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- PDB-3fru: NEONATAL FC RECEPTOR, PH 6.5 -

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Basic information

Entry
Database: PDB / ID: 3fru
TitleNEONATAL FC RECEPTOR, PH 6.5
Components
  • BETA-2-MICROGLOBULIN
  • NEONATAL FC RECEPTOR
KeywordsCOMPLEX (IMMUNOGLOBULIN/BINDING PROTEIN) / COMPLEX (IMMUNOGLOBULIN-BINDING PROTEIN) / COMPLEX (IMMUNOGLOBULIN-BINDING PROTEIN) complex
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / IgG receptor activity / IgG binding / Neutrophil degranulation / humoral immune response ...Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / IgG receptor activity / IgG binding / Neutrophil degranulation / humoral immune response / beta-2-microglobulin binding / response to cadmium ion / cellular response to iron ion / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / response to xenobiotic stimulus / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / protein homodimerization activity / extracellular space / identical protein binding
Similarity search - Function
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 ...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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Beta-2-microglobulin / IgG receptor FcRn large subunit p51
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsVaughn, D.E. / Burmeister, W.P. / Bjorkman, P.J.
Citation
Journal: Structure / Year: 1998
Title: Structural basis of pH-dependent antibody binding by the neonatal Fc receptor.
Authors: Vaughn, D.E. / Bjorkman, P.J.
#1: Journal: Nature / Year: 1994
Title: Crystal Structure at 2.2 A Resolution of the Mhc-Related Neonatal Fc Receptor
Authors: Burmeister, W.P. / Gastinel, L.N. / Simister, N.E. / Blum, M.L. / Bjorkman, P.J.
History
DepositionDec 22, 1997Processing site: BNL
SupersessionJun 10, 1998ID: 1FRU
Revision 1.0Jun 10, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEONATAL FC RECEPTOR
B: BETA-2-MICROGLOBULIN
C: NEONATAL FC RECEPTOR
D: BETA-2-MICROGLOBULIN
E: NEONATAL FC RECEPTOR
F: BETA-2-MICROGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,31515
Polymers125,9266
Non-polymers3,3899
Water11,169620
1
A: NEONATAL FC RECEPTOR
B: BETA-2-MICROGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7277
Polymers41,9752
Non-polymers1,7525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-10 kcal/mol
Surface area20420 Å2
MethodPISA
2
C: NEONATAL FC RECEPTOR
D: BETA-2-MICROGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5355
Polymers41,9752
Non-polymers1,5593
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint4 kcal/mol
Surface area20300 Å2
MethodPISA
3
E: NEONATAL FC RECEPTOR
F: BETA-2-MICROGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0533
Polymers41,9752
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-17 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.500, 191.700, 149.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHIS ENTRY CONSISTS OF THREE FCRN HETERODIMERS AS THEY ARE ARRANGED IN THE ASYMMETRIC UNIT. THE HEAVY CHAINS COMPRISE RESIDUES A 1 - A 269, C 1 - C 269, AND E 5 - E 269. WITHIN EACH HEAVY CHAIN THERE ARE THREE DOMAINS: ALPHA1 (1 - 87), ALPHA2 (88 - 179) AND ALPHA3 (179 - 269). THE LIGHT CHAINS ARE B 1 - B 99 (ASSOCIATED WITH HEAVY CHAIN A), D 1 - D 99 (ASSOCIATED WITH HEAVY CHAIN C) AND F 1 - F 99 (ASSOCIATED WITH HEAVY CHAIN E).

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein NEONATAL FC RECEPTOR / FCRN / BRAMBELL RECEPTOR


Mass: 30322.887 Da / Num. of mol.: 3 / Fragment: EXTRACELLULAR LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GLUTAMINE SYNTHETASE SELECTION / Cell line (production host): CHO-K1 / Cellular location (production host): SECRETED / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P13599
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11652.282 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GLUTAMINE SYNTHETASE SELECTION / Cell line (production host): CHO-K1 / Cellular location (production host): SECRETED / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P07151

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Sugars , 3 types, 4 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...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


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6DManpb1-4DGlcpNAca1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,7,6/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-2-3-4-1-5-6/a4-b1_a6-g1_b4-c1_c6-d1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...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


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-2DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-4-5-6/a4-b1_a6-g1_b4-c1_c6-d1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 625 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 66 %
Crystal growpH: 6.5 / Details: PH 6.5
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMPIPES1drop
30.02 %1dropNaN3
415 %PEG30001reservoir
5100 mMTris-HCl1reservoir
6100 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 83821 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Num. measured all: 436000

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
CCP4model building
CNSDEVELOPMENTALrefinement
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 -5 %RANDOM
Rwork0.232 ---
obs0.232 83821 86 %-
Solvent computationSolvent model: FLAT / Bsol: 82.37 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.408 Å20 Å20 Å2
2--13.022 Å20 Å2
3----5.614 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8877 0 220 620 9717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev position: 30 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2PARAM3.CHO
Software
*PLUS
Name: 'CNS DEVELOPMENTAL' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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