8SR0: Therapeutic antibody

CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3 local refined. Determined by electron microscopy at 3.53 Å resolution. Released 6 Sept 2023.

Method: Electron microscopy
Resolution: 3.53 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 5,988
Mol. weight: 221.78 kDa
Ligands: NAG
Released: 6 Sept 2023

Explore 8SR0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SR0 contains 10 α-helices and 84 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 D: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	30	1
β-strand	31	1	18
β-strand	40-42	3	19
β-strand	63-66	4	18
β-strand	100	1	18
β-strand	134-136	3	19
α-helix	141-143	3
β-strand	146-149	4	18
β-strand	162-163	2	18
β-strand	171-173	3	20
β-strand	185-189	5	20
α-helix	196-197	2
β-strand	199-202	4	21
β-strand	220-221	2	20
β-strand	226-228	3	20
β-strand	238-244	7	21
β-strand	251-256	6	21

Chain H: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	22
β-strand	20-25	6	22
β-strand	33-39	7	23
β-strand	45-51	7	23
β-strand	58-60	3	23
β-strand	70-73	4	22
β-strand	78-81	4	22
β-strand	93-100	8	23
β-strand	105-109	5	23
β-strand	114	1	23

Chain L: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	24
β-strand	10-11	2	25
β-strand	19-20	2	26
β-strand	22-24	3	24
β-strand	37-42	6	25
β-strand	49-53	5	25
β-strand	57-58	2	25
α-helix	59	1
α-helix	64-66	3
β-strand	74	1	24
β-strand	78-79	2	26
β-strand	89-94	6	25
β-strand	101	1	25
β-strand	106-108	3	25

Chain X: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	1
β-strand	40-43	4	2
β-strand	62-65	4	3
β-strand	99-102	4	3
β-strand	133-136	4	2
β-strand	147-150	4	3
β-strand	166-167	2	1
β-strand	171	1	4
β-strand	185-186	2	5
β-strand	189	1	4
α-helix	196-197	2
β-strand	199-203	5	6
β-strand	212	1	6
β-strand	220-221	2	5
β-strand	226-228	3	5
α-helix	233-235	3
β-strand	238	1	7
β-strand	240-244	5	6
β-strand	250-253	4	6
β-strand	256	1	7

Chain Y: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	8
α-helix	7-9	3
β-strand	12	1	9
β-strand	18-21	4	10
β-strand	24-25	2	8
β-strand	34-39	6	11
β-strand	46-51	6	11
β-strand	58	1	11
β-strand	68-73	6	10
β-strand	78-83	6	10
β-strand	92-98	7	11
β-strand	108	1	11
β-strand	110	1	8
β-strand	113-115	3	11
β-strand	117	1	9

Chain Z: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-11	2	13
β-strand	19-20	2	14
β-strand	22-24	3	12
β-strand	38-42	5	15
α-helix	47-48	2
β-strand	49-50	2	15
β-strand	52-53	2	16
β-strand	57-58	2	16
α-helix	59	1
β-strand	67	1	14
β-strand	71	1	12
β-strand	74	1	12
β-strand	78-79	2	14
β-strand	89-93	5	15
β-strand	94	1	17
β-strand	101	1	17
β-strand	107-108	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lymphocyte activation gene 3 protein	D, X	protein	525	Homo sapiens	P18627 (AlphaFold model)
favezelimab Fab heavy chain	H, Y	protein	252	Mus musculus
favezelimab Fab light chain	L, Z	protein	238	Mus musculus

Sequence of entity 1 (D, X), FASTA

>8SR0_1 Lymphocyte activation gene 3 protein (chains D, X)
MWEAQFLGLLFLQPLWVAPVKPLQPGAEVPVVWAQEGAPAQLPCSPTIPLQDLSLLRRAG
VTWQHQPDSGPPAAAPGHPLAPGPHPAAPSSWGPRPRRYTVLSVGPGGLRSGRLPLQPRV
QLDERGRQRGDFSLWLRPARRADAGEYRAAVHLRDRALSCRLRLRLGQASMTASPPGSLR
ASDWVILNCSFSRPDRPASVHWFRNRGQGRVPVRESPHHHLAESFLFLPQVSPMDSGPWG
CILTYRDGFNVSIMYNLTVLGLEPPTPLTVYAGAGSRVGLPCRLPAGVGTRSFLTAKWTP
PGGGPDLLVTGDNGDFTLRLEDVSQAQAGTYTCHIHLQEQQLNATVTLAIITVTPKSFGS
PGSLGKLLCEVTPVSGQERFVWSSLDTPSQRSFSGPWLEAQEAQLLSQPWQCQLYQGERL
LGAAVYFTELSSPGAQRSGRAPGALPAGHLLLFLILGVLSLLLLVTGAFGFHLWRRQWRP
RRFSALEQGIHPPQAQSKIEELEQEPEPEPEPEPEPEPEPEPEQL

Sequence of entity 2 (H, Y), FASTA

>8SR0_2 favezelimab Fab heavy chain (chains H, Y)
MGWTWIFLFFLSGTAGVLSEVLLLQSGPELVKPGTSVKIPCKASGYTFTDYNVDWVKQRH
GKGLEWIGDINPNNGGTIYSQKFKGKATLTVDKSSSTAFMELRSLTSEDTAVYFCARNYR
WFGAMDHWGQGTSVTVSSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSG
ALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCD
KTAGWSHPQFEK

Sequence of entity 3 (L, Z), FASTA

>8SR0_3 favezelimab Fab light chain (chains L, Z)
METDTILLWVLLLWVPGSTGDIVLTQSPASLAVSPGQRATISCKASQSLDYEGDSDMNWY
QQKPGQPPRLLISGASNLESGIPARFSGSGSGTDFTVNIHPVEEEDAATYYCQQSTEDPR
TFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKYQWKVDNALQS
GNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3 determined using a bivalent Fab as fiducial marker. Mishra, A.K., Shahid, S., Karade, S.S. et al. Structure (2023) 31:1149. DOI 10.1016/j.str.2023.07.013 · PubMed

Other PDB entries of the same protein (UniProt P18627 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UM3 2.4 Å, Crystal structure of a Fab in complex with a peptide derived from the LAG-3 D1 domain…
7TZH 2.43 Å, Structure of human LAG3 domains 3-4 in complex with antibody single chain-variable…
9BF9 3.4 Å, Human LAG-3-HLA-DR1 complex
8SO3 3.61 Å, CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3
7TZG 3.71 Å, Structure of human LAG3 in complex with antibody single-chain variable fragment

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