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- PDB-2qlu: Crystal structure of Activin receptor type II kinase domain from human -

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Basic information

Entry
Database: PDB / ID: 2qlu
TitleCrystal structure of Activin receptor type II kinase domain from human
ComponentsActivin receptor type IIB
KeywordsTRANSFERASE / TGF-beta / ActRIIB / serine/threonine kinase receptor / Alternative splicing / ATP-binding / Disease mutation / Glycoprotein / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Serine/threonine-protein kinase / Transmembrane
Function / homology
Function and homology information


Regulation of signaling by NODAL / activin receptor activity / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / venous blood vessel development / lymphangiogenesis / trophoblast cell migration / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex ...Regulation of signaling by NODAL / activin receptor activity / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / venous blood vessel development / lymphangiogenesis / trophoblast cell migration / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex / artery development / 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 / transforming growth factor beta receptor activity, type II / transforming growth factor beta receptor activity, type III / activin binding / pattern specification process / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / Signaling by NODAL / gastrulation with mouth forming second / pancreas development / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / insulin secretion / negative regulation of cold-induced thermogenesis / anterior/posterior pattern specification / skeletal system morphogenesis / cell surface receptor protein serine/threonine kinase signaling pathway / organ growth / growth factor binding / mesoderm development / odontogenesis of dentin-containing tooth / roof of mouth 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 / intracellular iron ion homeostasis / 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 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENINE / Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHan, S.
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structure of activin receptor type IIB kinase domain from human at 2.0 Angstrom resolution
Authors: Han, S. / Loulakis, P. / Griffor, M. / Xie, Z.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activin receptor type IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1234
Polymers35,7961
Non-polymers3273
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.217, 98.217, 71.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

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Components

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


Mass: 35796.023 Da / Num. of mol.: 1 / Fragment: Protein kinase domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q13705, receptor protein serine/threonine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 45mM MES, 90mM ammonium sulfate, 11% polyethylene glycol monomethyl ether 5000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 24186 / % possible obs: 99.3 % / Redundancy: 5.76 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 2→2 Å / Redundancy: 5.33 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.8 / % possible all: 97.4

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1228 -random
Rwork0.216 ---
all0.219 ---
obs-22785 99.3 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 21 140 2539

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