6VY2

Cryo-EM structure of M1214_N1 Fab in complex with CH505 TF chimeric 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, C, E (A, C, E)	Glycoprotein 120	polymer	487	54540.4	3	UniProt (A0A0A7I3C6) Pfam (PF00516)	Human immunodeficiency virus 1	Surface protein gp120, SU, gp120
2	B, D, F (B, D, F)	Glycoprotein 41	polymer	160	18146.7	3	UniProt (Q2N0S5) Pfam (PF00517)	Human immunodeficiency virus 1	Transmembrane protein gp41, TM, gp41
3	G, H, I (H, I, J)	M1214 N1 Fab heavy chain	polymer	226	24210.1	3		Homo sapiens (Human)
4	J, K, L (L, M, N)	M1214 N1 Fab light chain	polymer	214	22876.4	3		Homo sapiens (Human)
5	BA, CA, CB, DA, FA... (b, c, 2, d, f...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	15	In PDB GlyTouCan (G42666HT)
6	AA, AB, BB, DB, EA... (a, 0, 1, 3, e...)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	21	In PDB GlyTouCan (G15407YE)
7	GA, Q, WA (g, Q, w)	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		910.8	3	In PDB GlyTouCan (G94626GC)
8	IA, S, YA (i, S, y)	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)
9	JA, T, ZA (j, T, 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)
10	EB, OA, Y (4, o, Y)	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		1235.1	3	In PDB GlyTouCan (G84881ST)
11	AC, BC, CC, DC, EC... (E, F, A, B, C...)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	24	Chemie (NAG)

Sequence modifications

A, C, E: 35 - 506 (UniProt: A0A0A7I3C6)

PDB	External Database	Details
Met 7	-	initiating methionine
Pro 8	-	expression tag
Met 9	-	expression tag
Gly 10	-	expression tag
Ser 11	-	expression tag
Leu 12	-	expression tag
Gln 13	-	expression tag
Pro 14	-	expression tag
Leu 15	-	expression tag
Ala 16	-	expression tag
Thr 17	-	expression tag
Leu 18	-	expression tag
Tyr 19	-	expression tag
Leu 20	-	expression tag
Leu 21	-	expression tag
Gly 22	-	expression tag
Met 23	-	expression tag
Leu 24	-	expression tag
Val 25	-	expression tag
Ala 26	-	expression tag
Ser 27	-	expression tag
Val 28	-	expression tag
Leu 29	-	expression tag
Ala 30	-	expression tag
Ala 31	-	expression tag
Glu 32	-	expression tag
Asn 33	-	expression tag
Leu 34	-	expression tag
Lys 64	Glu 60	conflict
Trp 316	Ala 301	conflict
Lys 490	Glu 473	conflict
Ile 491	Val 474	conflict
Glu 492	Lys 475	conflict
Arg 500	Asn 483	conflict
Cys 501	Ala 484	conflict
Lys 502	Arg 485	conflict

B, D, F: 511 - 664 (UniProt: Q2N0S5)

PDB	External Database	Details
Gly 505	-	expression tag
Arg 506	-	expression tag
Arg 507	-	expression tag
Arg 508	-	expression tag
Arg 509	-	expression tag
Arg 510	-	expression tag
Pro 559	Ile 556	conflict
Cys 605	Thr 602	conflict

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	359321.0
Branched	Number of molecules	48
	Total formula weight	30099.7
Non-Polymers*	Number of molecules	24
	Total formula weight	5309.0
All*	Total formula weight	394729.7

*Water molecules are not included.