6YYE: TREM2 extracellular domain

TREM2 extracellular domain (19-131) in complex with single-chain variable fragment (scFv-2). Determined by X-ray diffraction at 3.36 Å resolution. Released 17 Feb 2021.

Method: X-ray diffraction
Resolution: 3.36 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,052
Mol. weight: 78.53 kDa
Ligands: NAG
Released: 17 Feb 2021

Explore 6YYE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YYE contains 12 α-helices and 62 β-strands across 4 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: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	1
β-strand	32-37	6	2
β-strand	47-53	7	1
β-strand	60-65	6	1
α-helix	71-74	4
β-strand	77-79	3	2
β-strand	82-87	6	2
β-strand	92-97	6	2
α-helix	102-104	3
β-strand	106-114	9	1
β-strand	117-129	13	1

Chain B: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
β-strand	23-27	5	3
β-strand	32-37	6	4
β-strand	48-53	6	3
β-strand	60-65	6	3
β-strand	77-78	2	4
β-strand	82-87	6	4
β-strand	92-97	6	4
α-helix	102-104	3
β-strand	106-114	9	3
β-strand	117-129	13	3

Chain C: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	5
β-strand	12-13	2	6
β-strand	20-27	8	5
β-strand	36-41	6	6
β-strand	47-53	7	6
β-strand	60-62	3	6
β-strand	70-75	6	5
β-strand	80-85	6	5
α-helix	90-92	3
β-strand	94-100	7	6
β-strand	114	1	6
β-strand	118-121	4	6
β-strand	143-146	4	7
β-strand	149-152	4	8
β-strand	158-164	7	7
β-strand	172-177	6	8
β-strand	185-188	4	8
β-strand	192-193	2	8
α-helix	194	1
β-strand	201-206	6	7
β-strand	209-214	6	7
α-helix	219-221	3
β-strand	223-229	7	8
α-helix	237	1
β-strand	238	1	8
α-helix	239	1
β-strand	242-246	5	8

Chain D: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	9
β-strand	12-14	3	10
β-strand	20-27	8	9
β-strand	36-41	6	10
β-strand	47-53	7	10
β-strand	60-62	3	10
β-strand	70-75	6	9
β-strand	80-85	6	9
α-helix	90-92	3
β-strand	94-100	7	10
β-strand	114	1	10
β-strand	118-122	5	10
β-strand	143-146	4	11
β-strand	149-152	4	12
β-strand	158-164	7	11
β-strand	172-177	6	12
β-strand	183-188	6	12
β-strand	192-193	2	12
α-helix	194	1
β-strand	201-206	6	11
β-strand	209-214	6	11
α-helix	219-221	3
β-strand	224-229	6	12
β-strand	238	1	12
β-strand	242-246	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Triggering receptor expressed on myeloid cells 2	A, B	protein	116	Homo sapiens	Q9NZC2 (AlphaFold model)
TREM2 Single chain variable 2	C, D	protein	247	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6YYE_1 Triggering receptor expressed on myeloid cells 2 (chains A, B)
ETGHNTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFL
RRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLAD

Sequence of entity 2 (C, D), FASTA

>6YYE_2 TREM2 Single chain variable 2 (chains C, D)
SMEVQLLESGGGLVQPGGSLRLSCAASGFTFYSSYMGWVRQAPGKGLEWVSYISSSGSST
YYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARVGGYYSWGNGIDYWGQGTLV
TVSSGGGGSGGGGSGGGGSDIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPG
KAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYGVYYPFTFGQ
GTKLEIK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Selection and structural characterization of anti-TREM2 scFvs that reduce levels of shed ectodomain. Szykowska, A., Chen, Y., Smith, T.B. et al. Structure (2021) 29:1241-1252.e5. DOI 10.1016/j.str.2021.06.010 · PubMed

Other PDB entries of the same protein (UniProt Q9NZC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
5UD8 1.8 Å, Crystal Structure of Mutant Ig-like Domain
9PWN 1.8 Å, Crystal structure of Fabs 7411 in complex with TREM2 peptide
8T51 1.9 Å, Crystal structure of Fab 3.10C2 bound to TREM2
8T59 2.0 Å, Crystal structure of Para.09 bound to TREM2
6B8O 2.2 Å, WT Ig-like V Domain with Phosphatidylserine
5UD7 2.2 Å, Crystal Structure of Wild-Type Ig-like Domain
6Y6C 2.26 Å, TREM2 extracellular domain (19-174) in complex with single-chain variable fragment…
6YMQ 3.07 Å, TREM2 extracellular domain (19-131) in complex with single-chain variable 4 (scFv-4)
5ELI 3.1 Å, Triggering receptor expressed on myeloid cells 2
9PX5 3.7 Å, Crystal structure of Fab 7268 in complex with MBP-TREM2 Ig domain fusion
6Z0G Structure of TREM2 transmembrane helix in DPC micelles

Browse structure collections

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