3FRU

NEONATAL FC RECEPTOR, PH 6.5

PDB DOI: https://doi.org/10.2210/pdb3FRU/pdb
Entry: 3FRU supersedes: 1FRU

Classification: COMPLEX (IMMUNOGLOBULIN/BINDING PROTEIN)
Organism(s): Rattus norvegicus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 1997-12-22 Released: 1998-06-10
Deposition Author(s): Vaughn, D.E., Burmeister, W.P., Bjorkman, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.276
R-Value Work: 0.232
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structural basis of pH-dependent antibody binding by the neonatal Fc receptor.

Vaughn, D.E., Bjorkman, P.J.

(1998) Structure 6: 63-73

PubMed: 9493268 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(98)00008-2
Primary Citation of Related Structures:
3FRU

PubMed Abstract:
The neonatal Fc receptor (FcRn) mediates the transcytosis of maternal immunoglobulin G (IgG) across fetal and/or neonatal tissues for the acquisition of passive immunity. In adults, FcRn is involved in the maintenance of high serum IgG levels. Both processes are mediated by pH-dependent IgG binding to FcRn-FcRn binds to IgG with nanomolar affinity at pH 6, but shows no detectable binding at pH 7.5. At pH 6, FcRn is more thermally stable and the dissociation rate of its light chain is an order of magnitude slower than at pH 8.0. Comparison of the structures of FcRn at pH 6.5 and pH 8 allows an analysis of the structural basis for the receptor's pH-dependent ligand binding and stability.

Organizational Affiliation

Division of Biology, California Institute of Technology, Pasadena 91125, USA.

Macromolecule Content

Total Structure Weight: 129.31 kDa
Atom Count: 9,717
Modelled Residue Count: 1,104
Deposited Residue Count: 1,104
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEONATAL FC RECEPTOR	A, C, E	269	Rattus norvegicus	Mutation(s): 0 Gene Names: GLUTAMINE SYNTHETASE SELECTION
UniProt
Find proteins for P13599 (Rattus norvegicus) Explore P13599 Go to UniProtKB: P13599
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13599
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2-MICROGLOBULIN	B, D, F	99	Rattus norvegicus	Mutation(s): 0 Gene Names: GLUTAMINE SYNTHETASE SELECTION
UniProt
Find proteins for P07151 (Rattus norvegicus) Explore P07151 Go to UniProtKB: P07151
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07151
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	7		N-Glycosylation	Interactions Focus chain G
Glycosylation Resources
GlyTouCan: G13680ZF GlyCosmos: G13680ZF GlyGen: G13680ZF

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	7		N-Glycosylation	Interactions Focus chain H
Glycosylation Resources
GlyTouCan: G13380TW GlyCosmos: G13380TW GlyGen: G13380TW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C]	I [auth A], M [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	J [auth A], K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth E] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth E]	L [auth B], N [auth C], O [auth E]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.276
R-Value Work: 0.232
R-Value Observed: 0.232
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.5	α = 90
b = 191.7	β = 90
c = 149.6	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
CCP4	model building
CNS	refinement
CCP4	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1998-06-10

Deposition Author(s):

Vaughn, D.E.

Burmeister, W.P.

Bjorkman, P.J.

This entry supersedes: 1FRU

Revision History (Full details and data files)

Version 1.0: 1998-06-10
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary