8D9R

AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	C, H, Z, J, X...	ADP-ribosylation factor 1	polymer	181	20800.9	18	UniProt (P84077) Pfam (PF00025) In PDB	Homo sapiens (human)
2	N, L, o, e, p...	Protein Nef	polymer	213	24364.4	12	UniProt (Q90VU7) Pfam (PF00469) In PDB	Human immunodeficiency virus 1	3'ORF,Negative factor,F-protein
3	Y, y, z, 0, 1...	HLA class I histocompatibility antigen, A alpha chain	polymer	44	4558.9	6	UniProt (P04439) Pfam (PF06623) In PDB	Homo sapiens (human)	Human leukocyte antigen A,HLA-A
4	B, A, D, E, F...	AP-1 complex subunit beta-1	polymer	949	104736.5	6	UniProt (Q10567) Pfam (PF01602) Pfam (PF02883) Pfam (PF09066) In PDB	Homo sapiens (human)	Adaptor protein complex AP-1 subunit beta-1,Adaptor-related protein complex 1 subunit beta-1,Beta-1-adaptin,Beta-adaptin 1,Clathrin assembly protein complex 1 beta large chain,Golgi adaptor HA1/AP1 adaptin beta subunit
5	G, R, T, U, V...	AP-1 complex subunit gamma-1	polymer	601	68194.1	6	UniProt (P22892) Pfam (PF01602) In PDB	Mus musculus (house mouse)	Adaptor protein complex AP-1 subunit gamma-1,Adaptor-related protein complex 1 subunit gamma-1,Clathrin assembly protein complex 1 gamma-1 large chain,Gamma-adaptin,Gamma1-adaptin,Golgi adaptor HA1/AP1 adaptin subunit gamma-1
6	M, j, k, l, m...	AP-1 complex subunit mu-1	polymer	423	48606.7	6	UniProt (P35585) Pfam (PF01217) Pfam (PF00928) In PDB	Mus musculus (house mouse)	AP-mu chain family member mu1A,Adaptor protein complex AP-1 subunit mu-1,Adaptor-related protein complex 1 subunit mu-1,Clathrin assembly protein complex 1 mu-1 medium chain 1,Clathrin coat assembly protein AP47,Clathrin coat-associated protein AP47,Golgi adaptor HA1/AP1 adaptin mu-1 subunit,Mu-adaptin 1,Mu1A-adaptin
7	S, t, u, v, w...	AP-1 complex subunit sigma-3	polymer	154	18305.3	6	UniProt (Q96PC3) Pfam (PF01217) In PDB	Homo sapiens (human)	Adaptor protein complex AP-1 subunit sigma-1C,Adaptor-related protein complex 1 subunit sigma-1C,Clathrin assembly protein complex 1 sigma-1C small chain,Golgi adaptor HA1/AP1 adaptin sigma-1C subunit,Sigma 1C subunit of AP-1 clathrin,Sigma-adaptin 1C,Sigma1C-adaptin
8	O, b, 5, P, C...	GUANOSINE-5'-TRIPHOSPHATE	non-polymer		523.2	18	Chemie (GTP)
9	O, b, 5, P, C...	MAGNESIUM ION	non-polymer		24.3	18	Chemie (MG)

Sequence modifications

C, H, Z, J, X, 3, K, a, 4, O, b, 5, P, c, 6, Q, d, 7: 2 - 181 (UniProt: P84077)

PDB	External Database	Details
Myr 1	-	modified residue

N, L, o, e, p, f, q, g, r, h, s, i: 2 - 206 (UniProt: Q90VU7)

PDB	External Database	Details
Myr 1	-	modified residue
Gly 207	-	expression tag
His 208	-	expression tag
His 209	-	expression tag
His 210	-	expression tag
His 211	-	expression tag
His 212	-	expression tag
His 213	-	expression tag

Y, y, z, 0, 1, 2: 334 - 365 (UniProt: P04439)

PDB	External Database	Details
Gly 328	-	expression tag
Ala 329	-	expression tag
Met 330	-	expression tag
Gly 331	-	expression tag
Ser 332	-	expression tag
Cys 333	-	expression tag
Ser 345	Thr 345	engineered mutation
Gly 349	Ser 349	engineered mutation
Ser 355	Gly 355	engineered mutation
Ser 363	Cys 363	engineered mutation
His 366	-	expression tag
His 367	-	expression tag
His 368	-	expression tag
His 369	-	expression tag
His 370	-	expression tag
His 371	-	expression tag

B, A, D, E, F, I: 1 - 949 (UniProt: Q10567)

PDB	External Database	Details
Arg 359	Lys 359	engineered mutation
Lys 476	Glu 476	engineered mutation

G, R, T, U, V, W: 1 - 595 (UniProt: P22892)

PDB	External Database	Details
Glu 596	-	expression tag
Asn 597	-	expression tag
Leu 598	-	expression tag
Tyr 599	-	expression tag
Phe 600	-	expression tag
Gln 601	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	60
	Total formula weight	2133197.7
Non-Polymers*	Number of molecules	36
	Total formula weight	9854.7
All*	Total formula weight	2143052.5

*Water molecules are not included.