6D84

Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B, I, J (T, L, R, O)	Bone marrow stromal antigen 2,Protein Nef	polymer	264	29880.2	4	UniProt (Q10589) UniProt (Q90VU7) Pfam (PF00469)	Homo sapiens (Human)	BST-2,HM1.24 antigen,Tetherin,3'ORF,Negative factor,F-protein
2	C, K (B, F)	AP-1 complex subunit beta-1	polymer	586	66152.5	2	UniProt (Q10567) Pfam (PF01602)	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
3	D, F, L, N (C, H, I, N)	ADP-ribosylation factor 1	polymer	193	22314.3	4	UniProt (P84077) Pfam (PF00025)	Homo sapiens (Human)
4	E, M (G, K)	AP-1 complex subunit gamma-1	polymer	601	68194.1	2	UniProt (P22892) Pfam (PF01602)	Mus musculus (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
5	G, O (M, P)	AP-1 complex subunit mu-1	polymer	423	48606.7	2	UniProt (P35585) Pfam (PF01217) Pfam (PF00928)	Mus musculus (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
6	H, P (S, Q)	AP-1 complex subunit sigma-3	polymer	154	18321.3	2	UniProt (Q96PC3) Pfam (PF01217)	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
7	Q, S, U, W (C, H, I, N)	GUANOSINE-5'-TRIPHOSPHATE	non-polymer		523.2	4	Chemie (GTP)
8	R, T, V, X (C, H, I, N)	MAGNESIUM ION	non-polymer		24.3	4	Chemie (MG)

Sequence modifications

T, L, R, O: 2 - 21 (UniProt: Q10589)

PDB	External Database	Details
Met -26	-	expression tag
Ser -25	-	expression tag
Tyr -24	-	expression tag
Tyr -23	-	expression tag
His -22	-	expression tag
His -21	-	expression tag
His -20	-	expression tag
His -19	-	expression tag
His -18	-	expression tag
His -17	-	expression tag
Asp -16	-	expression tag
Tyr -15	-	expression tag
Asp -14	-	expression tag
Ile -13	-	expression tag
Pro -12	-	expression tag
Thr -11	-	expression tag
Thr -10	-	expression tag
Glu -9	-	expression tag
Asn -8	-	expression tag
Leu -7	-	expression tag
Tyr -6	-	expression tag
Phe -5	-	expression tag
Gln -4	-	expression tag
Gly -3	-	expression tag
Ala -2	-	expression tag
Met -1	-	expression tag
Gly 0	-	expression tag
Ser 1	-	expression tag
Gly 22	-	linker
Ser 23	-	linker
Asp 24	-	linker
Glu 25	-	linker
Ala 26	-	linker
Ser 27	-	linker
Glu 28	-	linker
Gly 29	-	linker
Ser 30	-	linker
Gly 31	-	linker

T, L, R, O: 32 - 237 (UniProt: Q90VU7)

PDB	External Database	Details
Ala 195	Leu 164	engineered mutation
Ala 196	Leu 165	engineered mutation

B, F: 1 - 584 (UniProt: Q10567)

PDB	External Database	Details
Gly -1	-	expression tag
Ser 0	-	expression tag
Arg 359	Lys 359	conflict
Lys 476	Glu 476	conflict

C, H, I, N: 17 - 181 (UniProt: P84077)

PDB	External Database	Details
Met -11	-	expression tag
Ser -10	-	expression tag
Tyr -9	-	expression tag
Tyr -8	-	expression tag
His -7	-	expression tag
His -6	-	expression tag
His -5	-	expression tag
His -4	-	expression tag
His -3	-	expression tag
His -2	-	expression tag
Asp -1	-	expression tag
Tyr 0	-	expression tag
Asp 1	-	expression tag
Ile 2	-	expression tag
Pro 3	-	expression tag
Thr 4	-	expression tag
Thr 5	-	expression tag
Glu 6	-	expression tag
Asn 7	-	expression tag
Leu 8	-	expression tag
Tyr 9	-	expression tag
Phe 10	-	expression tag
Gln 11	-	expression tag
Gly 12	-	expression tag
Ala 13	-	expression tag
Met 14	-	expression tag
Gly 15	-	expression tag
Ser 16	-	expression tag
Leu 71	Gln 71	conflict

G, K: 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

S, Q: 1 - 154 (UniProt: Q96PC3)

PDB	External Database	Details
Cys 148	Ser 148	conflict

Contents of the asymmetric unit

Polymers	Number of chains	16
	Total formula weight	611327.1
Non-Polymers*	Number of molecules	8
	Total formula weight	2189.9
All*	Total formula weight	613517.0

*Water molecules are not included.