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- PDB-5nhr: CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING ... -

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Basic information

Entry
Database: PDB / ID: 5nhr
TitleCRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, CUBIC CRYSTAL FORM
Components
  • Activin receptor type-2B
  • Bimagrumab Fv Light-Chain
  • Bimagrumab Fv heavy-chain
KeywordsIMMUNE SYSTEM / three-finger toxin fold / antibody Fv fragment
Function / homology
Function and homology information


Regulation of signaling by NODAL / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / activin receptor activity / venous blood vessel development / lymphangiogenesis / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex ...Regulation of signaling by NODAL / activin receptor activity, type II / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / activin receptor activity / venous blood vessel development / lymphangiogenesis / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex / artery development / receptor protein serine/threonine kinase / Signaling by BMP / activin binding / activin receptor signaling pathway / Signaling by Activin / Signaling by NODAL / kinase activator activity / gastrulation with mouth forming second / pancreas development / determination of left/right symmetry / skeletal system morphogenesis / negative regulation of cold-induced thermogenesis / insulin secretion / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / organ growth / roof of mouth development / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / blood vessel remodeling / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to glucose / protein serine/threonine/tyrosine kinase activity / post-embryonic development / kidney development / lung development / cellular response to growth factor stimulus / heart development / receptor complex / phosphorylation / protein serine/threonine kinase activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å
Model detailsCUBIC CRYSTAL FORM
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 1.2Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Bimagrumab Fv Light-Chain
H: Bimagrumab Fv heavy-chain
B: Bimagrumab Fv Light-Chain
A: Bimagrumab Fv heavy-chain
C: Activin receptor type-2B
D: Activin receptor type-2B


Theoretical massNumber of molelcules
Total (without water)75,1696
Polymers75,1696
Non-polymers00
Water00
1
L: Bimagrumab Fv Light-Chain
H: Bimagrumab Fv heavy-chain
C: Activin receptor type-2B


Theoretical massNumber of molelcules
Total (without water)37,5853
Polymers37,5853
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-19 kcal/mol
Surface area14400 Å2
MethodPISA
2
B: Bimagrumab Fv Light-Chain
A: Bimagrumab Fv heavy-chain
D: Activin receptor type-2B


Theoretical massNumber of molelcules
Total (without water)37,5853
Polymers37,5853
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-19 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.826, 187.826, 187.826
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

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Components

#1: Antibody Bimagrumab Fv Light-Chain


Mass: 12513.700 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING domain
Source method: isolated from a genetically manipulated source
Details: VL domain / Source: (gene. exp.) Homo sapiens (human) / Details (production host): C-terminal Strep tag
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
#2: Antibody Bimagrumab Fv heavy-chain


Mass: 13423.935 Da / Num. of mol.: 2 / Fragment: VH
Source method: isolated from a genetically manipulated source
Details: periplasmic expression / Source: (gene. exp.) Homo sapiens (human) / Details (production host): C-terminal His6 tag
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
#3: Protein Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


Mass: 11646.901 Da / Num. of mol.: 2 / Fragment: VL, UNP residues 24-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2B / Details (production host): Thioredoxin-fusion / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): Shuffle
References: UniProt: Q13705, receptor protein serine/threonine kinase

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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: 7.35 Å3/Da / Mosaicity: 0.707 ° / Mosaicity esd: 0.003 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6 / Details: 1.4M AMMONIUM SULFATE, 0.1M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→100 Å / Num. obs: 28995 / % possible obs: 90.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.093 / Χ2: 1.066 / Net I/σ(I): 8.2 / Num. measured all: 96966
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
3.35-3.473.20.4820.797193.9
3.47-3.613.20.3320.779193.3
3.61-3.773.30.2550.978192.9
3.77-3.973.30.1830.987192.4
3.97-4.223.40.1211.053191.7
4.22-4.553.40.0881.299191.3
4.55-53.40.0751.274190.2
5-5.733.40.0631.21189.4
5.73-7.223.50.0611.246187.6
7.22-1003.50.0320.994184

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.35 Å45.55 Å
Translation3.35 Å45.55 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
CNSrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H64

2h64


Resolution: 3.35→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.229 1421 4.4 %
Rwork0.2156 --
obs-28995 90.6 %
Displacement parametersBiso max: 112.3 Å2 / Biso mean: 72.1553 Å2 / Biso min: 45.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 0 0 4918
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d0.942
X-RAY DIFFRACTIONc_mcbond_it1.1811.5
X-RAY DIFFRACTIONc_scbond_it1.5672
X-RAY DIFFRACTIONc_mcangle_it2.0862
X-RAY DIFFRACTIONc_scangle_it2.6212.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4ion.top

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