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- PDB-4n0f: Human FcRn complexed with human serum albumin -

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Basic information

Entry
Database: PDB / ID: 4n0f
TitleHuman FcRn complexed with human serum albumin
Components
  • Beta-2-microglobulin
  • IgG receptor FcRn large subunit p51
  • Serum albumin
KeywordsIMMUNE SYSTEM / alpha/beta / receptor / IgG constant domain / membrane
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / bilirubin transport / Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / IgG binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / bilirubin transport / Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / IgG binding / molecular carrier activity / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / beta-2-microglobulin binding / Scavenging of heme from plasma / toxic substance binding / Recycling of bile acids and salts / platelet alpha granule lumen / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / fatty acid binding / cellular response to starvation / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / Post-translational protein phosphorylation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / HFE-transferrin receptor complex / Cytoprotection by HMOX1 / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / response to nutrient levels / negative regulation of neurogenesis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / MHC class II protein complex binding / T cell differentiation in thymus / Platelet degranulation / DAP12 signaling / pyridoxal phosphate binding / late endosome membrane / negative regulation of neuron projection development / protein refolding / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / blood microparticle / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / copper ion binding / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin ...Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Albumin / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsOganesyan, V. / Wu, H. / Dall'Acqua, W.F.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Insights into Neonatal Fc Receptor-based Recycling Mechanisms.
Authors: Oganesyan, V. / Damschroder, M.M. / Cook, K.E. / Li, Q. / Gao, C. / Wu, H. / Dall'acqua, W.F.
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Other
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
D: Serum albumin
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
G: Serum albumin
H: IgG receptor FcRn large subunit p51
I: Beta-2-microglobulin
J: Serum albumin
K: IgG receptor FcRn large subunit p51
L: Beta-2-microglobulin
M: Serum albumin


Theoretical massNumber of molelcules
Total (without water)433,76112
Polymers433,76112
Non-polymers00
Water00
1
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
D: Serum albumin


Theoretical massNumber of molelcules
Total (without water)108,4403
Polymers108,4403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-23 kcal/mol
Surface area44080 Å2
MethodPISA
2
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
G: Serum albumin


Theoretical massNumber of molelcules
Total (without water)108,4403
Polymers108,4403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-24 kcal/mol
Surface area44040 Å2
MethodPISA
3
H: IgG receptor FcRn large subunit p51
I: Beta-2-microglobulin
J: Serum albumin


Theoretical massNumber of molelcules
Total (without water)108,4403
Polymers108,4403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-25 kcal/mol
Surface area44190 Å2
MethodPISA
4
K: IgG receptor FcRn large subunit p51
L: Beta-2-microglobulin
M: Serum albumin


Theoretical massNumber of molelcules
Total (without water)108,4403
Polymers108,4403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-24 kcal/mol
Surface area44180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.469, 115.925, 186.237
Angle α, β, γ (deg.)90.00, 104.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21E
12A
22H
13A
23K
14B
24F
15B
25I
16B
26L
17D
27G
18D
28J
19D
29M
110E
210H
111E
211K
112F
212I
113F
213L
114G
214J
115G
215M
116H
216K
117I
217L
118J
218M

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLEULEUAA4 - 2671 - 264
21HISHISLEULEUED4 - 2671 - 264
12HISHISLEULEUAA4 - 2671 - 264
22HISHISLEULEUHG4 - 2671 - 264
13HISHISLEULEUAA4 - 2671 - 264
23HISHISLEULEUKJ4 - 2671 - 264
14ILEILEMETMETBB1 - 991 - 99
24ILEILEMETMETFE1 - 991 - 99
15ILEILEMETMETBB1 - 991 - 99
25ILEILEMETMETIH1 - 991 - 99
16ILEILEMETMETBB1 - 991 - 99
26ILEILEMETMETLK1 - 991 - 99
17HISHISLEULEUDC3 - 5853 - 585
27HISHISLEULEUGF3 - 5853 - 585
18HISHISLEULEUDC3 - 5853 - 585
28HISHISLEULEUJI3 - 5853 - 585
19HISHISLEULEUDC3 - 5853 - 585
29HISHISLEULEUML3 - 5853 - 585
110HISHISLEULEUED4 - 2671 - 264
210HISHISLEULEUHG4 - 2671 - 264
111HISHISLEULEUED4 - 2671 - 264
211HISHISLEULEUKJ4 - 2671 - 264
112ILEILEMETMETFE1 - 991 - 99
212ILEILEMETMETIH1 - 991 - 99
113ILEILEMETMETFE1 - 991 - 99
213ILEILEMETMETLK1 - 991 - 99
114HISHISLEULEUGF3 - 5853 - 585
214HISHISLEULEUJI3 - 5853 - 585
115HISHISLEULEUGF3 - 5853 - 585
215HISHISLEULEUML3 - 5853 - 585
116HISHISLEULEUHG4 - 2671 - 264
216HISHISLEULEUKJ4 - 2671 - 264
117ILEILEMETMETIH1 - 991 - 99
217ILEILEMETMETLK1 - 991 - 99
118HISHISLEULEUJI3 - 5853 - 585
218HISHISLEULEUML3 - 5853 - 585

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Protein
IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 30120.838 Da / Num. of mol.: 4 / Fragment: unp residues 27-297 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55899
#2: Protein
Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 4 / Fragment: unp residues 21-119 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61769
#3: Protein
Serum albumin


Mass: 66571.219 Da / Num. of mol.: 4 / Fragment: unp residues 25-609 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.2
Details: 4% Tacsimate, pH 4.0, 12% PEG3350, 30 mM Sodium Acetate, pH 5.2, HSA/FcRn 10 mg/ml, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 110127 / Num. obs: 110017 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.997 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26003 5501 5 %RANDOM
Rwork0.22325 ---
obs0.22511 104460 99.14 %-
all-110127 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.372 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å20 Å20.61 Å2
2---2 Å20 Å2
3---4.92 Å2
Refinement stepCycle: LAST / Resolution: 3.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30181 0 0 0 30181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0230988
X-RAY DIFFRACTIONr_bond_other_d0.0050.0221568
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.96241956
X-RAY DIFFRACTIONr_angle_other_deg1.143.00652384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49553772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85924.4721476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45155424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.51515164
X-RAY DIFFRACTIONr_chiral_restr0.0830.24500
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02134324
X-RAY DIFFRACTIONr_gen_planes_other0.0040.026272
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A100540.04
12E100540.04
21A99580.06
22H99580.06
31A100530.04
32K100530.04
41B38570.06
42F38570.06
51B38310.06
52I38310.06
61B38540.04
62L38540.04
71D236490.05
72G236490.05
81D236040.05
82J236040.05
91D236190.05
92M236190.05
101E100040.04
102H100040.04
111E100530.04
112K100530.04
121F38440.06
122I38440.06
131F38660.05
132L38660.05
141G237000.04
142J237000.04
151G237650.03
152M237650.03
161H99990.04
162K99990.04
171I38490.05
172L38490.05
181J236650.04
182M236650.04
LS refinement shellResolution: 3.017→3.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 375 -
Rwork0.375 6640 -
obs--89.86 %

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