Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5FYJ

Crystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1 Clade G X1193.c1 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (B)	GP41 ENV ECTODOMAIN	polymer	161	17990.4	1	UniProt (C6ZIG9) Pfam (PF00517)	HUMAN IMMUNODEFICIENCY VIRUS 1
2	B (D)	35O22	polymer	243	26170.5	1		HOMO SAPIENS (HUMAN)
3	C (E)	35O22	polymer	216	23318.8	1		HOMO SAPIENS (HUMAN)
4	D (G)	GP120 ENV ECTODOMAIN	polymer	484	54536.0	1	UniProt (C6ZIG9) Pfam (PF00516)	HUMAN IMMUNODEFICIENCY VIRUS 1
5	E (H)	PGT122	polymer	244	26465.9	1		HOMO SAPIENS (HUMAN)
6	F (L)	PGT122	polymer	213	22880.3	1		HOMO SAPIENS (HUMAN)
7	G, H (U, V)	VRC01	polymer	240	26153.3	2		HOMO SAPIENS (HUMAN)
8	DA, I, J, L (d, A, C, I)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	4	In PDB GlyTouCan (G42666HT)
9	K, Q, Z (F, O, Z)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	3	In PDB GlyTouCan (G15407YE)
10	M (J)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1397.2	1	In PDB GlyTouCan (G80966KZ)
11	N, T (K, R)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1883.7	2	In PDB GlyTouCan (G60230HH)
12	O, P, X (M, N, X)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1721.5	3	In PDB GlyTouCan (G91704UR)
13	R (P)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1073.0	1	In PDB GlyTouCan (G56014GC)
14	S (Q)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1235.1	1	In PDB GlyTouCan (G07617FP)
15	U (S)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1559.4	1	In PDB GlyTouCan (G04216GB)
16	V (T)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1559.4	1	In PDB GlyTouCan (G83161QT)
17	EA, FA, W (e, f, W)	alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1073.0	3	In PDB GlyTouCan (G34442SS)
18	Y (Y)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1235.1	1	In PDB GlyTouCan (G16404YH)
19	AA (a)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1559.4	1	In PDB GlyTouCan (G37135JQ)
20	BA (b)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1721.5	1	In PDB GlyTouCan (G89864BN)
21	CA (c)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1235.1	1	In PDB GlyTouCan (G46836GH)
22	GA, KA, MA (B, G)	CITRIC ACID	non-polymer		192.1	3	Chemie (CIT)
23	HA, LA (D, G)	1,2-ETHANEDIOL	non-polymer		62.1	2	Chemie (EDO)
24	IA, JA, NA (G)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	3	Chemie (NAG)
25	OA, PA, QA, RA, SA... (B, D, E, G, H...)	water	water		18.0	12	Chemie (HOH)

Sequence modifications

B: 512 - 665 (UniProt: C6ZIG9)

PDB	External Database	Details
Pro 559	Ile 557	engineered mutation
Cys 605	Thr 603	engineered mutation
Gly 666	-	expression tag
Gly 667	-	expression tag
Gly 668	-	expression tag
Leu 669	-	expression tag
Val 670	-	expression tag
Pro 671	-	expression tag
Arg 672	-	expression tag

G: 33 - 508 (UniProt: C6ZIG9)

PDB	External Database	Details
Ala 29	-	expression tag
Leu 30	-	expression tag
Ala 31	-	expression tag
Gly 32	-	expression tag
Cys 459	Gly 455	engineered mutation
Cys 501	Ala 499	engineered mutation
Arg 509	-	expression tag
Arg 510	-	expression tag
Arg 511	-	expression tag
Arg 512	-	expression tag
Arg 513	-	expression tag

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	8
Polymers	Total formula weight	223668.5
Branched	Number of molecules	24
Branched	Total formula weight	28183.2
Non-Polymers*	Number of molecules	8
Non-Polymers*	Total formula weight	1364.1
All*	Total formula weight	253215.9

*Water molecules are not included.

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