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- PDB-1j88: HUMAN HIGH AFFINITY FC RECEPTOR FC(EPSILON)RI(ALPHA), TETRAGONAL ... -

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Basic information

Entry
Database: PDB / ID: 1j88
TitleHUMAN HIGH AFFINITY FC RECEPTOR FC(EPSILON)RI(ALPHA), TETRAGONAL CRYSTAL FORM 1
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 / Fc epsilon receptor (FCERI) signaling / type 2 immune response / mast cell degranulation / immunoglobulin mediated 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 / Fc epsilon receptor (FCERI) signaling / type 2 immune response / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / cell surface receptor signaling pathway / external side of plasma membrane / 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 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
High affinity immunoglobulin epsilon receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)110,48835
Polymers99,7515
Non-polymers10,73730
Water00
1
A: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7988
Polymers19,9501
Non-polymers2,8487
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)21,8467
Polymers19,9501
Non-polymers1,8966
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)22,0497
Polymers19,9501
Non-polymers2,0996
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)22,2117
Polymers19,9501
Non-polymers2,2616
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)21,5846
Polymers19,9501
Non-polymers1,6345
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.080, 145.080, 62.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2
DetailsThe biological assembly is a protein monomer with attached carbohydrate

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Components

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Protein , 1 types, 5 molecules ABCDE

#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

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Sugars , 5 types, 30 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 6
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
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 17
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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Details

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: 3.31 Å3/Da / Density % sol: 50 %
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, VAPOR DIFFUSION, HANGING DROP
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
11.4-1.6 Mammonium sulfate1reservoir
2100 mMTris1reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 21, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 21357 / Num. obs: 21357 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 79.8 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 20
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.363 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 159490
Reflection shell
*PLUS
% possible obs: 87.2 % / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F2Q

1f2q


Resolution: 3.2→30.69 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1760998.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: 300 KCAL/MOL/A^2 NCS RESTRAINTS APPLIED TO ALL PROTEIN ATOMS EXCEPT THOSE IN FLEXIBLE LOOPS, IN CRYSTAL CONTACTS, OR WITH ATTACHED CARBOHYDRATE. NCS GROUP 1 REPRESENTS DOMAIN 1; GROUP2 REPRESENTS DOMAIN2.
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1065 5 %SHELLS
Rwork0.262 ---
obs0.262 21343 97.5 %-
all-21343 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 108.5 Å2 / ksol: 0.203 e/Å3
Displacement parametersBiso mean: 126.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å20 Å2
2--2.64 Å20 Å2
3----5.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.2→30.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6905 0 701 0 7606
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it14.112
X-RAY DIFFRACTIONc_mcangle_it19.913
X-RAY DIFFRACTIONc_scbond_it18.793
X-RAY DIFFRACTIONc_scangle_it28.594
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev position (Å)Weight Biso Weight position
11X-RAY DIFFRACTION0.042300
22X-RAY DIFFRACTION0.042300
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 125 3.9 %
Rwork0.356 3107 -
obs-3232 90.4 %
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 % / Rfactor Rfree: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it3
X-RAY DIFFRACTIONc_mcangle_it3
X-RAY DIFFRACTIONc_scangle_it4
LS refinement shell
*PLUS
Rfactor Rfree: 0.393 / % reflection Rfree: 3.9 % / Rfactor Rwork: 0.356

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