6CDE

Cryo-EM structure at 3.8 A resolution of vaccine-elicited antibody vFP20.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	h, H, 3	vFP20.01 Heavy Chain	polymer	211	22673.6	3		Homo sapiens (human)
2	l, L, 4	vFP20.01 Light chain	polymer	216	23826.7	3		Homo sapiens (human)
3	M, m, 7	PGT122 Heavy chain	polymer	228	24710.8	3		Homo sapiens (human)
4	N, n, 8	PGT122 Light Chain	polymer	210	22560.9	3		Homo sapiens (human)
5	R, r, 6	VRC03 Light Chain	polymer	208	23043.7	3		Homo sapiens (human)
6	Q, q, 5	VRC03 Heavy Chain	polymer	227	24653.8	3		Homo sapiens (human)
7	D, d, 1	Glycoprotein 41	polymer	153	17162.5	3	UniProt (Q2N0S7) Pfam (PF00517) In PDB	Human immunodeficiency virus 1
8	C, c, 2	Glycoprotein 120	polymer	473	52987.0	3	UniProt (Q2N0S5) Pfam (PF00516) In PDB	Human immunodeficiency virus 1
9	s, u, w, x, 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	18	In PDB GlyTouCan (G15407YE)
10	E, F, K, S, 0...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	12	In PDB GlyTouCan (G42666HT)
11	G, AA, f	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	3	In PDB GlyTouCan (G81315DD)
12	I, BA, g	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	3	In PDB GlyTouCan (G56014GC)
13	J, CA, i	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	3	In PDB GlyTouCan (G83582BK)
14	O, EA, k	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	3	In PDB GlyTouCan (G22768VO)
15	P, FA, o	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	3	In PDB GlyTouCan (G33303XH)
16	t, U, IA	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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		1559.4	3	In PDB GlyTouCan (G63337SS)
17	v, W, KA	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		748.7	3	In PDB GlyTouCan (G22573RC)
18	C, d, c, 1, 2...	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	9	Chemie (NAG)
19	c, 2, C	alpha-D-mannopyranose	non-polymer		180.2	3	Chemie (MAN)

Sequence modifications

D, d, 1: 512 - 664 (UniProt: Q2N0S7)

PDB	External Database	Details
Cys 605	Thr 602	conflict

C, c, 2: 31 - 505 (UniProt: Q2N0S5)

PDB	External Database	Details
Cys 201	Ile 200	conflict
Asn 332	Thr 330	conflict
Cys 433	Ala 430	conflict
Cys 501	Ala 498	conflict

Contents of the asymmetric unit

Polymers	Number of chains	24
	Total formula weight	634856.9
Branched	Number of molecules	51
	Total formula weight	39155.6
Non-Polymers*	Number of molecules	12
	Total formula weight	2531.3
All*	Total formula weight	676543.9

*Water molecules are not included.