Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5FYK

Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade B JR-FL 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)	JR-FL, GP41 ENV ECTODOMAIN	polymer	161	18074.5	1	UniProt (Q6BC19) Pfam (PF00517) UniProt (by SIFTS) (Q75760)	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)	JR-FL, GP120 ENV ECTODOMAIN	polymer	475	53732.0	1	UniProt (Q75760) 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	I (A)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	1	In PDB GlyTouCan (G15407YE)
9	J (C)	alpha-D-mannopyranose-(1-3)-[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		1235.1	1	In PDB GlyTouCan (G55220VL)
10	K, O (F, M)	alpha-D-mannopyranose-(1-2)-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		1559.4	2	In PDB GlyTouCan (G68668TB)
11	L (I)	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		1235.1	1	In PDB GlyTouCan (G91845HM)
12	M (J)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 (G94559IJ)
13	N, V (K, T)	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		748.7	2	In PDB GlyTouCan (G81315DD)
14	P (N)	alpha-D-mannopyranose-(1-2)-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		1397.2	1	In PDB GlyTouCan (G83582BK)
15	Q (O)	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		910.8	1	In PDB GlyTouCan (G22768VO)
16	R (P)	alpha-D-mannopyranose-(1-2)-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		1397.2	1	In PDB GlyTouCan (G33303XH)
17	S (Q)	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	1	In PDB GlyTouCan (G91704UR)
18	T, U (R, S)	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		1235.1	2	In PDB GlyTouCan (G23799GS)
19	W (W)	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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		1397.2	1	In PDB GlyTouCan (G61846BY)
20	X (X)	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		1073.0	1	In PDB GlyTouCan (G09724ZC)
21	AA, Y (a, Y)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	2	In PDB GlyTouCan (G42666HT)
22	Z (Z)	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 (G47410OF)
23	BA (b)	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	1	In PDB GlyTouCan (G34442SS)
24	CA, DA, EA, FA, GA (B, G, H)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	5	Chemie (NAG)

Sequence modifications

B: 512 - 664 (UniProt: Q6BC19)

PDB	External Database	Details
Pro 559	Ile 550	engineered mutation
Glu 563	Gln 554	conflict
Cys 605	Thr 596	engineered mutation
Gly 665	-	expression tag
Gly 666	-	expression tag
Leu 667	-	expression tag
Glu 668	-	expression tag
Val 669	-	expression tag
Leu 670	-	expression tag
Phe 671	-	expression tag
Gln 672	-	expression tag

G: 31 - 506 (UniProt: Q75760)

PDB	External Database	Details
Lys 168	Glu 165	engineered mutation
Ile 430	Val 421	conflict
Cys 459	Gly 450	engineered mutation
Cys 501	Ala 492	engineered mutation
Gly 507	-	expression tag
Arg 508	-	expression tag
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	222948.7
Branched	Number of molecules	20
Branched	Total formula weight	22270.0
Non-Polymers*	Number of molecules	5
Non-Polymers*	Total formula weight	1106.0
All*	Total formula weight	246324.7

*Water molecules are not included.

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