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- PDB-9g6r: Fab-IP8 in complex with rocuronium -

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Basic information

Entry
Database: PDB / ID: 9g6r
TitleFab-IP8 in complex with rocuronium
Components
  • Fab-IP8 Heavy chain
  • Fab-IP8 Light chain
KeywordsIMMUNE SYSTEM / immunotherapy / anaphylaxis
Function / homologyrocuronium
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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

Downloads & links

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Assembly

Deposited unit
H: Fab-IP8 Heavy chain
L: Fab-IP8 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5653
Polymers48,0352
Non-polymers5301
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-26 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.496, 55.170, 76.892
Angle α, β, γ (deg.)90.00, 104.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab-IP8 Heavy chain


Mass: 24046.760 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-IP8 Light chain


Mass: 23988.676 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.: 354 / 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

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 60 % (w/v) MPD 0.01 M CaCl2 0.1 M Na Acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785657 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785657 Å / Relative weight: 1
ReflectionResolution: 1.72→44.3 Å / Num. obs: 48808 / % possible obs: 99.3 % / Redundancy: 8.5 % / CC1/2: 0.999 / Net I/σ(I): 13.9
Reflection shellResolution: 1.72→1.76 Å / Num. unique obs: 3369 / CC1/2: 0.706

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→39.47 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.859 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20281 1489 3.1 %RANDOM
Rwork0.16222 ---
obs0.16345 47138 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.06 Å2
2---1.71 Å20 Å2
3---1.96 Å2
Refinement stepCycle: 1 / Resolution: 1.72→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 38 354 3773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123505
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163199
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.8244770
X-RAY DIFFRACTIONr_angle_other_deg0.5681.7597430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3565439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.922512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95810561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6884.6391762
X-RAY DIFFRACTIONr_mcbond_other3.6724.6391762
X-RAY DIFFRACTIONr_mcangle_it4.6418.3242199
X-RAY DIFFRACTIONr_mcangle_other4.648.3252200
X-RAY DIFFRACTIONr_scbond_it4.6414.9791743
X-RAY DIFFRACTIONr_scbond_other4.644.9781744
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7068.9352572
X-RAY DIFFRACTIONr_long_range_B_refined8.20346.023826
X-RAY DIFFRACTIONr_long_range_B_other8.14945.253760
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.742 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.302 53 -
Rwork0.302 1701 -
obs--98.93 %

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