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- PDB-7yru: ALK2 antibody complex -

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Basic information

Entry
Database: PDB / ID: 7yru
TitleALK2 antibody complex
Components
  • Activin receptor type-1
  • antibody heavy chain
  • antibody light chain
KeywordsTRANSFERASE/IMMUNE SYSTEM / ALK2 / PROTEIN BINDING / TRANSFERASE-IMMUNE SYSTEM complex / IMMUNE SYSTEM
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition ...endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / activin receptor complex / endocardial cushion formation / smooth muscle cell differentiation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / transforming growth factor beta binding / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / ventricular septum morphogenesis / SMAD binding / germ cell development / peptide hormone binding / positive regulation of SMAD protein signal transduction / mesoderm formation / regulation of ossification / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / negative regulation of signal transduction / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / negative regulation of extrinsic apoptotic signaling pathway / cellular response to growth factor stimulus / positive regulation of peptidyl-tyrosine phosphorylation / apical part of cell / heart development / in utero embryonic development / protein kinase activity / positive regulation of cell migration / cadherin binding / phosphorylation / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKawaguchi, Y. / Nakamura, K. / Suzuki, M. / Tsuji, S. / Katagiri, T.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2023
Title: A blocking monoclonal antibody reveals dimerization of intracellular domains of ALK2 associated with genetic disorders.
Authors: Katagiri, T. / Tsukamoto, S. / Kuratani, M. / Tsuji, S. / Nakamura, K. / Ohte, S. / Kawaguchi, Y. / Takaishi, K.
History
DepositionAug 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activin receptor type-1
H: antibody heavy chain
L: antibody light chain


Theoretical massNumber of molelcules
Total (without water)59,9733
Polymers59,9733
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-34 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.048, 37.299, 118.638
Angle α, β, γ (deg.)90.000, 92.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Activin receptor type-1 / Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine- ...Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine-protein kinase receptor R1 / SKR1 / TGF-B superfamily receptor type I / TSR-I


Mass: 12327.843 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1, ACVRLK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q04771, receptor protein serine/threonine kinase
#2: Antibody antibody heavy chain


Mass: 24514.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Homo sapiens (human)
#3: Antibody antibody light chain


Mass: 23130.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 2% Tacsimate pH 7.0, 0.1 M HEPES pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→43.3 Å / Num. obs: 16127 / % possible obs: 98.3 % / Redundancy: 2.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.057 / Rrim(I) all: 0.1 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.384 / Num. unique obs: 1987 / CC1/2: 0.88 / Rpim(I) all: 0.265 / Rrim(I) all: 0.469 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.3 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 912 5.7 %RANDOM
Rwork0.2453 ---
obs0.2468 15215 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.06 Å2 / Biso mean: 49.498 Å2 / Biso min: 24.25 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-2.02 Å2
2--6.02 Å20 Å2
3----3.57 Å2
Refinement stepCycle: final / Resolution: 2.6→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 0 55 3913
Biso mean---39.76 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023960
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9495386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22924.379153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2915625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5451513
X-RAY DIFFRACTIONr_chiral_restr0.0690.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212960
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 63 -
Rwork0.385 1128 -
all-1191 -
obs--99.42 %

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