6CDI

Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 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	A, I, Q (c, A, D)	Glycoprotein gp41	polymer	153	17162.5	3	UniProt (Q2N0S7) Pfam (PF00517)	Human immunodeficiency virus 1
2	B, J, R (d, 2, C)	Glycoprotein 120	polymer	473	52987.0	3	UniProt (Q2N0S5) Pfam (PF00516)	Human immunodeficiency virus 1
3	C, K, S (n, 6, N)	PGT122 Light Chain	polymer	107	11591.7	3		Homo sapiens (human)
4	D, L, T (m, 5, M)	PGT122 Heavy Chain	polymer	132	14838.7	3		Homo sapiens (human)
5	E, M, U (r, 7, R)	VRC03 light chain	polymer	102	11386.8	3		Homo sapiens (human)
6	F, N, V (q, 8, Q)	VRC03 Heavy Chain	polymer	227	24653.8	3		Homo sapiens (human)
7	G, O, W (h, 3, H)	vFP16.02 Heavy Chain	polymer	211	22455.2	3		Homo sapiens (human)
8	H, P, X (l, 4, L)	vFP16.02 Light Chain	polymer	216	23752.5	3		Homo sapiens (human)
9	AB, FA, GB, JA, NB... (t, O, z, U, DA...)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	9	In PDB GlyTouCan (G15407YE)
10	BA, FB, HB, JB, OA... (G, y, 0, 9, Z...)	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	9	In PDB GlyTouCan (G81315DD)
11	AA, CB, EB, HA, IA... (F, v, x, S, T...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	15	In PDB GlyTouCan (G42666HT)
12	BB, CA, KA, KB, SB... (u, I, V, AA, IA...)	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	6	In PDB GlyTouCan (G22768VO)
13	DA, LB, UA (J, BA, 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	EA, MB, VA (K, CA, j)	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)
15	GA, OB, XA (P, EA, o)	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)
16	DB, MA, UB (w, X, KA)	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	3	In PDB GlyTouCan (G68668TB)
17	AC, BC, CC, XB, YB... (2, D, C, c, d...)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	6	Chemie (NAG)

Sequence modifications

d, 2, C: 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

c, A, D: 512 - 664 (UniProt: Q2N0S7)

PDB	External Database	Details
Cys 605	Thr 602	conflict

Contents of the asymmetric unit

Polymers	Number of chains	24
	Total formula weight	536484.7
Branched	Number of molecules	51
	Total formula weight	38182.8
Non-Polymers*	Number of molecules	6
	Total formula weight	1327.2
All*	Total formula weight	575994.8

*Water molecules are not included.