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- PDB-5nhw: CRYSTAL STRUCTURE OF THE BIMAGRUMAB Fab -

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Basic information

Entry
Database: PDB / ID: 5nhw
TitleCRYSTAL STRUCTURE OF THE BIMAGRUMAB Fab
Components
  • anti-human ActRII Bimagrumab Fab heavy-chain
  • anti-human ActRII Bimagrumab Fab light-chain
KeywordsIMMUNE SYSTEM / immunoglobulin / antibody Fab fragment / anti-Activin receptor type-2 antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsRondeau, J.-M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Blockade of activin type II receptors with a dual anti-ActRIIA/IIB antibody is critical to promote maximal skeletal muscle hypertrophy.
Authors: Morvan, F. / Rondeau, J.M. / Zou, C. / Minetti, G. / Scheufler, C. / Scharenberg, M. / Jacobi, C. / Brebbia, P. / Ritter, V. / Toussaint, G. / Koelbing, C. / Leber, X. / Schilb, A. / Witte, ...Authors: Morvan, F. / Rondeau, J.M. / Zou, C. / Minetti, G. / Scheufler, C. / Scharenberg, M. / Jacobi, C. / Brebbia, P. / Ritter, V. / Toussaint, G. / Koelbing, C. / Leber, X. / Schilb, A. / Witte, F. / Lehmann, S. / Koch, E. / Geisse, S. / Glass, D.J. / Lach-Trifilieff, E.
History
DepositionMar 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti-human ActRII Bimagrumab Fab heavy-chain
L: anti-human ActRII Bimagrumab Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1934
Polymers48,0092
Non-polymers1842
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-25 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.021, 78.016, 131.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody anti-human ActRII Bimagrumab Fab heavy-chain


Mass: 25370.207 Da / Num. of mol.: 1 / Fragment: Fab heavy-chain / Mutation: R212K
Source method: isolated from a genetically manipulated source
Details: C-terminal FLAG-His6 tag / Source: (gene. exp.) Homo sapiens (human) / Details (production host): periplasmic expression / Production host: Escherichia coli (E. coli) / Variant (production host): TG1
#2: Antibody anti-human ActRII Bimagrumab Fab light-chain


Mass: 22638.949 Da / Num. of mol.: 1 / Fragment: Fab light-chain / Mutation: C216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Details (production host): periplasmic expression / Production host: Escherichia coli (E. coli) / Variant (production host): TG1
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.61 % / Mosaicity: 1.606 ° / Mosaicity esd: 0.007 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 18% PEG 5000 MME, 50mM TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.78→100 Å / Num. obs: 44353 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.45 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.008 / Net I/σ(I): 6 / Num. measured all: 276646
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.78-1.8460.470.621100
1.84-1.9260.360.681100
1.92-260.2820.761100
2-2.1160.2260.8931100
2.11-2.246.10.191.0311100
2.24-2.426.10.1681.104199.9
2.42-2.666.30.1421.2151100
2.66-3.046.40.0991.2351100
3.04-3.836.60.0651.2341100
3.83-1006.80.0471.192199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0
Highest resolutionLowest resolution
Rotation2.5 Å41.74 Å
Translation2.5 Å41.74 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
BUSTER2.11.5refinement
PDB_EXTRACT3.22data extraction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JB5

2jb5


Resolution: 1.78→41.74 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9341 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.119 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2229 5.04 %RANDOM
Rwork0.178 ---
obs0.1794 44230 99.97 %-
Displacement parametersBiso max: 109.93 Å2 / Biso mean: 23.9 Å2 / Biso min: 7 Å2
Baniso -1Baniso -2Baniso -3
1--4.8641 Å20 Å20 Å2
2--1.8757 Å20 Å2
3---2.9885 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: final / Resolution: 1.78→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 12 433 3620
Biso mean--37.59 35.16 -
Num. residues----426
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1046SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it3268HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion435SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4003SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3268HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4454HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.2
X-RAY DIFFRACTIONt_other_torsion14.65
LS refinement shellResolution: 1.78→1.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2101 153 4.73 %
Rwork0.192 3085 -
all0.1928 3238 -
obs--99.97 %

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