3M17: Human FcRn with a monomeric peptide inhibitor

Crystal structure of human FcRn with a monomeric peptide inhibitor. Determined by X-ray diffraction at 2.6 Å resolution. Released 16 Jun 2010.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 12
Atoms: 11,581
Mol. weight: 172.03 kDa
Released: 16 Jun 2010

Explore 3M17 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M17 contains 47 α-helices and 127 β-strands across 12 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	7-14	8	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	60-78	19
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	132-143	12
α-helix	147-152	6
α-helix	153-158	6
α-helix	159-169	11
α-helix	171-175	5
β-strand	178	1	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	217-220	4	4
β-strand	225-228	4	3
β-strand	234-243	10	3
α-helix	247-249	3
β-strand	250-255	6	4
β-strand	263-265	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
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
α-helix	90	1
β-strand	91-94	4	7

Chain C: 11 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	60-78	19
α-helix	79-81	3
β-strand	89-98	10	8
β-strand	104-112	9	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	209-215	7	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	263-265	3	11

Chains D and H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain E: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	15
α-helix	17-18	2
β-strand	24-30	7	15
β-strand	33-39	7	15
β-strand	46-47	2	15
α-helix	49-53	5
α-helix	60-78	19
α-helix	79-81	3
β-strand	89-98	10	15
β-strand	104-112	9	15
β-strand	115-121	7	15
β-strand	126-128	3	15
α-helix	132-143	12
α-helix	147-152	6
α-helix	153-158	6
α-helix	159-169	11
α-helix	171-174	4
β-strand	178	1	16
α-helix	179-180	2
β-strand	181-188	8	17
β-strand	193-203	11	17
β-strand	204	1	16
β-strand	209-214	6	18
β-strand	217-218	2	18
β-strand	223-228	6	17
β-strand	234-243	10	17
β-strand	250-255	6	18
β-strand	263-266	4	18

Chain F: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	19
α-helix	4-5	2
β-strand	6-11	6	20
β-strand	21-30	10	20
β-strand	31	1	19
β-strand	36-41	6	21
β-strand	44-45	2	21
β-strand	50-51	2	20
β-strand	55-56	2	20
β-strand	62-70	9	20
β-strand	78-84	7	21
β-strand	87-94	8	21

Chain G: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	22
α-helix	17-18	2
β-strand	24-30	7	22
β-strand	33-39	7	22
β-strand	46-47	2	22
α-helix	49-53	5
α-helix	60-78	19
α-helix	79-81	3
β-strand	89-97	9	22
β-strand	98	1	23
β-strand	104	1	23
β-strand	107-112	6	22
β-strand	115-121	7	22
β-strand	126-128	3	22
α-helix	132-143	12
α-helix	147-153	7
α-helix	154-158	5
α-helix	159-169	11
α-helix	171-174	4
β-strand	178	1	24
β-strand	181-188	8	25
β-strand	194-203	10	25
β-strand	204	1	24
β-strand	209-214	6	26
β-strand	217-220	4	26
β-strand	223	1	25
β-strand	226-228	3	25
β-strand	234-242	9	25
β-strand	250-255	6	26
β-strand	263-266	4	26

Chains I, J, K and L: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	30
β-strand	10-12	3	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG receptor FcRn large subunit p51	A, C, E, G	protein	267	Homo sapiens	P55899 (AlphaFold model)
Beta-2-microglobulin	B, D, F, H	protein	99	Homo sapiens	P61769 (AlphaFold model)
monomeric peptide inhibitor	I, J, K, L	protein	15

Sequence of entity 1 (A, C, E, G), FASTA

>3M17_1 IgG receptor FcRn large subunit p51 (chains A, C, E, G)
AESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLSYNSLRGEAEPCGAWVWENQVSWY
WEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCELGPDNTSVPTAKFALNGEEFMNF
DLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLFSCPHRLREHLERGRGNLEWKEPP
SMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGTGQGDFGPNSDGSFHASSSL
TVKSGDEHHYCCIVQHAGLAQPLRVEL

Sequence of entity 2 (B, D, F, H), FASTA

>3M17_2 Beta-2-microglobulin (chains B, D, F, H)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (I, J, K, L), FASTA

>3M17_3 monomeric peptide inhibitor (chains I, J, K, L)
XRFXTGHFGGLYPCX

Primary citation

X-ray crystal structures of monomeric and dimeric peptide inhibitors in complex with the human neonatal Fc receptor, FcRn. Mezo, A.R., Sridhar, V., Badger, J. et al. J Biol Chem (2010) 285:27694-27701. DOI 10.1074/jbc.M110.120667 · 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
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

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