9NPM

Composite map of three pairs of dimeric VRC36 Fabs bound to HIV-1 BG505.T332N DS-SOSIP.664 Env trimer

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, G, M (C, E, A)	HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp120	polymer	473	53200.5	3	UniProt (A0A6H1VH54)	Human immunodeficiency virus 1	Env polyprotein
2	B, H, N (D, F, B)	HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp41	polymer	153	17146.5	3	UniProt (Q2N0S5)	Human immunodeficiency virus 1
3	C, E, I, K, O... (K, M, O, Q, G...)	VRC36 Fab heavy chain	polymer	223	24125.2	6		Homo sapiens
4	D, F, J, L, P... (L, N, P, R, H...)	VRC36 Fab light chain	polymer	214	23380.9	6		Homo sapiens
5	DA, EA, GA, HA, OA... (d, e, g, h, o...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	12	In PDB GlyTouCan (G42666HT)
6	FA, QA, U (f, q, U)	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)
7	IA, TA, X (i, t, X)	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)
8	JA, KA, VA, Y, Z (j, k, v, Y, Z)	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	5	In PDB GlyTouCan (G83582BK)
9	AA, BA, LA, MA, WA... (a, b, l, m, w...)	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	6	In PDB GlyTouCan (G09724ZC)
10	CA, NA, ZA (c, n, z)	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)
11	UA (u)	alpha-D-mannopyranose-(1-2)-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		1073.0	1	In PDB GlyTouCan (G01760ZU)
12	YA (y)	alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	branched		342.3	1	In PDB GlyTouCan (G00891MP)
13	AB, BB, CB, DB, EB... (C, E, A)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	15	Chemie (NAG) PubChem (24139)

Sequence modifications

C, E, A: 31 - 508 (UniProt: A0A6H1VH54)

PDB	External Database	Details
-	Asn 178	deletion
-	Gln 179	deletion
-	Gly 180	deletion
-	Asn 181	deletion
-	Arg 182	deletion
-	Ser 183	deletion
-	Asn 184	deletion
-	Asn 185	deletion
Cys 201	Ile 200	conflict
Ser 375	Tyr 373	conflict
Cys 433	Ala 430	conflict
Cys 501	Ala 498	conflict
Arg 509	-	expression tag
Arg 510	-	expression tag
Arg 511	-	expression tag
Arg 512	-	expression tag
Arg 513	-	expression tag

D, F, B: 512 - 664 (UniProt: Q2N0S5)

PDB	External Database	Details
Pro 559	Ile 556	engineered mutation
Cys 605	Thr 602	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	18
	Total formula weight	496077.3
Branched	Number of molecules	34
	Total formula weight	29588.8
Non-Polymers*	Number of molecules	15
	Total formula weight	3318.1
All*	Total formula weight	528984.2

*Water molecules are not included.