342	11
α-helix	351-361	11
α-helix	367-383	17
α-helix	385-399	15
α-helix	404-420	17
α-helix	429-432	4
α-helix	436-438	3
α-helix	442-454	13
α-helix	462-468	7
α-helix	478-493	16
α-helix	496-498	3
α-helix	500-511	12
α-helix	517-530	14
α-helix	554-556	3
α-helix	557-563	7
α-helix	564-566	3
α-helix	570-572	3

Chain C: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	15
α-helix	30-38	9
β-strand	52-57	6	15
β-strand	62-67	6	15
α-helix	72-74	3
α-helix	76-81	6
β-strand	87-90	4	15
β-strand	91-93	3	16
α-helix	97-99	3
α-helix	100-111	12
β-strand	120-123	4	15
β-strand	124-126	3	16
α-helix	136-142	7
α-helix	145-147	3
β-strand	153-155	3	15
β-strand	159	1	17
β-strand	164	1	17
α-helix	166-177	12

Chain M: 7 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
β-strand	14-19	6	1
α-helix	29-31	3
α-helix	33-42	10
β-strand	49-51	3	1
β-strand	56-62	7	1
β-strand	65-71	7	1
α-helix	77-94	18
α-helix	100-117	18
β-strand	119	1	2
β-strand	122	1	2
α-helix	129-131	3
α-helix	149-154	6
β-strand	170-177	8	3
β-strand	178-180	3	4
β-strand	183	1	5
β-strand	189	1	5
β-strand	193	1	4
β-strand	196-203	8	3
β-strand	209	1	6
β-strand	210	1	7
β-strand	212-213	2	8
β-strand	236-238	3	3
β-strand	242	1	7
α-helix	244-247	4
β-strand	255	1	7
β-strand	261-267	7	3
β-strand	281-286	6	9
β-strand	290-295	6	9
β-strand	298	1	10
β-strand	307-314	8	11
β-strand	331-335	5	11
β-strand	340-348	9	11
β-strand	353	1	10
β-strand	356-357	2	9
β-strand	379	1	11
β-strand	382	1	12
β-strand	394-395	2	8
β-strand	398	1	6
β-strand	407-411	5	3
β-strand	413	1	12
β-strand	414-417	4	4

Chain S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	13
β-strand	14-19	6	13
α-helix	25-40	16
β-strand	49-52	4	13
β-strand	55-62	8	13
β-strand	65-72	8	13
α-helix	77-95	19
α-helix	101-105	5
α-helix	107-115	9
β-strand	118-119	2	14
β-strand	122-123	2	14
α-helix	129-136	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-1 complex subunit gamma-1	A	protein	601	Mus musculus	P22892 (AlphaFold model)
AP-1 complex subunit beta-1	B	protein	586	Homo sapiens	Q10567 (AlphaFold model)
AP-1 complex subunit mu-1	M	protein	423	Mus musculus	P35585 (AlphaFold model)
AP-1 complex subunit sigma-3	S	protein	154	Homo sapiens	Q96PC3 (AlphaFold model)
ADP-ribosylation factor 1	C	protein	172	Homo sapiens	P84077

Sequence of entity 1 (A), FASTA

>4HMY_1 AP-1 complex subunit gamma-1 (chains A)
MPAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLG
YPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQG
LALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATK
NLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGI
SDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIK
SESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVS
IKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHID
TIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCI
GEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCT
VNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVMEKVTTNGPENLYF
Q

Sequence of entity 2 (B), FASTA

>4HMY_2 AP-1 complex subunit beta-1 (chains B)
GSMTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCM
QTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKI
TEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVA
NAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQ
SICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPEL
QYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAEL
REYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIF
RKYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKST
QVQLQLLTAFVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAK
EVVLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVEG

Sequence of entity 3 (M), FASTA

>4HMY_3 AP-1 complex subunit mu-1 (chains M)
MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI
KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF
GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN
LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ
FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF
GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQL
RTQ

Sequence of entity 4 (S), FASTA

>4HMY_4 AP-1 complex subunit sigma-3 (chains S)
MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYK
RYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIG
GEIQETSKKIAVKAIEDSDMLQEVSTVCQTMGER

Sequence of entity 5 (C), FASTA

>4HMY_5 ADP-ribosylation factor 1 (chains C)
MHHHHHHEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVG
GLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQD
LPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Structural Basis for Recruitment and Activation of the AP-1 Clathrin Adaptor Complex by Arf1. Ren, X., Farias, G.G., Canagarajah, B.J. et al. Cell (2013) 152:755-767. DOI 10.1016/j.cell.2012.12.042 · 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
4P6Z 3.0 Å, Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic…
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

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