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- PDB-9g6s: Fab-IP2 in complex with rocuronium -

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Basic information

Entry
Database: PDB / ID: 9g6s
TitleFab-IP2 in complex with rocuronium
Components
  • Fab-IP2 H chain
  • Fab-IP2 L chain
KeywordsIMMUNE SYSTEM / Fab
Function / homologyrocuronium
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.373 Å
AuthorsHaouz, A. / Saul, F.A. / Bruhns, P.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur Institute France
CitationJournal: J.Allergy Clin.Immunol. / Year: 2025
Title: Antibody-secreting cell repertoires hold high-affinity anti-rocuronium specificities that can induce anaphylaxis in vivo.
Authors: Dejoux, A. / Zhu, Q. / Woolfe, A. / Godon, O. / Ellouze, S. / Mottet, G. / Castrillon, C. / Gillis, C. / Pecalvel, C. / Ganneau, C. / Iannascoli, B. / Lemoine, F. / Saul, F. / England, P. / ...Authors: Dejoux, A. / Zhu, Q. / Woolfe, A. / Godon, O. / Ellouze, S. / Mottet, G. / Castrillon, C. / Gillis, C. / Pecalvel, C. / Ganneau, C. / Iannascoli, B. / Lemoine, F. / Saul, F. / England, P. / Reber, L.L. / Gouel-Cheron, A. / de Chaisemartin, L. / Haouz, A. / Millot, G.A. / Bay, S. / Gerard, A. / Jonsson, F. / Chollet-Martin, S. / Bruhns, P.
History
DepositionJul 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab-IP2 H chain
L: Fab-IP2 L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0413
Polymers46,5112
Non-polymers5301
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-23 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.638, 131.638, 95.24
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody Fab-IP2 H chain


Mass: 23311.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK 293-F Cells / Production host: Homo sapiens (human)
#2: Antibody Fab-IP2 L chain


Mass: 23198.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK 293-F Cells / Production host: Homo sapiens (human)
#3: Chemical ChemComp-RBR / rocuronium


Mass: 529.774 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H53N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10 % (w/v) PEG 4K 5 %w/v 2-PropOH 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.373→114.002 Å / Num. obs: 16351 / % possible obs: 89.7 % / Redundancy: 5.5 % / CC1/2: 0.985 / Net I/σ(I): 5.6
Reflection shellResolution: 2.373→2.795 Å / Num. unique obs: 818 / CC1/2: 0.676

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.373→30.01 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.869 / SU R Cruickshank DPI: 0.696 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.717 / SU Rfree Blow DPI: 0.358 / SU Rfree Cruickshank DPI: 0.362
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 785 -RANDOM
Rwork0.2077 ---
obs0.2098 16325 42 %-
Displacement parametersBiso mean: 39.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.9397 Å20 Å20 Å2
2---0.9397 Å20 Å2
3---1.8794 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.373→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 38 122 3338
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073305HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024515HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1088SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes535HARMONIC5
X-RAY DIFFRACTIONt_it3305HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion447SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2574SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion20.63
LS refinement shellResolution: 2.373→2.69 Å
RfactorNum. reflection% reflection
Rfree0.3599 29 -
Rwork0.2887 --
obs--3.5 %

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