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- PDB-8s4k: Crystal structure of Fab-2B1 in complex with rocuronium -

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Basic information

Entry
Database: PDB / ID: 8s4k
TitleCrystal structure of Fab-2B1 in complex with rocuronium
Components
  • Fab-2B1 VH
  • Fab-2B1 VL
KeywordsIMMUNE SYSTEM / NeuroMuscular Blocking Agents Rocuronium-induced anaphylaxis
Function / homologyrocuronium
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSaul, F.A. / Haouz, A. / Bruhns, P.
Funding support France, European Union, 3items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM)EQU202203014631 France
Agence Nationale de la Recherche (ANR)ANR-21-CE15-0027 France
European Research Council (ERC)ERC-2013-CoG 616050European Union
CitationJournal: Sci Transl Med / Year: 2024
Title: Rocuronium-specific antibodies drive perioperative anaphylaxis but can also function as reversal agents in preclinical models.
Authors: Dejoux, A. / Zhu, Q. / Ganneau, C. / Goff, O.R. / Godon, O. / Lemaitre, J. / Relouzat, F. / Huetz, F. / Sokal, A. / Vandenberghe, A. / Pecalvel, C. / Hunault, L. / Derenne, T. / Gillis, C.M. ...Authors: Dejoux, A. / Zhu, Q. / Ganneau, C. / Goff, O.R. / Godon, O. / Lemaitre, J. / Relouzat, F. / Huetz, F. / Sokal, A. / Vandenberghe, A. / Pecalvel, C. / Hunault, L. / Derenne, T. / Gillis, C.M. / Iannascoli, B. / Wang, Y. / Rose, T. / Mertens, C. / Nicaise-Roland, P. / England, P. / Mahevas, M. / de Chaisemartin, L. / Le Grand, R. / Letscher, H. / Saul, F. / Pissis, C. / Haouz, A. / Reber, L.L. / Chappert, P. / Jonsson, F. / Ebo, D.G. / Millot, G.A. / Bay, S. / Chollet-Martin, S. / Gouel-Cheron, A. / Bruhns, P.
History
DepositionFeb 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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-2B1 VH
L: Fab-2B1 VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4294
Polymers49,6612
Non-polymers7682
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-23 kcal/mol
Surface area19070 Å2
Unit cell
Length a, b, c (Å)161.568, 40.517, 69.772
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-331-

HOH

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Components

#1: Antibody Fab-2B1 VH


Mass: 25359.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab-2B1 VL


Mass: 24301.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 70% (v/v) MPD 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979261 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979261 Å / Relative weight: 1
ReflectionResolution: 1.6→68.63 Å / Num. obs: 59091 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.996 / Net I/σ(I): 7.9
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 8520 / CC1/2: 0.666

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.466 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20551 1198 2 %RANDOM
Rwork0.1785 ---
obs0.17907 57787 99.72 %-
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: 26.518 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20.4 Å2
2---0.72 Å20 Å2
3---1.88 Å2
Refinement stepCycle: 1 / Resolution: 1.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 46 341 3628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173047
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.674634
X-RAY DIFFRACTIONr_angle_other_deg1.4191.67126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3835421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29222.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9515542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7281513
X-RAY DIFFRACTIONr_chiral_restr0.1750.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
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_it2.1562.5891690
X-RAY DIFFRACTIONr_mcbond_other2.1512.5881689
X-RAY DIFFRACTIONr_mcangle_it3.0353.8742106
X-RAY DIFFRACTIONr_mcangle_other3.0363.8752107
X-RAY DIFFRACTIONr_scbond_it3.3542.9311703
X-RAY DIFFRACTIONr_scbond_other3.3532.9311703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0544.2462526
X-RAY DIFFRACTIONr_long_range_B_refined6.67231.4353652
X-RAY DIFFRACTIONr_long_range_B_other6.52731.0613602
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.62 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.439 45 -
Rwork0.35 2029 -
obs--93.09 %

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