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- PDB-1rpq: High Affinity IgE Receptor (alpha chain) Complexed with Tight-Bin... -

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Basic information

Entry
Database: PDB / ID: 1rpq
TitleHigh Affinity IgE Receptor (alpha chain) Complexed with Tight-Binding E131 'zeta' Peptide from Phage Display
Components
  • High affinity immunoglobulin epsilon receptor alpha-subunit precursor
  • Peptide E131
KeywordsMEMBRANE PROTEIN / receptor-peptide complex
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
triacetyl-beta-chitotriose / CITRIC ACID / High affinity immunoglobulin epsilon receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStamos, J. / Eigenbrot, C. / Nakamura, G.R. / Reynolds, M.E. / Yin, J.P. / Lowman, H.B. / Fairbrother, W.J. / Starovasnik, M.A.
Citation
Journal: Structure / Year: 2004
Title: Convergent Recognition of the IgE Binding Site on the High-Affinity IgE Receptor.
Authors: Stamos, J. / Eigenbrot, C. / Nakamura, G.R. / Reynolds, M.E. / Yin, J.P. / Lowman, H.B. / Fairbrother, W.J. / Starovasnik, M.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Stable "Zeta" Peptides that Act as Potent Antagonists of the High-Affinity Ige Receptor
Authors: Nakamura, G.R. / Reynolds, M.E. / Chen, Y.M. / Starovasnik, M.A. / Lowman, H.B.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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 precursor
B: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
C: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
D: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
W: Peptide E131
X: Peptide E131
Y: Peptide E131
Z: Peptide E131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,56528
Polymers92,0118
Non-polymers9,55520
Water0
1
A: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
W: Peptide E131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4457
Polymers23,0032
Non-polymers2,4425
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint22 kcal/mol
Surface area12770 Å2
MethodPISA
2
B: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
X: Peptide E131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3496
Polymers23,0032
Non-polymers2,3464
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint21 kcal/mol
Surface area12530 Å2
MethodPISA
3
C: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
Y: Peptide E131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3387
Polymers23,0032
Non-polymers2,3355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint8 kcal/mol
Surface area12420 Å2
MethodPISA
4
D: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
Z: Peptide E131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4348
Polymers23,0032
Non-polymers2,4316
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint12 kcal/mol
Surface area12700 Å2
MethodPISA
5
A: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
C: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
W: Peptide E131
Y: Peptide E131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,78314
Polymers46,0054
Non-polymers4,77710
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint17 kcal/mol
Surface area23060 Å2
MethodPISA
6
B: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
D: High affinity immunoglobulin epsilon receptor alpha-subunit precursor
X: Peptide E131
Z: Peptide E131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,78314
Polymers46,0054
Non-polymers4,77710
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint21 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.700, 149.700, 104.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDWXYZ

#1: Protein
High affinity immunoglobulin epsilon receptor alpha-subunit precursor / FcERI / IgE Fc receptor / alpha-subunit / Fc-epsilon RI-alpha


Mass: 20462.738 Da / Num. of mol.: 4 / Fragment: alpha chain extracellular domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCER1A, FCE1A / Plasmid: pAcGP67B / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12319
#2: Protein/peptide
Peptide E131


Mass: 2539.898 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Random peptide sequences displayed on phage, selected for binding to Fc(epsilon)RI(alpha)

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Sugars , 5 types, 16 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Polysaccharide
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-4]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c4-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(4+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 4
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
#6: 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.: 2
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
#7: 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.: 4
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 , 2 types, 4 molecules

#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7

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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: 4.23 Å3/Da / Density % sol: 70.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 2000 monomethyl ether, ammonium sulfate, sodium citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 5, 2001
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 30473 / Num. obs: 30473 / % possible obs: 96.5 % / Observed criterion σ(F): -10 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 85.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / Num. unique all: 2644 / % possible all: 85

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Processing

Software
NameVersionClassification
X-PLOR98.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F2Q

1f2q


Resolution: 3→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.349 968 3.2 %RANDOM
Rwork0.294 ---
all0.296 30473 --
obs0.294 30473 96.5 %-
Displacement parametersBiso mean: 70.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2---0.08 Å20 Å2
3----2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6125 0 632 0 6757
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_mcbond_it2.533
X-RAY DIFFRACTIONx_mcangle_it4.423
X-RAY DIFFRACTIONx_scbond_it2.443
X-RAY DIFFRACTIONx_scangle_it3.893
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 2.7 Å2 / Weight Biso : 3 / Weight position: 1000

Ens-IDDom-IDNCS model detailsRms dev position (Å)
11RESTRAINED, PARTS OF CHAINS A, B, C, D0
220.01
330.01
440.01
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
3-3.110.433813.10.38825630.048264485
3.11-3.230.41880.37304996.5
3.23-3.380.361020.35306497
3.38-3.560.35840.33305096.6
3.56-3.780.36900.3308797.8
3.78-4.070.32970.28307897.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MSI_XPLOR_PARHCSDX.PROMSI_XPLOR_TOPHCSDX.PRO
X-RAY DIFFRACTION2MSI_XPLOR_PARAM3.CHOMSI_XPLOR_TOPH3.CHO
X-RAY DIFFRACTION3PARAM.SO4
X-RAY DIFFRACTION4CIT.PAR

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