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- PDB-1j89: HUMAN HIGH AFFINITY FC RECEPTOR FC(EPSILON)RI(ALPHA), TETRAGONAL ... -

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Basic information

Entry
Database: PDB / ID: 1j89
TitleHUMAN HIGH AFFINITY FC RECEPTOR FC(EPSILON)RI(ALPHA), TETRAGONAL CRYSTAL FORM 2
ComponentsHIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
KeywordsIMMUNE SYSTEM / Fc Receptor / IgE receptor / Glycoprotein
Function / homology
Function and homology information


high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / type 2 immune response / Fc epsilon receptor (FCERI) signaling / mast cell degranulation / regulation of immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization ...high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / type 2 immune response / Fc epsilon receptor (FCERI) signaling / mast cell degranulation / regulation of immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / transmembrane signaling receptor activity / cell surface receptor signaling pathway / cell surface / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
High affinity immunoglobulin epsilon receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 4.1 Å
AuthorsGarman, S.C. / Sechi, S. / Kinet, J.P. / Jardetzky, T.S.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The analysis of the human high affinity IgE receptor Fc epsilon Ri alpha from multiple crystal forms.
Authors: Garman, S.C. / Sechi, S. / Kinet, J.P. / Jardetzky, T.S.
History
DepositionMay 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
B: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
C: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
D: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
E: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,35240
Polymers99,7515
Non-polymers11,60135
Water0
1
A: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2708
Polymers19,9501
Non-polymers2,3207
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2708
Polymers19,9501
Non-polymers2,3207
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2708
Polymers19,9501
Non-polymers2,3207
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2708
Polymers19,9501
Non-polymers2,3207
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2708
Polymers19,9501
Non-polymers2,3207
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.500, 150.500, 74.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43
DetailsThe biological assembly is a protein monomer with attached carbohydrate

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Components

#1: Protein
HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT / FC(EPSILON)RI(ALPHA) / IGE FC RECEPTOR / ALPHA-SUBUNIT / FC-EPSILON RI-ALPHA


Mass: 19950.135 Da / Num. of mol.: 5 / Fragment: EXTRACELLULAR FRAGMENT
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATED PROTEIN, CHAIN A BY SUGARS F, B BY SUGARS G, C BY SUGARS H, D BY SUGARS I, E BY SUGARS J
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): LDLD.LEC1 / Organ (production host): OVARY / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P12319
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 20
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 10000, Ammonium Citrate, Sodium Chloride, pH 5.6. VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8.5 / Details: Garman, S.C., (2000) Nature, 406, 259.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 MTris1reservoir
31.4-1.6 Mammonium sulfate1reservoir
48 mMCHAPS1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 4.1→40 Å / Num. all: 11510 / Num. obs: 11510 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 204.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.4
Reflection shellResolution: 4.1→4.25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3 / % possible all: 83.2
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 25057
Reflection shell
*PLUS
% possible obs: 83.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J88

1j88


Resolution: 4.1→36.5 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2780561.23 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Synchrotron beam failed during data collection, causing poor data completeness and redundancy. 300 kcal/mol/A^2 NCS restraints applied to all atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 740 5.1 %SHELLS
Rwork0.273 ---
obs0.273 11510 86.8 %-
all-11510 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 199.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å20 Å20 Å2
2---2.89 Å20 Å2
3---5.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.91 Å
Refinement stepCycle: LAST / Resolution: 4.1→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6905 0 755 0 7660
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
Refine LS restraints NCSRms dev position: 0.04 Å / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 4.1→4.36 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 72 4 %
Rwork0.312 1729 -
obs-2208 83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.369 / % reflection Rfree: 4 % / Rfactor Rwork: 0.312

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