9VBI

Cryo-EM structure of PLD3 bound to ssDNA (poly(A))

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, C (C, B)	DNA (5'-D(*AP*AP*AP*AP*A)-3')	polymer	49	15302.2	2		synthetic construct
2	B, D (A, D)	5'-3' exonuclease PLD3	polymer	436	48467.5	2	UniProt (Q8IV08)	Homo sapiens (human)	(S,S)-bis(monoacylglycero)phosphate synthase PLD3,HindIII K4L homolog,Hu-K4,Phospholipase D3
3	E, H, I, L (E, H, I, L)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	4	In PDB GlyTouCan (G42666HT)
4	F, J (F, 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	2	In PDB GlyTouCan (G15407YE)
5	G, K (G, K)	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	2	In PDB GlyTouCan (G22768VO)

Sequence modifications

A, D: 61 - 490 (UniProt: Q8IV08)

PDB	External Database	Details
Ala 201	His 201	engineered mutation
Ala 416	His 416	engineered mutation
Leu 491	-	expression tag
Glu 492	-	expression tag
Val 493	-	expression tag
Leu 494	-	expression tag
Phe 495	-	expression tag
Gln 496	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	4
	Total formula weight	127539.4
Branched	Number of molecules	8
	Total formula weight	4692.3
All*	Total formula weight	132231.7

*Water molecules are not included.