8SO3: Therapeutic antibody

CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3. Determined by electron microscopy at 3.61 Å resolution. Released 6 Sept 2023.

Method: Electron microscopy
Resolution: 3.61 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,771
Mol. weight: 222.22 kDa
Ligands: NAG
Released: 6 Sept 2023

Explore 8SO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SO3 contains 24 α-helices and 128 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: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	41-42	2	1
β-strand	62-66	5	2
β-strand	99-103	5	2
β-strand	134-135	2	1
β-strand	146-147	2	2
β-strand	185-187	3	3
β-strand	199-203	5	4
β-strand	205	1	5
α-helix	207-209	3
β-strand	211	1	5
β-strand	220-221	2	3
β-strand	226-228	3	3
β-strand	238-239	2	6
β-strand	240-244	5	4
β-strand	255-256	2	6

Chain H: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	14	1	9
β-strand	16	1	9
β-strand	19-25	7	7
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68	1	11
β-strand	71-73	3	7
β-strand	78-82	5	7
β-strand	83	1	11
β-strand	93-100	8	10
β-strand	105-109	5	10
β-strand	113-114	2	10
β-strand	115-117	3	8
β-strand	121	1	12
β-strand	124-128	5	13
β-strand	141-147	7	13
β-strand	150	1	12
β-strand	154-158	5	14
α-helix	159-161	3
β-strand	167-169	3	13
α-helix	170-172	3
β-strand	173-174	2	13
β-strand	180-187	8	13
α-helix	190-192	3
β-strand	199-204	6	14
β-strand	209-214	6	14

Chain L: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	15
β-strand	10	1	16
β-strand	13	1	17
β-strand	19-20	2	18
β-strand	24-25	2	15
β-strand	37-42	6	16
β-strand	49-53	5	16
β-strand	57-58	2	16
α-helix	59	1
α-helix	64-66	3
β-strand	74	1	15
β-strand	78-79	2	18
β-strand	89-94	6	16
β-strand	101	1	16
β-strand	105-107	3	16
β-strand	110	1	17
β-strand	115	1	19
α-helix	116-117	2
β-strand	118-122	5	20
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	20
β-strand	144	1	19
β-strand	149-154	6	21
β-strand	158	1	21
β-strand	163-167	5	20
β-strand	177-186	10	20
α-helix	187-192	6
β-strand	196-201	6	21
β-strand	209-213	5	21

Chain X: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	30-31	2
β-strand	40-43	4	22
β-strand	61-67	7	23
β-strand	99-100	2	23
β-strand	133-136	4	22
β-strand	145-151	7	23
β-strand	159-161	3	23
β-strand	172-173	2	24
β-strand	185-186	2	25
β-strand	187-188	2	24
α-helix	196-197	2
β-strand	199-203	5	26
β-strand	216	1	27
β-strand	219	1	27
β-strand	220-221	2	25
β-strand	226-228	3	25
α-helix	233-235	3
β-strand	240-244	5	26
β-strand	251-253	3	26

Chain Y: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	28
α-helix	7-9	3
β-strand	10-12	3	29
β-strand	19-21	3	30
β-strand	24-25	2	28
α-helix	29-31	3
β-strand	34-39	6	29
β-strand	46-51	6	29
β-strand	58-60	3	29
β-strand	69-73	5	30
β-strand	78-82	5	30
β-strand	92-100	9	29
β-strand	105-109	5	29
β-strand	110	1	28
β-strand	113-117	5	29
β-strand	124-128	5	31
β-strand	140-149	10	31
β-strand	155-158	4	32
α-helix	159-161	3
β-strand	163	1	32
β-strand	168-169	2	31
α-helix	170-172	3
β-strand	173-174	2	31
β-strand	180-188	9	31
α-helix	190-194	5
β-strand	198-204	7	32
β-strand	209-215	7	32

Chain Z: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	33
β-strand	10-12	3	34
β-strand	19-20	2	35
β-strand	24-25	2	33
β-strand	31	1	36
β-strand	34	1	36
β-strand	37-42	6	34
β-strand	49-53	5	34
β-strand	57-58	2	34
α-helix	59	1
β-strand	66-67	2	35
β-strand	71	1	33
β-strand	74	1	33
β-strand	78-79	2	35
β-strand	89-94	6	34
β-strand	101	1	34
β-strand	106-109	4	34
β-strand	115	1	37
β-strand	118-122	5	38
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-141	9	38
β-strand	144	1	37
β-strand	148-154	7	39
β-strand	158	1	39
β-strand	163-167	5	38
α-helix	168-170	3
β-strand	178-186	9	38
α-helix	187-191	5
β-strand	196-202	7	39
β-strand	209-213	5	39

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

>8SO3_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

>8SO3_2 favezelimab Fab heavy chain (chains H, Y)
MGWTWIFLFFLSGTAGVLSEVLLLQSGPELVKPGTSVKIPCKASGYTFTDYNVDWVKQRH
GKGLEWIGDINPNNGGTIYSQKFKGKATLTVDKSSSTAFMELRSLTSEDTAVYFCARNYR
WFGAMDHWGQGTSVTVSSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSG
ALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCD
KTAGWSHPQFEK

Sequence of entity 3 (L, Z), FASTA

>8SO3_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	4

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
8SR0 3.53 Å, CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3 local refined
7TZG 3.71 Å, Structure of human LAG3 in complex with antibody single-chain variable fragment

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