5I8H

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, C	BG505 SOSIP.664 gp120	polymer	481	54064.3	2	UniProt (Q2N0S6) Pfam (PF00516) In PDB	Human immunodeficiency virus 1	Endogenous retrovirus group K member 113 Env polyprotein,Endogenous retrovirus group K member 13-1 Env polyprotein,Endogenous retrovirus group K member 18 Env polyprotein,Endogenous retrovirus group K member 19 Env polyprotein,Endogenous retrovirus group K member 21 Env polyprotein,Endogenous retrovirus group K member 24 Env polyprotein,Endogenous retrovirus group K member 25 Env polyprotein,Endogenous retrovirus group K member 6 Env polyprotein,Endogenous retrovirus group K member 8 Env polyprotein,Endogenous retrovirus group K member 9 Env polyprotein
2	B, D	BG505 SOSIP.664 gp41	polymer	153	17162.5	2	UniProt (Q2N0S6) Pfam (PF00517) In PDB	Human immunodeficiency virus 1	Endogenous retrovirus group K member 113 Env polyprotein,Endogenous retrovirus group K member 13-1 Env polyprotein,Endogenous retrovirus group K member 18 Env polyprotein,Endogenous retrovirus group K member 19 Env polyprotein,Endogenous retrovirus group K member 21 Env polyprotein,Endogenous retrovirus group K member 24 Env polyprotein,Endogenous retrovirus group K member 25 Env polyprotein,Endogenous retrovirus group K member 6 Env polyprotein,Endogenous retrovirus group K member 8 Env polyprotein,Endogenous retrovirus group K member 9 Env polyprotein
3	L, J	PGT122 Fab light chain	polymer	210	22560.9	2		Homo sapiens
4	E, G	VRC34.01 Fab heavy chain	polymer	223	23797.6	2		Homo sapiens
5	F, H	VRC34.01 Fab light chain	polymer	212	23138.8	2		Homo sapiens
6	I, K	PGT122 Fab heavy chain	polymer	235	25434.7	2		Homo sapiens
7	M, Z	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	2	In PDB GlyTouCan (G55220VL)
8	a, N	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	2	In PDB GlyTouCan (G22768VO)
9	b, c, d, f, g...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	14	In PDB GlyTouCan (G42666HT)
10	e, R	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	2	In PDB GlyTouCan (G56014GC)
11	k, l, S, Y	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	4	In PDB GlyTouCan (G15407YE)
12	h, U	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	2	In PDB GlyTouCan (G91704UR)
13	m	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	1	In PDB GlyTouCan (G81315DD)
14	D, I, K, A, B...	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	16	Chemie (NAG)

Sequence modifications

A, C: 31 - 511 (UniProt: Q2N0S6)

PDB	External Database	Details
Asn 332	Thr 330	conflict
Cys 501	Ala 498	conflict
Arg 509	Glu 506	conflict
Arg 510	Lys 507	conflict
Arg 512	-	expression tag
Arg 513	-	expression tag

B, D: 512 - 664 (UniProt: Q2N0S6)

PDB	External Database	Details
Cys 605	Thr 602	conflict

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	332317.6
Branched	Number of molecules	27
	Total formula weight	18917.3
Non-Polymers*	Number of molecules	16
	Total formula weight	3539.3
All*	Total formula weight	354774.3

*Water molecules are not included.