8DVD

Cryo-EM structure of SIVmac239 SOS-2P Env trimer in complex with human bNAb PGT145

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, B, C	Envelope glycoprotein gp160	polymer	148	16822.2	3	UniProt (A0A0C5JYT4) Pfam (PF00517) In PDB	Simian immunodeficiency virus	Env polyprotein
2	E, F, G	Envelope glycoprotein gp160	polymer	500	57195.5	3	UniProt (A0A4Y5TGK0) Pfam (PF00516) In PDB	Simian immunodeficiency virus
3	H	PGT145 Heavy	polymer	244	26393.4	1		Homo sapiens
4	L	PGT145 Light	polymer	219	23953.8	1		Homo sapiens
5	QA, d, 5, g, 7...	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	18	In PDB GlyTouCan (G81315DD)
6	b, 1, RA, 6, J...	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	15	In PDB GlyTouCan (G15407YE)
7	a, 0, 4, j, 9...	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	16	In PDB GlyTouCan (G22768VO)
8	2, 3, h, i, 8...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	11	In PDB GlyTouCan (G42666HT)
9	EA, t, Y	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)
10	c	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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		1397.2	1	In PDB GlyTouCan (G81980VO)
11	e, f, KA	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		1397.2	3	In PDB GlyTouCan (G80966KZ)
12	FA, u	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	2	In PDB GlyTouCan (G22573RC)
13	IA, x	alpha-D-mannopyranose-(1-2)-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	2	In PDB GlyTouCan (G23799GS)
14	z	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		1235.1	1	In PDB GlyTouCan (G07617FP)
15	E, F, G	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	3	Chemie (NAG)
16	F	alpha-D-mannopyranose	non-polymer		180.2	1	Chemie (MAN)

Sequence modifications

A, B, C: 512 - 664 (UniProt: A0A0C5JYT4)

PDB	External Database	Details
Pro 559	Val 447	conflict
Pro 569	Thr 457	conflict
Cys 605	His 493	conflict

E, F, G: 33 - 511 (UniProt: A0A4Y5TGK0)

PDB	External Database	Details
Thr 169	Lys 180	conflict
Cys 501	Val 512	conflict

Contents of the asymmetric unit

Polymers	Number of chains	8
	Total formula weight	272400.2
Branched	Number of molecules	72
	Total formula weight	55526.5
Non-Polymers*	Number of molecules	4
	Total formula weight	843.8
All*	Total formula weight	328770.5

*Water molecules are not included.