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- PDB-9g6q: scFv IP11 in complex with rocuronium -

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Basic information

Entry
Database: PDB / ID: 9g6q
TitlescFv IP11 in complex with rocuronium
Components(scFv-IP11) x 2
KeywordsIMMUNE SYSTEM / immunotherapy / anaphylaxis
Function / homologyrocuronium
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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: scFv-IP11
L: scFv-IP11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6163
Polymers27,0862
Non-polymers5301
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-10 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.879, 63.685, 80.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody scFv-IP11


Mass: 13323.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody scFv-IP11


Mass: 13762.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#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.: 288 / 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: 48.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20 % (w/v) PEG 4K 10 % (v/v) 2-PropOH 0.1 M HEPES pH 7.5

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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: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.2→50.8 Å / Num. obs: 81866 / % possible obs: 99.2 % / Redundancy: 7.2 % / CC1/2: 0.998 / Net I/σ(I): 12.1
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 3978 / CC1/2: 0.668

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→49.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.613 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18893 1579 1.9 %RANDOM
Rwork0.16825 ---
obs0.16862 80214 99.11 %-
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: 13.93 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-0 Å20 Å2
2---0.57 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.2→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 38 288 2112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161731
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.8382589
X-RAY DIFFRACTIONr_angle_other_deg0.691.7814003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.035239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.714510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99510298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2880.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
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_it1.7851.771945
X-RAY DIFFRACTIONr_mcbond_other1.7841.77945
X-RAY DIFFRACTIONr_mcangle_it2.6293.5621181
X-RAY DIFFRACTIONr_mcangle_other2.6283.5671182
X-RAY DIFFRACTIONr_scbond_it3.722.169955
X-RAY DIFFRACTIONr_scbond_other3.7182.171956
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3374.2341406
X-RAY DIFFRACTIONr_long_range_B_refined6.48115.632124
X-RAY DIFFRACTIONr_long_range_B_other6.31314.152034
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.215 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.261 61 -
Rwork0.277 2945 -
obs--97.79 %

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