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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-microglobulinBeta-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 / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / IgG binding / Prednisone ADME ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / IgG binding / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / toxic substance binding / Scavenging of heme from plasma / beta-2-microglobulin binding / Recycling of bile acids and salts / cellular response to starvation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / platelet alpha granule lumen / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / fatty acid binding / Post-translational protein phosphorylation / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / Cytoprotection by HMOX1 / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / pyridoxal phosphate binding / Platelet degranulation / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / blood microparticle / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / immune response / copper ion binding / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / protein-containing complex
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 / Immunoglobulins / Immunoglobulin-like fold / 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

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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
Water0
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
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 267
2010E4 - 267
1020A4 - 267
2020H4 - 267
1030A4 - 267
2030K4 - 267
1040B1 - 99
2040F1 - 99
1050B1 - 99
2050I1 - 99
1060B1 - 99
2060L1 - 99
1070D3 - 585
2070G3 - 585
1080D3 - 585
2080J3 - 585
1090D3 - 585
2090M3 - 585
10100E4 - 267
20100H4 - 267
10110E4 - 267
20110K4 - 267
10120F1 - 99
20120I1 - 99
10130F1 - 99
20130L1 - 99
10140G3 - 585
20140J3 - 585
10150G3 - 585
20150M3 - 585
10160H4 - 267
20160K4 - 267
10170I1 - 99
20170L1 - 99
10180J3 - 585
20180M3 - 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 / 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

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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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