3M1B | pdb_00003m1b

Crystal structure of human FcRn with a dimeric peptide inhibitor

PDB DOI: https://doi.org/10.2210/pdb3M1B/pdb

Classification: IMMUNE SYSTEM/INHIBITOR
Organism(s): Homo sapiens
Expression System: Cricetinae
Mutation(s): No

Deposited: 2010-03-04 Released: 2010-06-16
Deposition Author(s): Mezo, A.R., Sridhar, V., Badger, J., Sakorafas, P., Nienaber, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.397 (Depositor), 0.395 (DCC)
R-Value Work:
0.314 (Depositor), 0.306 (DCC)
R-Value Observed:
0.318 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

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., Sakorafas, P., Nienaber, V.

(2010) J Biological Chem 285: 27694-27701

PubMed: 20592032 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M110.120667
Primary Citation Related Structures:
3M17, 3M1B

PubMed Abstract:
The neonatal Fc receptor, FcRn, is responsible for the long half-life of IgG molecules in vivo and is a potential therapeutic target for the treatment of autoimmune diseases. A family of peptides comprising the consensus motif GHFGGXY, where X is preferably a hydrophobic amino acid, was shown previously to inhibit the human IgG:human FcRn protein-protein interaction (Mezo, A. R., McDonnell, K. A., Tan Hehir, C. A., Low, S. C., Palombella, V. J., Stattel, J. M., Kamphaus, G. D., Fraley, C., Zhang, Y., Dumont, J. A., and Bitonti, A. J. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 2337-2342). Herein, the x-ray crystal structure of a representative monomeric peptide in complex with human FcRn was solved to 2.6 A resolution. The structure shows that the peptide binds to human FcRn at the same general binding site as does the Fc domain of IgG. The data correlate well with structure-activity relationship data relating to how the peptide family binds to human FcRn. In addition, the x-ray crystal structure of a representative dimeric peptide in complex with human FcRn shows how the bivalent ligand can bridge two FcRn molecules, which may be relevant to the mechanism by which the dimeric peptides inhibit FcRn and increase IgG catabolism in vivo. Modeling of the peptide:FcRn structure as compared with available structural data on Fc and FcRn suggest that the His-6 and Phe-7 (peptide) partially mimic the interaction of His-310 and Ile-253 (Fc) in binding to FcRn, but using a different backbone topology.

Organizational Affiliation

Biogen Idec, Syntonix Subsidiary, Waltham, Massachusetts 02451, USA. adam.mezo@biogenidec.com

Macromolecule Content

Total Structure Weight: 169.21 kDa
Atom Count: 11,241
Modeled Residue Count: 1,471
Deposited Residue Count: 1,496
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG receptor FcRn large subunit p51	A, C, E, G	267	Homo sapiens	Mutation(s): 0 Gene Names: FCGRT, FCRN
UniProt & NIH Common Fund Data Resources
Find proteins for P55899 (Homo sapiens) Explore P55899 Go to UniProtKB: P55899
PHAROS: P55899 GTEx: ENSG00000104870
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55899
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D, F, H	99	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DIMERIC PEPTIDE INHIBITOR	I, J	16	N/A	Mutation(s): 0

Small Molecules

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LE1 Query on LE1	I, J	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ S		VAL
MLE Query on MLE	I, J	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
SAR Query on SAR	I, J	PEPTIDE LINKING	C₃ H₇ N O₂		GLY

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000816 Query on PRD_000816	I, J	DIMERIC PEPTIDE INHIBITOR	Polypeptide / Inhibitor		Interactions Focus chain I Focus chain J Interactions & Density Focus chain I Focus chain J

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.397 (Depositor), 0.395 (DCC)
R-Value Work: 0.314 (Depositor), 0.306 (DCC)
R-Value Observed: 0.318 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.05	α = 90
b = 158.431	β = 90.11
c = 82.539	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-06-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-08-24
Changes: Derived calculations
Version 1.3: 2012-12-12
Changes: Other
Version 1.4: 2022-05-04
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description
Version 1.6: 2023-11-22
Changes: Data collection