5V5V: Complex of NLGN2 with MDGA1 Ig1-Ig2

Complex of NLGN2 with MDGA1 Ig1-Ig2. Determined by X-ray diffraction at 4.11 Å resolution. Released 5 Jul 2017.

Method: X-ray diffraction
Resolution: 4.11 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 12
Atoms: 33,540
Mol. weight: 544.66 kDa
Released: 5 Jul 2017

Explore 5V5V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V5V contains 203 α-helices and 262 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B, C, D and E: 30 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	52	1	1
β-strand	54-56	3	2
β-strand	66-68	3	2
β-strand	70	1	3
β-strand	72-73	2	4
α-helix	86-88	3
α-helix	90-92	3
β-strand	98	1	1
β-strand	100	1	3
α-helix	102-104	3
β-strand	105	1	5
α-helix	106	1
α-helix	116-118	3
α-helix	121-125	5
α-helix	127-131	5
β-strand	137	1	5
β-strand	143-144	2	4
β-strand	145-149	5	2
β-strand	177-182	6	2
β-strand	187	1	6
β-strand	190	1	6
α-helix	193-195	3
α-helix	200-205	6
β-strand	208-211	4	2
α-helix	217-221	5
α-helix	233-245	13
α-helix	249-252	4
β-strand	254-264	11	2
α-helix	267-276	10
β-strand	286-290	5	2
α-helix	304-314	11
α-helix	322-331	10
α-helix	334-338	5
α-helix	364-370	7
β-strand	377-383	7	2
α-helix	388-391	4
α-helix	403-418	16
α-helix	424-435	12
α-helix	445-456	12
α-helix	457-461	5
α-helix	462-473	12
β-strand	478-483	6	2
α-helix	504-507	4
α-helix	510-512	3
β-strand	516	1	7
β-strand	519	1	7
α-helix	525-544	20
α-helix	571-573	3
β-strand	580-582	3	2
β-strand	588-590	3	2
α-helix	595-599	5
α-helix	600-604	5
α-helix	605-608	4

Chain F: 29 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	52	1	42
β-strand	54-56	3	43
β-strand	66-68	3	43
β-strand	70	1	44
β-strand	72-73	2	45
α-helix	86-88	3
α-helix	90-92	3
β-strand	98	1	42
β-strand	100	1	44
α-helix	102-104	3
β-strand	105	1	46
α-helix	106	1
α-helix	121-125	5
α-helix	127-131	5
β-strand	137	1	46
β-strand	143-144	2	45
β-strand	145-149	5	43
β-strand	177-182	6	43
β-strand	187	1	47
β-strand	190	1	47
α-helix	193-195	3
α-helix	200-205	6
β-strand	208-211	4	43
α-helix	217-221	5
α-helix	233-245	13
α-helix	249-252	4
β-strand	254-264	11	43
α-helix	267-276	10
β-strand	286-290	5	43
α-helix	304-314	11
α-helix	322-331	10
α-helix	334-338	5
α-helix	364-370	7
β-strand	377-383	7	43
α-helix	388-391	4
α-helix	403-418	16
α-helix	424-435	12
α-helix	445-456	12
α-helix	457-461	5
α-helix	462-473	12
β-strand	478-483	6	43
α-helix	504-507	4
α-helix	510-512	3
β-strand	516	1	48
β-strand	519	1	48
α-helix	525-544	20
α-helix	571-573	3
β-strand	580-582	3	43
β-strand	588-590	3	43
α-helix	595-599	5
α-helix	600-604	5
α-helix	605-608	4

Chains G and H: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	26-33	8	8
β-strand	47-51	5	9
β-strand	55-63	9	8
β-strand	69	1	10
β-strand	72-73	2	9
β-strand	87	1	9
β-strand	92-96	5	8
α-helix	100-102	3
β-strand	104-110	7	9
β-strand	111	1	10
α-helix	117	1
β-strand	118-127	10	9
β-strand	128-129	2	11
β-strand	133-139	7	12
β-strand	152-158	7	12
β-strand	161-162	2	11
β-strand	166-170	5	13
β-strand	184-187	4	12
β-strand	196-201	6	12
β-strand	212-217	6	13
α-helix	221-223	3
α-helix	224-226	3
β-strand	227	1	13
β-strand	230-231	2	13

Chains I, J, K and L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	26-33	8	55
β-strand	47-51	5	56
β-strand	55-63	9	55
β-strand	69	1	57
β-strand	72-73	2	56
β-strand	87	1	56
β-strand	92-96	5	55
α-helix	100-102	3
β-strand	104-110	7	56
β-strand	111	1	57
α-helix	117	1
β-strand	118-127	10	56
β-strand	128-129	2	58
β-strand	133-139	7	59
β-strand	152-158	7	59
β-strand	161-162	2	58
β-strand	166-170	5	60
β-strand	174	1	60
β-strand	184-187	4	59
β-strand	196-201	6	59
β-strand	212-217	6	60
α-helix	221-223	3
α-helix	224-226	3
β-strand	227	1	60
β-strand	230-231	2	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuroligin-2	A, B, C, D, E, F	protein	582	Rattus norvegicus	Q62888 (AlphaFold model)
MAM domain-containing glycosylphosphatidylinositol anchor protein 1	G, H, I, J, K, L	protein	230	Homo sapiens	Q8NFP4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>5V5V_1 Neuroligin-2 (chains A, B, C, D, E, F)
APVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRNAT
TLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKKRD
EATLNPPDTDIRDSGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVATLNYRLGVLG
FLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHS
EGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSTEAVECLRRKSSRELVDQ
DVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDG
VSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQW
VAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFP
CNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQY
LHIGLKPRVRDNYRANKVAFWLELVPHLHNLHASTSHHHHHH

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>5V5V_2 MAM domain-containing glycosylphosphatidylinositol anchor protein 1 (chains G, H, I, J, K, L)
VDYAPAQAQIVHAGQACVVKEDNISERVYTIREGDTLMLQCLVTGHPRPQVRWTKTAGSA
SDKFQETSVFNETLRIERIARTQGGRYYCKAENGVGVPAIKSIRVDVQYLDEPMLTVHQT
VSDVRGNFYQEKTVFLRCTVNSNPPARFIWKRGSDTLSHSQDNGVDIYEPLYTQGETKVL
KLKNLRPQDYASYTCQVSVRNVCGIPDKAITFRLTNTTGSASTSHHHHHH

Primary citation

Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges. Gangwar, S.P., Zhong, X., Seshadrinathan, S. et al. Neuron (2017) 94:1132-1141.e4. DOI 10.1016/j.neuron.2017.06.009 · PubMed

Browse structure collections

About this viewer

MolViewer shows 5V5V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.