8T51: Fab 3.10C2

Crystal structure of Fab 3.10C2 bound to TREM2. Determined by X-ray diffraction at 1.9 Å resolution. Released 19 Jun 2024.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,605
Mol. weight: 102.73 kDa
Ligands: ZN
Released: 19 Jun 2024

Explore 8T51 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T51 contains 41 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: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-39	6	3
β-strand	45-51	7	3
α-helix	54-56	3
β-strand	60-62	3	3
α-helix	64-66	3
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	3
β-strand	104	1	3
β-strand	108-110	3	3
β-strand	111-112	2	2
α-helix	116-117	2
β-strand	118	1	4
α-helix	119-120	2
β-strand	121-125	5	5
β-strand	136-146	11	5
β-strand	147	1	4
β-strand	152-155	4	6
α-helix	156-158	3
β-strand	164-166	3	5
α-helix	167-169	3
β-strand	170-171	2	5
β-strand	177-186	10	5
α-helix	187-189	3
β-strand	190	1	7
β-strand	193	1	7
β-strand	196-201	6	6
α-helix	202-204	3
β-strand	206-211	6	6

Chain B: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	30	1	10
β-strand	36	1	10
β-strand	38-43	6	9
β-strand	50-54	5	9
β-strand	58-59	2	9
α-helix	60	1
β-strand	67-72	6	8
β-strand	75-80	6	8
α-helix	85-87	3
β-strand	89-95	7	9
α-helix	101	1
β-strand	102-103	2	9
β-strand	107-111	5	9
β-strand	116	1	11
α-helix	117-118	2
β-strand	119-123	5	12
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	12
β-strand	145	1	11
β-strand	150-155	6	13
β-strand	158-159	2	13
α-helix	160	1
β-strand	164-168	5	12
α-helix	169-172	4
β-strand	178-187	10	12
α-helix	188-193	6
β-strand	196-202	7	13
β-strand	210-215	6	13

Chain C: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	18-25	8	14
β-strand	34-39	6	16
β-strand	45-51	7	16
α-helix	54-56	3
β-strand	60-62	3	16
α-helix	64-66	3
β-strand	70-75	6	14
α-helix	76-78	3
β-strand	80-85	6	14
α-helix	90-92	3
β-strand	94-99	6	16
β-strand	104	1	16
β-strand	108-110	3	16
β-strand	111-112	2	15
α-helix	116-117	2
β-strand	118	1	17
α-helix	119-120	2
β-strand	121-125	5	18
β-strand	136-146	11	18
β-strand	147	1	17
β-strand	152-155	4	19
α-helix	156-158	3
β-strand	160	1	19
β-strand	164-166	3	18
α-helix	167-169	3
β-strand	170-171	2	18
β-strand	177-186	10	18
α-helix	187-191	5
β-strand	196-201	6	19
α-helix	202-204	3
β-strand	206-211	6	19

Chain D: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
β-strand	10-13	4	21
β-strand	19-25	7	20
β-strand	30	1	22
β-strand	36	1	22
β-strand	38-43	6	21
β-strand	50-54	5	21
β-strand	58-59	2	21
α-helix	60	1
β-strand	67-72	6	20
β-strand	75-80	6	20
α-helix	85-87	3
β-strand	89-95	7	21
α-helix	101	1
β-strand	102-103	2	21
β-strand	107-111	5	21
β-strand	116	1	23
α-helix	117-118	2
β-strand	119-123	5	24
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	24
β-strand	145	1	23
β-strand	150-155	6	25
β-strand	158-159	2	25
α-helix	160	1
β-strand	164-168	5	24
α-helix	169-172	4
β-strand	178-187	10	24
α-helix	188-193	6
β-strand	196-202	7	25
β-strand	210-215	6	25

Chains E and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	159-162	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3.10C2 Fab heavy chain	A, C	protein	222	Homo sapiens
3.10C2 Fab light chain	B, D	protein	219	Homo sapiens
Triggering receptor expressed on myeloid cells 2 peptide	E, F	protein	20	Homo sapiens	Q9NZC2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8T51_1 3.10C2 Fab heavy chain (chains A, C)
EVQLVESGGGLVQPGGSLKLSCATSGFPFSNVWMHWVRQASGKGLEWIAHIKAKSDNYAT
YYAESVKGRFTISRDDSKTTIYLQMNSLKTEDTAVYYCTGLDYWGQGTTVTVSSASTKGP
SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS
SVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (B, D), FASTA

>8T51_2 3.10C2 Fab light chain (chains B, D)
DVVMTQSPLSLPVTPGEPASISCRSSRSLLTSKGITSLYWYLQKPGQSPQLLIYRMSNLA
SGIPDRFSGSGSGTDFTLKISRVEAEDVGVYYCAQFLVYPYTFGPGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E, F), FASTA

>8T51_3 Triggering receptor expressed on myeloid cells 2 peptide (chains E, F)
ESFEDAHVEHSISRSLLEEG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (PEG, ACT, GOL, SO4) 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
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
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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