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- PDB-5nh3: CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING ... -

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Basic information

Entry
Database: PDB / ID: 5nh3
TitleCRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV
Components
  • (anti-human ActRIIB mAb BYM338 Fv ...) x 2
  • Activin receptor type-2A
KeywordsTRANSFERASE / OTHER / EPITOPE MAPPING
Function / homology
Function and homology information


inhibin binding / Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / activin receptor activity / TGFBR3 regulates activin signaling / penile erection / positive regulation of activin receptor signaling pathway / sperm ejaculation / Sertoli cell proliferation / embryonic skeletal system development ...inhibin binding / Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / activin receptor activity / TGFBR3 regulates activin signaling / penile erection / positive regulation of activin receptor signaling pathway / sperm ejaculation / Sertoli cell proliferation / embryonic skeletal system development / activin receptor complex / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / transforming growth factor beta receptor activity, type III / activin binding / pattern specification process / cellular response to BMP stimulus / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / Signaling by NODAL / gastrulation with mouth forming second / regulation of nitric oxide biosynthetic process / determination of left/right symmetry / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / growth factor binding / mesoderm development / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of erythrocyte differentiation / PDZ domain binding / cellular response to growth factor stimulus / osteoblast differentiation / positive regulation of protein phosphorylation / spermatogenesis / receptor complex / protein serine/threonine kinase activity / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / identical protein 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 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Activin receptor type-2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsScheufler, C.
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 21, 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: Data collection / Polymer sequence / Category: chem_comp / entity_poly
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Oct 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
A: Activin receptor type-2A
B: Activin receptor type-2A
H: anti-human ActRIIB mAb BYM338 Fv heavy-chain
I: anti-human ActRIIB mAb BYM338 Fv heavy-chain
L: anti-human ActRIIB mAb BYM338 Fv light-chain
M: anti-human ActRIIB mAb BYM338 Fv light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,32310
Polymers80,2356
Non-polymers1,0884
Water6,503361
1
A: Activin receptor type-2A
H: anti-human ActRIIB mAb BYM338 Fv heavy-chain
L: anti-human ActRIIB mAb BYM338 Fv light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5605
Polymers40,1173
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-15 kcal/mol
Surface area14550 Å2
MethodPISA
2
B: Activin receptor type-2A
I: anti-human ActRIIB mAb BYM338 Fv heavy-chain
M: anti-human ActRIIB mAb BYM338 Fv light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7635
Polymers40,1173
Non-polymers6462
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-12 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.330, 108.207, 100.685
Angle α, β, γ (deg.)90.00, 98.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HILM

#2: Antibody anti-human ActRIIB mAb BYM338 Fv heavy-chain / MOR08159_germlined Fv


Mass: 13406.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody anti-human ActRIIB mAb BYM338 Fv light-chain / MOR08159_germlined Fv


Mass: 12513.700 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein / Non-polymers , 2 types, 363 molecules AB

#1: Protein Activin receptor type-2A / Activin receptor type IIA / ACTRIIA


Mass: 14196.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2A, ACVR2 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
References: UniProt: P27037, receptor protein serine/threonine kinase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate tribasic dihydrate pH3.5 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 38338 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45.93 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.9
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.11.4refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NGV

5ngv


Resolution: 2.35→47.55 Å / Cor.coef. Fo:Fc: 0.9448 / Cor.coef. Fo:Fc free: 0.9248 / SU R Cruickshank DPI: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.22 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 1917 5 %RANDOM
Rwork0.1658 ---
obs0.1679 38338 97.87 %-
Displacement parametersBiso mean: 39.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.8423 Å20 Å2-3.6651 Å2
2---8.6539 Å20 Å2
3---5.8116 Å2
Refine analyzeLuzzati coordinate error obs: 0.245 Å
Refinement stepCycle: LAST / Resolution: 2.35→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 70 361 5247
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015040HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.16861HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1645SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes753HARMONIC5
X-RAY DIFFRACTIONt_it5040HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion15.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion664SEMIHARMONIC5
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_contact5546SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.234 146 4.99 %
Rwork0.203 2777 -
all0.2047 2923 -
obs--97.87 %
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)
13.24051.2940.07511.9216-0.24516.5312-0.19820.0437-0.1969-0.17870.0285-0.17980.09660.28390.1697-0.117-0.00540.089-0.05270.0041-0.135421.991619.840418.5369
22.8191-0.6538-0.4731.5991.20835.71850.058-0.06840.0406-0.1703-0.0816-0.0857-0.27930.13080.0236-0.10990.00640.0495-0.0251-0.0157-0.14418.9485-24.2590.7904
32.81810.1814-0.82351.6531-0.38872.4875-0.06370.0974-0.0615-0.087-0.01030.18030.0598-0.22380.0741-0.0770.0025-0.0211-0.0042-0.0199-0.07323.582720.019934.2852
43.3460.2162-1.06211.2825-0.02162.7814-0.04980.2148-0.1897-0.0001-0.08820.16550.0637-0.37060.138-0.11110.0038-0.01480.0424-0.0792-0.09870.5649-25.332616.66
51.29050.1652-0.26741.34710.90992.7605-0.04310.09230.0059-0.0086-0.00720.013-0.23740.09410.0503-0.0419-0.0072-0.0259-0.02160.0155-0.065515.742733.354846.7205
61.4294-0.5767-0.32912.11390.8122.62620.00080.13280.05980.0683-0.0550.028-0.2594-0.03220.0542-0.0346-0.0026-0.0153-0.0222-0.0056-0.075112.7485-13.078330.2326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ H|* }
4X-RAY DIFFRACTION4{ I|* }
5X-RAY DIFFRACTION5{ L|* }
6X-RAY DIFFRACTION6{ M|* }

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