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- PDB-1fp5: CRYSTAL STRUCTURE ANALYSIS OF THE HUMAN IGE-FC CEPSILON3-CEPSILON... -

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Basic information

Entry
Database: PDB / ID: 1fp5
TitleCRYSTAL STRUCTURE ANALYSIS OF THE HUMAN IGE-FC CEPSILON3-CEPSILON4 FRAGMENT.
ComponentsIGE HEAVY CHAIN EPSILON-1
KeywordsIMMUNE SYSTEM / Antibody / Fc / Immunoglobin fold / "closed" IgE-Fc
Function / homology
Function and homology information


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / type 2 immune response / immunoglobulin receptor binding / immunoglobulin complex, circulating / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / immune response / inflammatory response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWurzburg, B.A. / Garman, S.C. / Jardetzky, T.S.
CitationJournal: Immunity / Year: 2000
Title: Structure of the human IgE-Fc C epsilon 3-C epsilon 4 reveals conformational flexibility in the antibody effector domains.
Authors: Wurzburg, B.A. / Garman, S.C. / Jardetzky, T.S.
History
DepositionAug 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGE HEAVY CHAIN EPSILON-1


Theoretical massNumber of molelcules
Total (without water)24,8211
Polymers24,8211
Non-polymers00
Water2,612145
1
A: IGE HEAVY CHAIN EPSILON-1

A: IGE HEAVY CHAIN EPSILON-1


Theoretical massNumber of molelcules
Total (without water)49,6422
Polymers49,6422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)105.600, 105.600, 47.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe asymmetric unit contains one chain of the Fc homodimer. The biological dimer can be generated from chain A.

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Components

#1: Antibody IGE HEAVY CHAIN EPSILON-1 / IGE-FC


Mass: 24821.018 Da / Num. of mol.: 1 / Fragment: CEPSILON3-CEPSILON4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PACGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01854
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlIgE-Fc1drop
210 mMTris1droppH8.0
325 mMsodium acetate1reservoirpH4.6
433 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.906
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 7, 1999 / Details: 1mm x 1mm slits, 25 m from crystal
RadiationMonochromator: Si (111), cryogenically-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 12322 / Num. obs: 12322 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 33.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 10.6 / Num. unique all: 1208 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 12340 / Num. measured all: 106855
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Density for the Cepsilon4 AB loop was particularly poor, especially from residues 453-457, and this region of the loop was built sterically. The B-factors were generally higher and the ...Details: Density for the Cepsilon4 AB loop was particularly poor, especially from residues 453-457, and this region of the loop was built sterically. The B-factors were generally higher and the electron density generally poorer for the BC- DE- and FG-loops of the Cepsilon3 domain that bind to the high affinity receptor. The residue K435 sits at the interdomain interface and the side chain may partially fill a gap in the space between the domains. This is not obvious from the structure, however, as all of the atoms could not be modeled for this residue. The structure contains two cis-Prolines : P471 and P533 There are N-linked carbohydrates attached to the protein at residues N371 and N394. Some electron density is observed for the carbohydrate attached to N394, but no electron density is observed for the carbohydrate attached to N371. Carbohydrates were not modeled in the structure and so they are not present in the PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1269 10.3 %random
Rwork0.242 ---
all-12322 --
obs-12322 99.7 %-
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.735 Å20 Å20 Å2
2--2.735 Å20 Å2
3----5.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 0 145 1763
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.77
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_improper_angle_d0.951
X-RAY DIFFRACTIONc_dihedral_angle_d26.21
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it3
X-RAY DIFFRACTIONc_scangle_it3.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 11053 / σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.242 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 51.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.951
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it3
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it3.5

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