7NDG

Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, F, I (A, G, D)	Netrin-1	polymer	441	49227.4	3	UniProt (O95631) Pfam (PF00055) Pfam (PF00053)	Homo sapiens (Human)	Epididymis tissue protein Li 131P,Netrin-1
2	B, G, J (B, H, E)	Neogenin	polymer	354	39268.2	3	UniProt (Q7TQG5) Pfam (PF00041)	Mus musculus (Mouse)
3	C, E, K (F, C, I)	Repulsive Guidance Molecule B (C-terminal region)	polymer	252	28104.5	3	UniProt (Q6NW40) Pfam (PF06535) Pfam (PF06534)	Homo sapiens (Human)	DRG11-responsive axonal guidance and outgrowth of neurite,DRAGON
4	D, H, L (N, M, O)	RGM domain family member B	polymer	119	13022.4	3	UniProt (Q6NW40) Pfam (PF06535)	Homo sapiens (Human)	DRG11-responsive axonal guidance and outgrowth of neurite,DRAGON
5	M, R, W (A, G, D)	CALCIUM ION	non-polymer		40.1	3	Chemie (CA)
6	AA, N, O, P, Q... (E, A, B, G, H...)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	12	Chemie (NAG)

Sequence modifications

A, G, D: 25 - 453 (UniProt: O95631)

PDB	External Database	Details
Gly 454	-	expression tag
Ser 455	-	expression tag
Gly 456	-	expression tag
Thr 457	-	expression tag
Glu 458	-	expression tag
Thr 459	-	expression tag
Ser 460	-	expression tag
Gln 461	-	expression tag
Val 462	-	expression tag
Ala 463	-	expression tag
Pro 464	-	expression tag
Ala 465	-	expression tag

B, H, E: 766 - 1123 (UniProt: Q7TQG5)

PDB	External Database	Details
Glu 763	-	expression tag
Thr 764	-	expression tag
Gly 765	-	expression tag
Gly 1124	-	expression tag
Thr 1125	-	expression tag
Lys 1126	-	expression tag
His 1127	-	expression tag
His 1128	-	expression tag
His 1129	-	expression tag
His 1130	-	expression tag
His 1131	-	expression tag
His 1132	-	expression tag

F, C, I: 169 - 412 (UniProt: Q6NW40)

PDB	External Database	Details
Thr 413	-	expression tag
Lys 414	-	expression tag
His 415	-	expression tag
His 416	-	expression tag
His 417	-	expression tag
His 418	-	expression tag
His 419	-	expression tag
His 420	-	expression tag

N, M, O: 53 - 169 (UniProt: Q6NW40)

PDB	External Database	Details
Glu 50	-	expression tag
Thr 51	-	expression tag
Gly 52	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	388867.4
Non-Polymers*	Number of molecules	15
	Total formula weight	2774.7
All*	Total formula weight	391642.1

*Water molecules are not included.