8T59: Para.09

Crystal structure of Para.09 bound to TREM2. Determined by X-ray diffraction at 2.0 Å resolution. Released 31 Jul 2024.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: synthetic construct, Homo sapiens
Chains: 6
Atoms: 7,534
Mol. weight: 101.86 kDa
Ligands: ZN
Released: 31 Jul 2024

Explore 8T59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T59 contains 38 α-helices and 93 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.

Chain A: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	46-51	6	2
α-helix	54-56	3
β-strand	60-62	3	2
β-strand	70-75	6	1
α-helix	76-78	3
β-strand	80-85	6	1
α-helix	90-92	3
β-strand	94-99	6	2
β-strand	105	1	2
β-strand	109-113	5	2
α-helix	116-118	3
β-strand	119	1	3
α-helix	120-121	2
β-strand	122-126	5	4
β-strand	137-147	11	4
β-strand	148	1	3
β-strand	153-156	4	5
α-helix	157-159	3
β-strand	161	1	5
β-strand	165-167	3	4
α-helix	168-170	3
β-strand	171-172	2	4
β-strand	178-187	10	4
α-helix	188-190	3
β-strand	191	1	6
β-strand	194	1	6
β-strand	197-202	6	5
α-helix	203-205	3
β-strand	207-212	6	5

Chains B and D: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	30	1	9
β-strand	36	1	9
β-strand	38-43	6	8
β-strand	50-54	5	8
β-strand	58-59	2	8
α-helix	60	1
β-strand	67-72	6	7
β-strand	75-80	6	7
α-helix	85-87	3
β-strand	89-95	7	8
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	116	1	10
α-helix	117-118	2
β-strand	119-123	5	11
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	11
β-strand	145	1	10
β-strand	150-155	6	12
β-strand	158-159	2	12
α-helix	160	1
β-strand	164-168	5	11
α-helix	169-172	4
β-strand	178-187	10	11
α-helix	188-191	4
β-strand	196-202	7	12
β-strand	210-215	6	12

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
β-strand	34-39	6	14
β-strand	46-51	6	14
α-helix	54-56	3
β-strand	60-62	3	14
α-helix	64-66	3
β-strand	70-75	6	13
β-strand	80-85	6	13
α-helix	90-92	3
β-strand	94-99	6	14
β-strand	105	1	14
β-strand	109-113	5	14
α-helix	116-118	3
β-strand	119	1	15
α-helix	120-121	2
β-strand	122-126	5	16
β-strand	133-134	2	16
β-strand	137-147	11	16
β-strand	148	1	15
β-strand	153-156	4	17
α-helix	157-159	3
β-strand	161	1	17
β-strand	165-167	3	16
α-helix	168-170	3
β-strand	171-172	2	16
β-strand	178-187	10	16
α-helix	188-190	3
β-strand	196-202	7	17
α-helix	203-205	3
β-strand	207-213	7	17

Chains E and F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	155-157	3
α-helix	159-162	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Para.09 heavy chain	A, C	protein	225	synthetic construct
Para.09 light chain	B, D	protein	219	synthetic construct
Triggering receptor expressed on myeloid cells 2	E, F	protein	19	Homo sapiens	Q9NZC2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8T59_1 Para.09 heavy chain (chains A, C)
EVQLVESGGGLVQPGGSLKLSCATSGFPFSNVWLHWVRQASGKGPEWVAHIKAKSDNYAT
YYAESVKGRFTISRDDSKNTVYLQMNSLKTEDTAVYYCTDILEYWGQGTLVTVSSASTKG
PSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSL
SSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTPK

Sequence of entity 2 (B, D), FASTA

>8T59_2 Para.09 light chain (chains B, D)
DVVMTQSPLSLPVTPGEPASISCRSSRSLLTSKGITSLYWYLQKPGQSPQLLIYRMSNLA
SGIPDRFSGSGSGTDFTLKISRVEAEDVGVYYCAQFLVYPYTFGPGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E, F), FASTA

>8T59_3 Triggering receptor expressed on myeloid cells 2 (chains E, F)
ESFEDAHVEHSISRSLLEG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

Water and common crystallization additives (GOL, PEG) are not listed.

Primary citation

Rapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining. Hsiao, Y.C., Wallweber, H.A., Alberstein, R.G. et al. Nat Commun (2024) 15:8382-8382. DOI 10.1038/s41467-024-52442-y · 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
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
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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