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- PDB-7sbd: Murine Fab/IgE in complex with profilin from Hevea brasieliensis ... -

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Basic information

Entry
Database: PDB / ID: 7sbd
TitleMurine Fab/IgE in complex with profilin from Hevea brasieliensis (Hev b 8)
Components
  • Fab/IgE Heavy chain
  • Fab/IgE Light chain
  • Profilin-2
KeywordsALLERGEN/IMMUNE SYSTEM / Antibody / Allergen / IgE/Fab fragment / complex / ALLERGEN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


sequestering of actin monomers / actin monomer binding / cell cortex / cytoskeleton
Similarity search - Function
: / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily
Similarity search - Domain/homology
Biological speciesHevea brasiliensis (rubber tree)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsRodriguez-Romero, A. / Garcia-Ramirez, B.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)087163 Mexico
CitationJournal: Commun Biol / Year: 2022
Title: A native IgE in complex with profilin provides insights into allergen recognition and cross-reactivity.
Authors: Garcia-Ramirez, B. / Mares-Mejia, I. / Rodriguez-Hernandez, A. / Cano-Sanchez, P. / Torres-Larios, A. / Ortega, E. / Rodriguez-Romero, A.
History
DepositionSep 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab/IgE Heavy chain
L: Fab/IgE Light chain
C: Profilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3744
Polymers61,4793
Non-polymers8951
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-15 kcal/mol
Surface area23740 Å2
Unit cell
Length a, b, c (Å)57.962, 77.468, 144.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Fab/IgE Heavy chain


Mass: 23226.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: Hybridome
#2: Antibody Fab/IgE Light chain


Mass: 23616.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: Hybridome
#3: Protein Profilin-2 / Pollen allergen Hev b 8.0102


Mass: 14636.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Gene: PRO2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9STB6
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2% Tacsimate, pH 6.0, 0.1 M Bis-Tris, pH 6.5, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.04→29.42 Å / Num. obs: 12929 / % possible obs: 99.02 % / Redundancy: 2 % / Biso Wilson estimate: 68.58 Å2 / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 7.12
Reflection shellResolution: 3.04→3.152 Å / Rmerge(I) obs: 0.271 / Num. unique obs: 1181 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1BAF & 5FDS

1baf

5fds


Resolution: 3.04→29.42 Å / SU ML: 0.3831 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2535 1293 10.01 %
Rwork0.2276 11627 -
obs0.2302 12920 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.99 Å2
Refinement stepCycle: LAST / Resolution: 3.04→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 60 0 4077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254176
X-RAY DIFFRACTIONf_angle_d0.6425715
X-RAY DIFFRACTIONf_chiral_restr0.0449658
X-RAY DIFFRACTIONf_plane_restr0.0043740
X-RAY DIFFRACTIONf_dihedral_angle_d5.6394638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.170.29291310.29791180X-RAY DIFFRACTION93.84
3.17-3.310.31261420.271278X-RAY DIFFRACTION99.93
3.31-3.480.32691440.25671285X-RAY DIFFRACTION100
3.48-3.70.28241420.24691288X-RAY DIFFRACTION99.79
3.7-3.990.25331420.22031273X-RAY DIFFRACTION99.86
3.99-4.390.25471460.19881306X-RAY DIFFRACTION99.86
4.39-5.020.21671430.19111299X-RAY DIFFRACTION99.86
5.02-6.310.27211480.2291326X-RAY DIFFRACTION99.8
6.32-29.420.20881550.2311392X-RAY DIFFRACTION99.49

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