6B8O: WT Ig-like V Domain with Phosphatidylserine

WT Ig-like V Domain with Phosphatidylserine. Determined by X-ray diffraction at 2.2 Å resolution. Released 27 Jun 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,416
Mol. weight: 120.09 kDa
Ligands: PSF, NAG
Released: 27 Jun 2018

Explore 6B8O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B8O contains 13 α-helices and 54 β-strands across 6 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 and C: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	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	117-128	12	1

Chains B, D and F: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	3
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

Chain E: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	9
β-strand	32-37	6	10
β-strand	48-52	5	9
α-helix	60	1
β-strand	61-65	5	9
α-helix	70-72	3
β-strand	77-79	3	10
β-strand	82-87	6	10
β-strand	92-97	6	10
α-helix	102-104	3
β-strand	106-114	9	9
β-strand	117-129	13	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Triggering receptor expressed on myeloid cells 2	A, B, C, D, E, F	protein	169	Homo sapiens	Q9NZC2 (AlphaFold model)

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

>6B8O_1 Triggering receptor expressed on myeloid cells 2 (chains A, B, C, D, E, F)
HDTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRW
NGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLADPLDHRDA
GDLWFPGESESFEDAHVEHSISRSLLEGEIPFPPTSENLYFQGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PSF	1,2-dicaproyl-sn-phosphatidyl-L-serine	C18 H34 N O10 P	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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

Primary citation

Molecular basis for the loss-of-function effects of the Alzheimer's disease-associated R47H variant of the immune receptor TREM2. Sudom, A., Talreja, S., Danao, J. et al. J Biol Chem (2018) 293:12634-12646. DOI 10.1074/jbc.RA118.002352 · 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
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
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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