6C99: FcRn

Crystal structure of FcRn bound to UCB-303. Determined by X-ray diffraction at 2.0 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,054
Mol. weight: 85.92 kDa
Ligands: CIT, NAG, EQY
Released: 30 May 2018

Explore 6C99 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C99 contains 24 α-helices and 58 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	132-142	11
α-helix	147-153	7
α-helix	154-158	5
α-helix	159-169	11
α-helix	171-175	5
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	209-214	6	4
β-strand	217-218	2	4
β-strand	223-228	6	3
β-strand	234-243	10	3
α-helix	247-249	3
β-strand	250-255	6	4
β-strand	263-266	4	4

Chains B and D: 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
α-helix	46	1
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

Chain C: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	8
α-helix	17-18	2
β-strand	24-30	7	8
β-strand	33-39	7	8
β-strand	46-47	2	8
α-helix	49-53	5
α-helix	60-80	21
β-strand	89-97	9	8
β-strand	105-112	8	8
β-strand	115-121	7	8
β-strand	126-128	3	8
α-helix	132-142	11
α-helix	147-153	7
α-helix	154-158	5
α-helix	159-169	11
α-helix	171-174	4
β-strand	178	1	9
α-helix	179-180	2
β-strand	181-188	8	10
β-strand	193-203	11	10
β-strand	204	1	9
β-strand	209-214	6	11
β-strand	217-218	2	11
β-strand	223-228	6	10
β-strand	234-243	10	10
α-helix	247-249	3
β-strand	250-255	6	11
β-strand	263-266	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG receptor FcRn large subunit p51	A, C	protein	274	Homo sapiens	P55899 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6C99_1 IgG receptor FcRn large subunit p51 (chains A, C)
AESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLSYNSLRGEAEPCGAWVWENQVSWY
WEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCELGPDNTSVPTAKFALNGEEFMNF
DLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLFSCPHRLREHLERGRGNLEWKEPP
SMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGTGQGDFGPNSDGSFHASSSL
TVKSGDEHHYCCIVQHAGLAQPLRVELESPAKSS

Sequence of entity 2 (B, D), FASTA

>6C99_2 Beta-2-microglobulin (chains B, D)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
EQY	methyl 7-(3,5-difluorophenyl)-5-(pyridin-3-yl)[1,2,4]triazolo[1,5-a]pyrimidine-…	C18 H11 F2 N5 O2	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR. Stoppler, D., Macpherson, A., Smith-Penzel, S. et al. PLoS Biol (2018) 16:e2006192-e2006192. DOI 10.1371/journal.pbio.2006192 · 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
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
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

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