5VN8

Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	G, D, E	Envelope glycoprotein gp160	polymer	516	57702.5	3	UniProt (B3UES2) Pfam (PF00516) In PDB	Human immunodeficiency virus 1
2	A, B, C	Envelope glycoprotein gp160	polymer	153	17357.8	3	UniProt (B3UEZ6) Pfam (PF00517) In PDB	Human immunodeficiency virus 1
3	H, F, I	b12 Fab heavy chain	polymer	230	24910.8	3		Homo sapiens
4	L, J, K	b12 Fab light chain	polymer	215	23707.4	3		Homo sapiens (Human)
5	b, c, d, g, h...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	21	In PDB GlyTouCan (G42666HT)
6	e, f, k, O, p...	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)
7	a, l, P	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)
8	A, D, B, E, G...	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	33	Chemie (NAG)

Sequence modifications

G, D, E: 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

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

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

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	371035.5
Branched	Number of molecules	33
	Total formula weight	16437.3
Non-Polymers*	Number of molecules	33
	Total formula weight	7299.9
All*	Total formula weight	394772.7

*Water molecules are not included.