5Z8Y: Human LRRTM2

Crystal structure of human LRRTM2 in complex with Neurexin 1beta. Determined by X-ray diffraction at 3.4 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 8
Atoms: 16,410
Mol. weight: 247.93 kDa
Ligands: CA, ZN, NAG
Released: 10 Oct 2018

Explore 5Z8Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z8Y contains 38 α-helices and 152 β-strands across 8 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, C, E and G: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	39-40	2	1
β-strand	44-46	3	1
α-helix	55-57	3
β-strand	65-67	3	1
β-strand	75-76	2	2
β-strand	89-91	3	1
β-strand	99-100	2	2
β-strand	113-115	3	1
β-strand	137-139	3	1
β-strand	161-163	3	1
β-strand	185-187	3	1
β-strand	209-211	3	1
β-strand	219-221	3	3
α-helix	222-225	4
β-strand	233-235	3	1
β-strand	243-245	3	3
β-strand	257-259	3	1
β-strand	267-268	2	3
β-strand	281-283	3	1
α-helix	294-297	4
β-strand	305-307	3	1
β-strand	314	1	4
α-helix	317-319	3
α-helix	320-328	9
β-strand	332-333	2	1
β-strand	338	1	5
β-strand	341	1	4
α-helix	343-345	3
β-strand	349	1	5
α-helix	350-356	7

Chains B and D: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	90-103	14	6
β-strand	112	1	7
β-strand	114-123	10	6
β-strand	127-135	9	6
α-helix	136	1
β-strand	142-148	7	6
β-strand	151-157	7	6
β-strand	162-166	5	6
β-strand	178-185	8	6
β-strand	188-192	5	6
α-helix	197-198	2
β-strand	199-201	3	6
β-strand	211	1	7
β-strand	214-219	6	6
β-strand	230-237	8	6
β-strand	240	1	6
α-helix	242-246	5
β-strand	254-260	7	6

Chains F and H: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	90-103	14	20
β-strand	112	1	21
β-strand	114-123	10	20
β-strand	127-135	9	20
β-strand	142-148	7	20
β-strand	151-157	7	20
β-strand	162-166	5	20
β-strand	178-185	8	20
β-strand	188-192	5	20
α-helix	197-198	2
β-strand	199-201	3	20
β-strand	211	1	21
β-strand	214-219	6	20
β-strand	230-237	8	20
β-strand	240	1	20
α-helix	242-246	5
β-strand	254-260	7	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat transmembrane neuronal protein 2	A, C, E, G	protein	346	Homo sapiens	O43300 (AlphaFold model)
Neurexin-1-beta	B, D, F, H	protein	193	Homo sapiens	P58400 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5Z8Y_1 Leucine-rich repeat transmembrane neuronal protein 2 (chains A, C, E, G)
CPPKCRCEKLLFYCDSQGFHSVPNATDKGSLGLSLRHNHITELERDQFASFSQLTWLHLD
HNQISTVKEDAFQGLYKLKELILSSNKIFYLPNTTFTQLINLQNLDLSFNQLSSLHPELF
YGLRKLQTLHLRSNSLRTIPVRLFWDCRSLEFLDLSTNRLRSLARNGFAGLIKLRELHLE
HNQLTKINFAHFLRLSSLHTLFLQWNKISNLTCGMEWTWGTLEKLDLTGNEIKAIDLTVF
ETMPNLKILLMDNNKLNSLDSKILNSLRSLTTVGLSGNLWECSARICALASWLGSFQGRW
EHSILCHSPDHTQGEDILDAVAGFQLCWNLSTTVTVMAGSHHHHHH

Sequence of entity 2 (B, D, F, H), FASTA

>5Z8Y_2 Neurexin-1-beta (chains B, D, F, H)
DAASHAGTTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGD
YLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIER
YPAGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRL
VGEVPGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
ZN	Zinc ion	Zn	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction. Yamagata, A., Goto-Ito, S., Sato, Y. et al. Nat Commun (2018) 9:3964-3964. DOI 10.1038/s41467-018-06333-8 · PubMed

Other PDB entries of the same protein (UniProt O43300 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5Z8X 3.15 Å, Crystal structure of human LRRTM2

Browse structure collections

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