6YMQ: TREM2 extracellular domain

TREM2 extracellular domain (19-131) in complex with single-chain variable 4 (scFv-4). Determined by X-ray diffraction at 3.07 Å resolution. Released 17 Feb 2021.

Method: X-ray diffraction
Resolution: 3.07 Å
Organism: Homo sapiens
Chains: 12
Atoms: 15,730
Mol. weight: 243.32 kDa
Ligands: NAG
Released: 17 Feb 2021

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

Secondary structure: helices and β-sheets

6YMQ contains 26 α-helices and 193 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.

Chain A: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	10	1
β-strand	20-27	8	1
β-strand	36-41	6	1
β-strand	47-53	7	1
β-strand	60-62	3	1
β-strand	70-75	6	1
β-strand	80-85	6	1
α-helix	90-92	3
β-strand	94-101	8	1
β-strand	104	1	2
β-strand	110-113	4	1
β-strand	117-121	5	1
β-strand	142-143	2	3
β-strand	148-150	3	4
β-strand	157-163	7	3
β-strand	171-176	6	4
β-strand	183-187	5	4
β-strand	191-192	2	4
α-helix	193	1
β-strand	200-205	6	3
β-strand	208-213	6	3
β-strand	223-228	6	4
β-strand	236	1	4
β-strand	241-243	3	4

Chain B: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	10	1
β-strand	20-27	8	1
β-strand	36-41	6	1
β-strand	47-53	7	1
β-strand	60-62	3	1
β-strand	67	1	1
β-strand	70-75	6	1
β-strand	80-85	6	1
α-helix	90-92	3
β-strand	94-101	8	1
β-strand	104	1	5
β-strand	110-113	4	1
β-strand	117-121	5	1
β-strand	142-144	3	6
β-strand	148-151	4	7
β-strand	157-163	7	6
β-strand	171-176	6	7
β-strand	183-187	5	7
β-strand	191-192	2	7
α-helix	193	1
β-strand	200-205	6	6
β-strand	208-213	6	6
α-helix	218-220	3
β-strand	223-228	6	7
β-strand	236	1	7
β-strand	240-244	5	7

Chain C: 1 helix, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	8
β-strand	20-27	8	8
β-strand	36-41	6	9
β-strand	47-53	7	9
β-strand	60-62	3	9
β-strand	70-75	6	8
β-strand	80-85	6	8
α-helix	90-92	3
β-strand	94-96	3	8
β-strand	97-101	5	9
β-strand	104	1	10
β-strand	110-113	4	9
β-strand	117-120	4	8
β-strand	142-144	3	11
β-strand	148-149	2	12
β-strand	157-163	7	11
β-strand	171-176	6	12
β-strand	183-187	5	12
β-strand	191-192	2	12
β-strand	200-205	6	11
β-strand	208-213	6	11
β-strand	223-228	6	12
β-strand	241-242	2	12

Chain D: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	8
β-strand	13-14	2	13
β-strand	19-27	9	8
β-strand	36-41	6	14
β-strand	47-53	7	14
β-strand	60-62	3	14
β-strand	67	1	8
β-strand	70-75	6	8
β-strand	80-86	7	8
α-helix	90-92	3
β-strand	94-101	8	14
β-strand	104	1	15
β-strand	110-113	4	14
β-strand	117-119	3	14
β-strand	120-121	2	13
β-strand	142-144	3	16
β-strand	148	1	17
β-strand	157-163	7	16
β-strand	171-176	6	17
β-strand	183-187	5	17
β-strand	191-192	2	17
α-helix	193	1
β-strand	200-205	6	16
β-strand	208-213	6	16
α-helix	218-220	3
β-strand	223-228	6	17
β-strand	240-241	2	17

Chain D000: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	25
β-strand	32-37	6	26
β-strand	47-53	7	25
β-strand	60-65	6	25
α-helix	76	1
β-strand	77-79	3	26
β-strand	82-87	6	26
β-strand	92-97	6	26
α-helix	102-104	3
β-strand	106-114	9	25
β-strand	117-129	13	25

Chain E: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	27
β-strand	12-14	3	28
β-strand	19-27	9	27
β-strand	36-41	6	29
β-strand	47-53	7	29
β-strand	60-62	3	29
β-strand	70-75	6	27
β-strand	80-86	7	27
β-strand	95-101	7	29
β-strand	110-113	4	29
β-strand	117-118	2	29
β-strand	119-121	3	28
β-strand	142-144	3	30
β-strand	148-151	4	31
β-strand	157-163	7	30
β-strand	171-176	6	31
β-strand	183-186	4	31
α-helix	191	1
β-strand	192	1	31
α-helix	193	1
β-strand	200-204	5	30
β-strand	208-213	6	30
α-helix	218-220	3
β-strand	223-228	6	31
β-strand	236	1	31
β-strand	240-244	5	31

Chain F: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	32
β-strand	13-14	2	33
β-strand	19-27	9	32
β-strand	35-41	7	34
β-strand	47-53	7	34
β-strand	60-62	3	34
β-strand	70-75	6	32
β-strand	80-86	7	32
β-strand	94-101	8	34
β-strand	110-113	4	34
β-strand	117-119	3	34
β-strand	120-121	2	33
β-strand	142-143	2	35
β-strand	148-151	4	36
β-strand	157-163	7	35
β-strand	171-176	6	36
β-strand	183-187	5	36
β-strand	191-192	2	36
α-helix	193	1
β-strand	200-201	2	35
β-strand	205	1	35
β-strand	208-213	6	35
β-strand	223-228	6	36
α-helix	235	1
β-strand	236	1	36
α-helix	237	1
β-strand	240-244	5	36

Chain G: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	2
β-strand	32-37	6	18
β-strand	47-53	7	2
β-strand	60-65	6	2
α-helix	70-72	3
β-strand	77-79	3	18
β-strand	82-87	6	18
β-strand	92-97	6	18
α-helix	102-104	3
β-strand	106-114	9	2
β-strand	117-129	13	2

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Single-chain variable 4	A, B, C, D, E, F	protein	245	Homo sapiens
Triggering receptor expressed on myeloid cells 2	D000, G, H, I, J, K	protein	125	Homo sapiens	Q9NZC2 (AlphaFold model)

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

>6YMQ_1 Single-chain variable 4 (chains A, B, C, D, E, F)
SMEVQLLESGGGLVQPGGSLRLSCAASGFTFSYYYMGWVRQAPGKGLEWVSGISPSSGYT
YYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYYYGYYYSHMDYWGQGTLVT
VSSGGGGSGGGGSGGGGSDIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGK
APKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSRSGLHTFGQGT
KLEIK

Sequence of entity 2 (D000, G, H, I, J, K), FASTA

>6YMQ_2 Triggering receptor expressed on myeloid cells 2 (chains D000, G, H, I, J, K)
ETGHNTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFL
RRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLADGTKH
HHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Water and common crystallization additives (MPD) are not listed.

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…
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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