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

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Basic information

Entry
Database: PDB / ID: 5ngv
TitleCRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, ORTHORHOMBIC CRYSTAL FORM
Components
  • Activin receptor type-2B
  • anti-human ActRIIB mAb BYM338 heavy-chain
  • anti-human ActRIIB mAb BYM338 light-chain
KeywordsTRANSFERASE / 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 / activin binding / Signaling by BMP / activin receptor signaling pathway / Signaling by Activin / kinase activator activity / Signaling by NODAL / gastrulation with mouth forming second / pancreas development / determination of left/right symmetry / negative regulation of cold-induced thermogenesis / insulin secretion / skeletal system morphogenesis / 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 osteoblast differentiation / positive regulation of bone mineralization / 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 / 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: 2 Å
Model detailsORTHORHOMBIC CRYSTAL FORM
AuthorsRondeau, J.-M. / Lehmann, S.
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 20, 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activin receptor type-2B
H: anti-human ActRIIB mAb BYM338 heavy-chain
L: anti-human ActRIIB mAb BYM338 light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7454
Polymers37,5503
Non-polymers1941
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-15 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 114.170, 117.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11L-318-

HOH

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Components

#1: Protein Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


Mass: 11646.901 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING domain
Source method: isolated from a genetically manipulated source
Details: expressed as thioredoxin-His6-fusion protein with a PreScission cleavage site after the His-tag
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2B / Production host: Escherichia coli (E. coli) / Variant (production host): Shuffle
References: UniProt: Q13705, receptor protein serine/threonine kinase
#2: Antibody anti-human ActRIIB mAb BYM338 heavy-chain


Mass: 13406.904 Da / Num. of mol.: 1 / Fragment: VH
Source method: isolated from a genetically manipulated source
Details: periplasmic expression / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Variant (production host): W3110
#3: Antibody anti-human ActRIIB mAb BYM338 light-chain


Mass: 12496.670 Da / Num. of mol.: 1 / Fragment: VL
Source method: isolated from a genetically manipulated source
Details: periplasmic expression / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Variant (production host): W3110
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.4 / Details: 0.1M PHOSPHATE-CITRATE, 40% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2→17.05 Å / Num. obs: 28674 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.439 % / Biso Wilson estimate: 33.4 Å2 / Rmerge F obs: 0.146 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.08 / Χ2: 0.956 / Net I/σ(I): 14.23 / Num. measured all: 127273 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2-2.054.3310.622.1820720.706100
2.05-2.114.4760.5232.6520360.59499.9
2.11-2.174.4950.443.2119940.49999.9
2.17-2.244.4630.3613.8919310.40999.8
2.24-2.314.5070.2824.9418890.3299.9
2.31-2.394.4830.2575.2918070.29199.9
2.39-2.484.4860.226.1717620.2599.9
2.48-2.584.50.1787.5716870.20199.9
2.58-2.74.5010.1399.4316260.15899.9
2.7-2.834.4640.10811.7315580.12399.8
2.83-2.984.4880.08514.8414540.09699.9
2.98-3.164.4570.06618.9714090.07599.9
3.16-3.384.4410.04924.2213300.05699.8
3.38-3.654.4710.03731.2312440.04399.8
3.65-44.3820.03334.9211300.03899.6
4-4.474.3970.03138.9610380.03599.5
4.47-5.164.3480.02941.339280.03399.3
5.16-6.324.3240.02938.557820.03399.2
6.32-8.944.1740.02839.426270.03299.7
8.94-17.053.7760.02442.363700.02998.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å41.05 Å
Translation2.5 Å41.05 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER1.3.1phasing
BUSTER2.11.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H64

2h64


Resolution: 2→17.05 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9259 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1431 5 %RANDOM
Rwork0.1768 ---
obs0.1779 28614 99.82 %-
Displacement parametersBiso max: 144.94 Å2 / Biso mean: 43.57 Å2 / Biso min: 22.35 Å2
Baniso -1Baniso -2Baniso -3
1-7.2596 Å20 Å20 Å2
2---15.272 Å20 Å2
3---8.0124 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: final / Resolution: 2→17.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 13 174 2656
Biso mean--45.76 46.11 -
Num. residues----319
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d854SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes377HARMONIC5
X-RAY DIFFRACTIONt_it2555HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion317SEMIHARMONIC5
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_contact2898SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2555HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3465HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion17.55
LS refinement shellResolution: 2→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2238 147 4.99 %
Rwork0.2122 2799 -
all0.2128 2946 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.74181.1340.48694.15041.04173.5502-0.1370.2233-0.4642-0.41310.4762-0.6070.14550.527-0.3392-0.0718-0.01410.0691-0.1344-0.1178-0.051611.83276.699718.3884
22.1670.913-0.1531.7276-0.0161.2748-0.06680.22080.1195-0.08360.11990.0004-0.09-0.0862-0.0531-0.07630.00730.0090.0260.0119-0.07868.870229.330824.2272
31.70640.06470.20220.84040.33662.3675-0.0021-0.2577-0.09680.04290.0055-0.07120.01750.0535-0.0034-0.07130.0026-0.00950.0360.0152-0.07942.527121.780243.7457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A25 - 117
2X-RAY DIFFRACTION2{ H|* }H1 - 114
3X-RAY DIFFRACTION3{ L|* }L1 - 112

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