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

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Basic information

Entry
Database: PDB / ID: 7sbg
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


actin monomer binding / cell cortex / cytoskeleton
Similarity search - Function
Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHevea brasiliensis (rubber tree)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsRodriguez-Romero, A. / Garcia-Ramirez, B.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)087163 Mexico
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2006
Title: HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.
Authors: Minor, W. / Cymborowski, M. / Otwinowski, Z. / Chruszcz, M.
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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)62,0494
Polymers61,4793
Non-polymers5711
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-16 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.325, 71.450, 132.518
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: Hybrydome
#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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
Has ligand of interestN
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: 1.9 Å3/Da / Density % sol: 35.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 0.2 M lithium acetate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.23→40.22 Å / Num. obs: 7675 / % possible obs: 98.85 % / Redundancy: 1.8 % / Biso Wilson estimate: 89.28 Å2 / CC1/2: 0.993 / Net I/σ(I): 16.65
Reflection shellResolution: 3.23→3.35 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.432 / Num. unique obs: 749 / CC1/2: 0.67 / % possible all: 91.89

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7SBD

7sbd


Resolution: 3.34→37.57 Å / SU ML: 0.5174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2978 979 12.99 %Random selection
Rwork0.2453 6560 --
obs0.2525 7539 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.1 Å2
Refinement stepCycle: LAST / Resolution: 3.34→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 38 0 3759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293856
X-RAY DIFFRACTIONf_angle_d0.62525304
X-RAY DIFFRACTIONf_chiral_restr0.0438611
X-RAY DIFFRACTIONf_plane_restr0.0049695
X-RAY DIFFRACTIONf_dihedral_angle_d6.2617602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.510.42721330.2994888X-RAY DIFFRACTION94.89
3.51-3.730.35471380.2548932X-RAY DIFFRACTION99.63
3.73-4.020.27671370.2591922X-RAY DIFFRACTION98.51
4.02-4.430.29761340.2325927X-RAY DIFFRACTION98.33
4.43-5.060.27671400.2123919X-RAY DIFFRACTION98.24
5.07-6.370.29011440.2547952X-RAY DIFFRACTION99.1
6.38-40.220.27881530.2461020X-RAY DIFFRACTION99.49

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