9MI6: Human FcRn

Crystal structure of human FcRn in complex with nipocalimab Fab fragment. Determined by X-ray diffraction at 2.41 Å resolution. Released 12 Feb 2025.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,337
Mol. weight: 88.88 kDa
Ligands: NAG
Released: 12 Feb 2025

Explore 9MI6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MI6 contains 30 α-helices and 77 β-strands across 4 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	1
α-helix	17-18	2
β-strand	24-30	7	1
β-strand	33-39	7	1
β-strand	46-47	2	1
α-helix	49-53	5
α-helix	60-82	23
β-strand	89-98	10	1
β-strand	104-112	9	1
β-strand	115-121	7	1
β-strand	126-128	3	1
α-helix	132-143	12
α-helix	147-153	7
α-helix	154-158	5
α-helix	159-167	9
α-helix	171-174	4
β-strand	178	1	2
α-helix	179-180	2
β-strand	181-190	10	3
β-strand	193-203	11	3
β-strand	204	1	2
β-strand	208-214	7	4
β-strand	217-220	4	4
β-strand	223-228	6	3
β-strand	234-243	10	3
α-helix	247-249	3
β-strand	250-256	7	4
β-strand	263-266	4	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7
α-helix	95-96	2

Chain H: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	105-106	2	10
β-strand	110-112	3	10
β-strand	113-114	2	9
α-helix	118-119	2
β-strand	120	1	11
α-helix	121-122	2
β-strand	123-127	5	12
β-strand	138-148	11	12
β-strand	149	1	11
β-strand	154-157	4	13
α-helix	158-160	3
β-strand	162	1	13
β-strand	166-168	3	12
α-helix	169-171	3
β-strand	172-173	2	12
β-strand	179-188	10	12
α-helix	189-191	3
β-strand	192	1	14
β-strand	195	1	14
β-strand	198-203	6	13
α-helix	204-206	3
β-strand	208-213	6	13
α-helix	215-217	3

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	15
β-strand	9-12	4	16
β-strand	18-23	6	15
β-strand	34-40	7	16
β-strand	47-50	4	16
β-strand	51	1	17
β-strand	55	1	17
α-helix	56-57	2
β-strand	64-69	6	15
β-strand	72-77	6	15
α-helix	82-84	3
β-strand	87-93	7	16
β-strand	99-101	3	16
β-strand	105-109	5	16
α-helix	112-114	3
β-strand	115	1	18
α-helix	116-117	2
β-strand	118-122	5	19
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	19
β-strand	144	1	18
β-strand	149-154	6	20
β-strand	157-159	3	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-184	9	19
α-helix	186-190	5
β-strand	195-201	7	20
β-strand	204-210	7	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG receptor FcRn large subunit p51	A	protein	280	Homo sapiens	P55899 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
nipocalimab Fab heavy chain	H	protein	220	Homo sapiens
nipocalimab Fab light chain	L	protein	216	Homo sapiens

Sequence of entity 1 (A), FASTA

>9MI6_1 IgG receptor FcRn large subunit p51 (chains A)
AESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLSYNSLRGEAEPCGAWVWENQVSWY
WEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCELGPDNTSVPTAKFALNGEEFMNF
DLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLFSCPHRLREHLERGRGNLEWKEPP
SMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGTGQGDFGPNSDGSFHASSSL
TVKSGDEHHYCCIVQHAGLAQPLRVELESPAKSSHHHHHH

Sequence of entity 2 (B), FASTA

>9MI6_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (H), FASTA

>9MI6_3 nipocalimab Fab heavy chain (chains H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSTYAMGWVRQAPGKGLEWVSSIGASGSQTRY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARLAIGDSYWGQGTMVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 4 (L), FASTA

>9MI6_4 nipocalimab Fab light chain (chains L)
QSALTQPASVSGSPGQSITISCTGTGSDVGSYNLVSWYQQHPGKAPKLMIYGDSERPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCSSYAGSGIYVFGTGTKVTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Nipocalimab, an immunoselective FcRn blocker that lowers IgG and has unique molecular properties. Seth, N.P., Xu, R., DuPrie, M. et al. MAbs (2025) 17:2461191-2461191. DOI 10.1080/19420862.2025.2461191 · PubMed

Other PDB entries of the same protein (UniProt P55899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6C98 1.85 Å, Crystal structure of FcRn bound to UCB-84
6QIO 1.95 Å, Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the…
6C97 2.0 Å, Crystal structure of FcRn at pH3
6C99 2.0 Å, Crystal structure of FcRn bound to UCB-303
9TF0 2.26 Å, Structure of echovirus 18 in complex with neonatal Fc receptor
6NHA 2.38 Å, Crystal structure of SYNT001, a human FcRn blocking monoclonal antibody
6LA6 2.39 Å, Cryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 7.4
4K71 2.4 Å, Crystal structure of a high affinity Human Serum Albumin variant bound to the Neonatal…
6WNA 2.4 Å, Next generation monomeric IgG4 Fc
6QIP 2.45 Å, Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the…
6WOL 2.49 Å, Next generation monomeric IgG4 Fc bound to neonatal Fc receptor
5WHK 2.5 Å, Crystal structure of Fab fragment of antibody DX-2507 bound to FcRn-B2M

Browse structure collections

About this viewer

MolViewer shows 9MI6 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.