6NHA: IgG receptor FcRn large subunit p51

Crystal structure of SYNT001, a human FcRn blocking monoclonal antibody. Determined by X-ray diffraction at 2.38 Å resolution. Released 25 Dec 2019.

Method: X-ray diffraction
Resolution: 2.38 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,263
Mol. weight: 90.4 kDa
Ligands: NHE
Released: 25 Dec 2019

Explore 6NHA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NHA contains 27 α-helices and 69 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	49-52	4
α-helix	59-78	20
α-helix	79-81	3
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	132-142	11
α-helix	147-153	7
α-helix	154-158	5
α-helix	159-165	7
β-strand	178	1	2
α-helix	179-180	2
β-strand	181-188	8	3
β-strand	193-203	11	3
β-strand	204	1	2
β-strand	208-214	7	4
β-strand	217-218	2	4
β-strand	223-228	6	3
β-strand	234-243	10	3
α-helix	246-249	4
β-strand	250-256	7	4
β-strand	263-265	3	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	35-41	7	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7

Chain H: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
β-strand	10-12	3	9
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	46-51	6	9
β-strand	58-60	3	9
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	108	1	9
β-strand	112-116	5	9
α-helix	119-121	3
α-helix	123-124	2
β-strand	125-129	5	14
β-strand	140-150	11	14
β-strand	156-159	4	15
α-helix	160-162	3
β-strand	168-170	3	14
α-helix	171-173	3
β-strand	174-175	2	14
β-strand	181-190	10	14
α-helix	191-194	4
β-strand	200-205	6	15
β-strand	210-215	6	15

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	85-90	6	9
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
β-strand	159-163	5	11
α-helix	165-167	3
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-197	7	12
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG receptor FcRn large subunit p51	A	protein	279	Homo sapiens	P55899 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
SYNT001-Fab light chain	L	protein	214	Homo sapiens
SYNT001-Fab heavy chain	H	protein	220	Homo sapiens

Sequence of entity 1 (A), FASTA

>6NHA_1 IgG receptor FcRn large subunit p51 (chains A)
AESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLSYNSLRGEAEPCGAWVWENQVSWY
WEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCELGPDATSVPTAKFALNGEEFMNF
DLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLFSCPHRLREHLERGRGNLEWKEPP
SMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGTGQGDFGPNSDGSFHASSSL
TVKSGDEHHYCCIVQHAGLAQPLRVELESPAKSENLYFQ

Sequence of entity 2 (B), FASTA

>6NHA_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (L), FASTA

>6NHA_3 SYNT001-Fab light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCKASDHINNWLAWYQQKPGQAPRLLISGATSLETGVPS
RFSGSGTGKDYTLTISSLQPEDFATYYCQQYWSTPYTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (H), FASTA

>6NHA_4 SYNT001-Fab heavy chain (chains H)
QVQLVQSGAELKKPGASVKLSCKASGYTFTSYGISWVKQATGQGLEWIGEIYPRSGNTYY
NEKFKGRATLTADKSTSTAYMELRSLRSEDSAVYFCARSTTVRPPGIWGTGTTVTVSSAS
TKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKY

Ligands and cofactors

ID	Name	Formula	Copies
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	3

Primary citation

Blocking FcRn in humans reduces circulating IgG levels and inhibits IgG immune complex-mediated immune responses. Blumberg, L.J., Humphries, J.E., Jones, S.D. et al. Sci Adv (2019) 5:eaax9586-eaax9586. DOI 10.1126/sciadv.aax9586 · 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
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
9MI6 2.41 Å, Crystal structure of human FcRn in complex with nipocalimab Fab fragment
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

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