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- PDB-8s4h: Crystal structure of scFv-1B6 in complex with rocuronium bromide -

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Basic information

Entry
Database: PDB / ID: 8s4h
TitleCrystal structure of scFv-1B6 in complex with rocuronium bromide
Components
  • ScFv-1B6 VL
  • scFv-1B6 VH
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: 1.7 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 1.1Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: scFv-1B6 VH
B: ScFv-1B6 VL
C: scFv-1B6 VH
D: ScFv-1B6 VL
H: scFv-1B6 VH
L: ScFv-1B6 VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8149
Polymers93,2256
Non-polymers1,5893
Water14,736818
1
A: scFv-1B6 VH
B: ScFv-1B6 VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6053
Polymers31,0752
Non-polymers5301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-11 kcal/mol
Surface area10820 Å2
2
C: scFv-1B6 VH
D: ScFv-1B6 VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6053
Polymers31,0752
Non-polymers5301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-11 kcal/mol
Surface area10850 Å2
3
H: scFv-1B6 VH
L: ScFv-1B6 VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6053
Polymers31,0752
Non-polymers5301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area10800 Å2
Unit cell
Length a, b, c (Å)135.467, 165.337, 127.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody scFv-1B6 VH


Mass: 17426.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody ScFv-1B6 VL


Mass: 13648.019 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila (fruit flies)
#3: Chemical ChemComp-RBR / rocuronium


Mass: 529.774 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H53N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 818 / 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, sitting drop / Details: 30%(v/v) PEG400 0.1M MES pH6.5 0.1 M Na Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 1.7→127.52 Å / Num. obs: 156312 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.027 / Rrim(I) all: 0.084 / Χ2: 1.02 / Net I/σ(I): 16.4 / Num. measured all: 1501870
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 1.707 / Num. measured all: 70880 / Num. unique obs: 7680 / CC1/2: 0.567 / Rpim(I) all: 0.594 / Rrim(I) all: 1.808 / Χ2: 1.04 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50.01 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.724 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18783 2378 1.5 %RANDOM
Rwork0.16637 ---
obs0.16669 153886 99.96 %-
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: 31.707 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--1.17 Å20 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5477 0 114 818 6409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135748
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185088
X-RAY DIFFRACTIONr_angle_refined_deg1.991.6817804
X-RAY DIFFRACTIONr_angle_other_deg1.5321.62311848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2665685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34722.03271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38315917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7281527
X-RAY DIFFRACTIONr_chiral_restr0.2830.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021288
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_it2.8443.0122767
X-RAY DIFFRACTIONr_mcbond_other2.8433.012766
X-RAY DIFFRACTIONr_mcangle_it3.824.4953443
X-RAY DIFFRACTIONr_mcangle_other3.824.4973444
X-RAY DIFFRACTIONr_scbond_it4.4913.432981
X-RAY DIFFRACTIONr_scbond_other4.493.432982
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4374.9564362
X-RAY DIFFRACTIONr_long_range_B_refined8.18736.5036677
X-RAY DIFFRACTIONr_long_range_B_other8.05135.6476515
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.722 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.286 99 -
Rwork0.299 5647 -
obs--100 %

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