5LFV: Myelin-associated glycoprotein

Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand. Determined by X-ray diffraction at 2.3 Å resolution. Released 14 Dec 2016.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Mus musculus
Chains: 2
Atoms: 5,095
Mol. weight: 74.62 kDa
Ligands: NAG, MAN
Released: 14 Dec 2016

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

Secondary structure: helices and β-sheets

5LFV contains 17 α-helices and 58 β-strands across 2 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.

Chain A: 12 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	1
β-strand	29-33	5	2
β-strand	38-40	3	3
β-strand	43-45	3	1
α-helix	48-50	3
β-strand	56-61	6	2
α-helix	70-71	2
β-strand	72-75	4	2
β-strand	89-91	3	3
α-helix	95-97	3
β-strand	99	1	1
β-strand	102-104	3	3
α-helix	109-111	3
β-strand	113-120	8	2
β-strand	126-138	13	2
α-helix	141	1
β-strand	142-144	3	4
β-strand	149-150	2	5
β-strand	155-162	8	4
α-helix	169-170	2
β-strand	171-175	5	6
α-helix	178-180	3
β-strand	184-190	7	4
α-helix	192-194	3
β-strand	196-204	9	4
α-helix	208-210	3
β-strand	214-220	7	6
β-strand	227-233	7	6
β-strand	236-237	2	5
β-strand	238-245	8	7
β-strand	249-252	4	8
β-strand	257-266	10	7
α-helix	268-269	2
β-strand	270-275	6	8
β-strand	278-284	7	8
β-strand	287-292	6	7
α-helix	297-299	3
β-strand	301-309	9	8
β-strand	312-324	13	8
α-helix	325-328	4

Chain B: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	9
β-strand	29-33	5	10
β-strand	38-40	3	11
β-strand	43-45	3	9
β-strand	56-61	6	10
α-helix	66-68	3
β-strand	72-75	4	10
α-helix	83-85	3
β-strand	89-92	4	11
β-strand	99	1	9
β-strand	101-104	4	11
α-helix	109-111	3
β-strand	113-120	8	10
β-strand	126-128	3	10
β-strand	133-138	6	10
β-strand	142-144	3	12
β-strand	149-150	2	13
β-strand	155-162	8	12
β-strand	171-175	5	14
β-strand	184-189	6	12
β-strand	197-204	8	12
α-helix	208-210	3
β-strand	214-220	7	14
β-strand	227-233	7	14
β-strand	236-237	2	13
β-strand	238-245	8	15
β-strand	249-252	4	16
β-strand	257-266	10	15
β-strand	270-275	6	17
β-strand	278-284	7	17
β-strand	287-292	6	15
β-strand	302-309	8	17
β-strand	312-319	8	17
β-strand	320-324	5	16
α-helix	325-328	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myelin-associated glycoprotein	A, B	protein	317	Mus musculus	P20917 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5LFV_1 Myelin-associated glycoprotein (chains A, B)
GSGHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWYFNSPYPKNYPPVVFKSR
TQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGDLGGYNQYTFSEHSVLDI
VNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGLGEPTVLGRLREDEGTWV
QVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPPVIVEMNSSVEAIEGSHV
SLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGEDGVYACLAENAYGQDNRT
VELSVMYAAAAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
MAN	alpha-D-mannopyranose	C6 H12 O6	2

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Structural basis of myelin-associated glycoprotein adhesion and signalling. Pronker, M.F., Lemstra, S., Snijder, J. et al. Nat Commun (2016) 7:13584-13584. DOI 10.1038/ncomms13584 · PubMed

Other PDB entries of the same protein (UniProt P20917 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GZL 1.95 Å, Complex between the dynein light chain DYNLL1/DLC8 and a peptide from the large…
6GZJ 1.98 Å, Complex between the dynein light chain DYNLL1/DLC8 and the specific domain of large…
5LFR 2.12 Å, Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3
5LF5 3.8 Å, Myelin-associated glycoprotein (MAG) deglycosylated full extracellular domain with…
5LFU 4.3 Å, Myelin-associated glycoprotein (MAG) glycosylated and lysine-methylated full…

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