6Y6C: TREM2 extracellular domain

TREM2 extracellular domain (19-174) in complex with single-chain variable fragment (scFv-4). Determined by X-ray diffraction at 2.26 Å resolution. Released 17 Feb 2021.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,771
Mol. weight: 98.32 kDa
Ligands: NAG
Released: 17 Feb 2021

Explore 6Y6C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y6C contains 21 α-helices and 69 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	21-27	7	1
β-strand	32-37	6	2
β-strand	48-53	6	1
β-strand	60-65	6	1
α-helix	70-72	3
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: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	3
α-helix	31	1
β-strand	32-37	6	4
β-strand	48-53	6	3
β-strand	60-65	6	3
α-helix	70-72	3
β-strand	77-79	3	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
α-helix	130	1

Chain C: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	5
β-strand	12-14	3	6
β-strand	20-27	8	5
α-helix	31-33	3
β-strand	36-41	6	6
β-strand	47-53	7	6
β-strand	60-62	3	6
α-helix	64-66	3
β-strand	70-75	6	5
β-strand	80-85	6	5
α-helix	90-92	3
β-strand	94-101	8	6
β-strand	104	1	3
β-strand	105	1	7
β-strand	107	1	7
β-strand	110-113	4	6
β-strand	117-121	5	6
β-strand	142-145	4	8
β-strand	148-151	4	9
β-strand	157-163	7	8
β-strand	171-176	6	9
β-strand	183-187	5	9
β-strand	191-192	2	9
α-helix	193	1
β-strand	200-205	6	8
β-strand	208-213	6	8
α-helix	218-220	3
β-strand	223-228	6	9
α-helix	235	1
β-strand	236	1	9
α-helix	237	1
β-strand	240-244	5	9

Chain D: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	10
β-strand	13-14	2	11
β-strand	20-27	8	10
α-helix	31-33	3
β-strand	36-41	6	12
β-strand	47-53	7	12
β-strand	60-62	3	12
α-helix	64-66	3
β-strand	70-75	6	10
α-helix	76-78	3
β-strand	80-85	6	10
α-helix	90-92	3
β-strand	94-101	8	12
β-strand	104	1	1
β-strand	105	1	13
β-strand	107	1	13
β-strand	110-113	4	12
β-strand	117-119	3	12
β-strand	120-121	2	11
β-strand	142-145	4	14
β-strand	148-151	4	15
β-strand	157-163	7	14
β-strand	171-176	6	15
β-strand	183-187	5	15
β-strand	191-192	2	15
α-helix	193	1
β-strand	200-205	6	14
β-strand	208-213	6	14
α-helix	218-220	3
β-strand	223-228	6	15
α-helix	235	1
β-strand	236	1	15
α-helix	237	1
β-strand	240-244	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Triggering receptor expressed on myeloid cells 2	A, B	protein	202	Homo sapiens	Q9NZC2 (AlphaFold model)
Single chain variable	C, D	protein	245	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6Y6C_1 Triggering receptor expressed on myeloid cells 2 (chains A, B)
ETGHHHHHHSSGVDLGTENLYFQSMHNTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQ
LGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSL
HGSEADTLRKVLVEVLADPLDHRDAGDLWFPGESESFEDAHVEHSISRSLLEGEIPFPPT
SSSKGGYGLNDIFEAQKIEWHE

Sequence of entity 2 (C, D), FASTA

>6Y6C_2 Single chain variable (chains C, D)
SMEVQLLESGGGLVQPGGSLRLSCAASGFTFSYYYMGWVRQAPGKGLEWVSGISPSSGYT
YYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYYYGYYYSHMDYWGQGTLVT
VSSGGGGSGGGGSGGGGSDIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGK
APKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSRSGLHTFGQGT
KLEIK

Ligands and cofactors

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

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
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
6YYE 3.36 Å, TREM2 extracellular domain (19-131) in complex with single-chain variable fragment…
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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