5VN3

Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, F, K (L, N, O)	17b Fab light chain	polymer	214	23425.9	3		Homo sapiens (Human)
2	B, G, L (A, B, D)	Envelope glycoprotein gp160	polymer	153	17357.8	3	UniProt (B3UEZ6) Pfam (PF00517)	Human immunodeficiency virus 1
3	C, H, M (G, I, J)	Envelope glycoprotein gp160	polymer	516	57702.5	3	UniProt (B3UES2) Pfam (PF00516)	Human immunodeficiency virus 1
4	D, I, N (C, E, F)	T-cell surface glycoprotein CD4	polymer	185	20503.3	3	UniProt (P01730) Pfam (PF00047) Pfam (PF05790)	Homo sapiens (Human)	T-cell surface antigen T4/Leu-3
5	E, J, O (H, K, M)	17b Fab heavy chain	polymer	229	24484.5	3		Homo sapiens
6	AA, EA, FA, JA, LA... (a, e, f, j, l...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	12	In PDB GlyTouCan (G42666HT)
7	BA, HA, IA, KA, MA... (b, h, i, k, m...)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	12	In PDB GlyTouCan (G15407YE)
8	CA, NA, R (c, n, R)	alpha-D-mannopyranose-(1-2)-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		1235.1	3	In PDB GlyTouCan (G46836GH)
9	DA, OA, S (d, o, S)	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)
10	GA, RA, V (g, r, V)	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)
11	AB, BB, CB, DB, EB... (G, B, I, D, J...)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	24	Chemie (NAG)

Sequence modifications

A, B, D: 512 - 664 (UniProt: B3UEZ6)

PDB	External Database	Details
Pro 559	Ile 563	engineered mutation
Cys 605	Thr 609	engineered mutation

G, I, J: 31 - 505 (UniProt: B3UES2)

PDB	External Database	Details
Met -4	-	initiating methionine
Asp -3	-	expression tag
Ala -2	-	expression tag
Met -1	-	expression tag
Lys 0	-	expression tag
Arg 1	-	expression tag
Gly 2	-	expression tag
Leu 3	-	expression tag
Cys 4	-	expression tag
Cys 5	-	expression tag
Val 6	-	expression tag
Leu 7	-	expression tag
Leu 8	-	expression tag
Leu 9	-	expression tag
Cys 10	-	expression tag
Gly 11	-	expression tag
Ala 12	-	expression tag
Val 13	-	expression tag
Phe 14	-	expression tag
Val 15	-	expression tag
Ser 16	-	expression tag
Pro 17	-	expression tag
Ser 18	-	expression tag
Gln 19	-	expression tag
Glu 20	-	expression tag
Ile 21	-	expression tag
His 22	-	expression tag
Ala 23	-	expression tag
Arg 24	-	expression tag
Phe 25	-	expression tag
Arg 26	-	expression tag
Arg 27	-	expression tag
Gly 28	-	expression tag
Ala 29	-	expression tag
Arg 30	-	expression tag
Cys 501	Ala 505	engineered mutation

C, E, F: 1 - 183 (UniProt: P01730)

PDB	External Database	Details
Asn 184	-	expression tag
Thr 185	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	15
	Total formula weight	430421.6
Branched	Number of molecules	33
	Total formula weight	20328.7
Non-Polymers*	Number of molecules	24
	Total formula weight	5309.0
All*	Total formula weight	456059.3

*Water molecules are not included.