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- PDB-6unp: Crystal structure of the kinase domain of BMPR2-D485G -

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Basic information

Entry
Database: PDB / ID: 6unp
TitleCrystal structure of the kinase domain of BMPR2-D485G
ComponentsBone morphogenetic protein receptor type-2
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


semi-lunar valve development / negative regulation of chondrocyte proliferation / regulation of lung blood pressure / activin receptor activity, type II / lymphatic endothelial cell differentiation / pulmonary valve development / chondrocyte development / tricuspid valve morphogenesis / negative regulation of cell proliferation involved in heart valve morphogenesis / aortic valve development ...semi-lunar valve development / negative regulation of chondrocyte proliferation / regulation of lung blood pressure / activin receptor activity, type II / lymphatic endothelial cell differentiation / pulmonary valve development / chondrocyte development / tricuspid valve morphogenesis / negative regulation of cell proliferation involved in heart valve morphogenesis / aortic valve development / BMP binding / atrial septum morphogenesis / negative regulation of muscle cell differentiation / venous blood vessel development / proteoglycan biosynthetic process / maternal placenta development / endochondral bone morphogenesis / positive regulation of cartilage development / endocardial cushion development / transforming growth factor beta receptor activity / lymphangiogenesis / mitral valve morphogenesis / BMP receptor activity / retina vasculature development in camera-type eye / positive regulation of axon extension involved in axon guidance / lung vasculature development / artery development / receptor protein serine/threonine kinase / cellular response to BMP stimulus / Signaling by BMP / endothelial cell apoptotic process / negative regulation of systemic arterial blood pressure / positive regulation of ossification / endothelial cell proliferation / limb development / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / negative regulation of vasoconstriction / lung alveolus development / growth factor binding / ventricular septum morphogenesis / blood vessel development / outflow tract morphogenesis / mesoderm formation / positive regulation of SMAD protein signal transduction / positive regulation of epithelial cell migration / blood vessel remodeling / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / clathrin-coated pit / protein tyrosine kinase binding / basal plasma membrane / cellular response to starvation / stem cell differentiation / adherens junction / negative regulation of smooth muscle cell proliferation / negative regulation of cell growth / caveola / cellular response to growth factor stimulus / osteoblast differentiation / regulation of cell population proliferation / cell differentiation / receptor complex / postsynaptic density / apical plasma membrane / cadherin binding / axon / neuronal cell body / dendrite / positive regulation of gene expression / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / ATP binding / metal ion binding / plasma membrane
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 / Protein kinase 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
ADENOSINE-5'-DIPHOSPHATE / Bone morphogenetic protein receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAgnew, C. / Jura, N.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization.
Authors: Agnew, C. / Ayaz, P. / Kashima, R. / Loving, H.S. / Ghatpande, P. / Kung, J.E. / Underbakke, E.S. / Shan, Y. / Shaw, D.E. / Hata, A. / Jura, N.
History
DepositionOct 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone morphogenetic protein receptor type-2
B: Bone morphogenetic protein receptor type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,82931
Polymers83,4442
Non-polymers2,38629
Water1,69394
1
A: Bone morphogenetic protein receptor type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,09714
Polymers41,7221
Non-polymers1,37513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bone morphogenetic protein receptor type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,73317
Polymers41,7221
Non-polymers1,01116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.497, 138.497, 109.992
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEU(chain 'A' and (resid 199 through 322 or (resid 323...AA199 - 28733 - 121
12LYSLYSPROPRO(chain 'A' and (resid 199 through 322 or (resid 323...AA289 - 366123 - 200
13GLUGLUASPASP(chain 'A' and (resid 199 through 322 or (resid 323...AA376 - 396210 - 230
14GLUGLUPROPRO(chain 'A' and (resid 199 through 322 or (resid 323...AA398 - 425232 - 259
15SERSERGLNGLN(chain 'A' and (resid 199 through 322 or (resid 323...AA428 - 495262 - 329
16ALAALAGLUGLU(chain 'A' and (resid 199 through 322 or (resid 323...AA497 - 499331 - 333
17METMETLEULEU(chain 'A' and (resid 199 through 322 or (resid 323...AA501 - 504335 - 338
18METMETTRPTRP(chain 'A' and (resid 199 through 322 or (resid 323...AA506 - 508340 - 342
21ASPASPLEULEU(chain 'B' and (resid 199 through 200 or (resid 201...BB199 - 28733 - 121
22LYSLYSPROPRO(chain 'B' and (resid 199 through 200 or (resid 201...BB289 - 366123 - 200
23GLUGLUASPASP(chain 'B' and (resid 199 through 200 or (resid 201...BB376 - 396210 - 230
24GLUGLUPROPRO(chain 'B' and (resid 199 through 200 or (resid 201...BB398 - 425232 - 259
25SERSERGLNGLN(chain 'B' and (resid 199 through 200 or (resid 201...BB428 - 495262 - 329
26ALAALAGLUGLU(chain 'B' and (resid 199 through 200 or (resid 201...BB497 - 499331 - 333
27METMETLEULEU(chain 'B' and (resid 199 through 200 or (resid 201...BB501 - 504335 - 338
28METMETTRPTRP(chain 'B' and (resid 199 through 200 or (resid 201...BB506 - 508340 - 342

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bone morphogenetic protein receptor type-2 / BMPR-2 / Bone morphogenetic protein receptor type II / BMPR-II


Mass: 41721.828 Da / Num. of mol.: 2 / Fragment: kinase domain / Mutation: D485G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR2, PPH1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13873, receptor protein serine/threonine kinase

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Non-polymers , 5 types, 123 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.68 Å3/Da / Density % sol: 66.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Na Cacodylate, pH 6.0, 0.3 M Ammonium sulfate, 22% w/v PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 2.3→49.99 Å / Num. obs: 54388 / % possible obs: 100 % / Redundancy: 20.4 % / Biso Wilson estimate: 48.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.049 / Rrim(I) all: 0.159 / Net I/σ(I): 16.3
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 21 % / Rmerge(I) obs: 2.62 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4391 / CC1/2: 0.65 / Rpim(I) all: 0.838 / Rrim(I) all: 2.752 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G2F

3g2f


Resolution: 2.3→49.99 Å / SU ML: 0.2619 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 2714 5 %
Rwork0.1885 51613 -
obs0.1897 54327 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 136 94 4977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814982
X-RAY DIFFRACTIONf_angle_d1.14296770
X-RAY DIFFRACTIONf_chiral_restr0.0597744
X-RAY DIFFRACTIONf_plane_restr0.0057856
X-RAY DIFFRACTIONf_dihedral_angle_d14.33142955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.33871530.29342678X-RAY DIFFRACTION99.93
2.34-2.390.30071490.27612693X-RAY DIFFRACTION99.89
2.39-2.440.30421390.26532650X-RAY DIFFRACTION99.89
2.44-2.490.27651260.24612718X-RAY DIFFRACTION100
2.49-2.550.26371360.24392675X-RAY DIFFRACTION99.82
2.55-2.610.25781230.24282741X-RAY DIFFRACTION100
2.61-2.680.28691300.22992681X-RAY DIFFRACTION100
2.68-2.760.23351380.21962723X-RAY DIFFRACTION100
2.76-2.850.25031610.20892657X-RAY DIFFRACTION99.89
2.85-2.950.24821320.22282734X-RAY DIFFRACTION100
2.95-3.070.26471320.2212713X-RAY DIFFRACTION100
3.07-3.210.26511280.22612718X-RAY DIFFRACTION100
3.21-3.380.24531150.2182736X-RAY DIFFRACTION100
3.38-3.590.23421590.19852702X-RAY DIFFRACTION100
3.59-3.870.18951440.17412726X-RAY DIFFRACTION100
3.87-4.250.18641530.15682731X-RAY DIFFRACTION100
4.25-4.870.1641550.13832730X-RAY DIFFRACTION100
4.87-6.130.16851780.15912748X-RAY DIFFRACTION100
6.13-49.990.18261630.16712859X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 0.508963949953 Å / Origin y: 109.173767733 Å / Origin z: -3.2511274513 Å
111213212223313233
T0.397206591493 Å2-0.0391039993286 Å20.0424087008851 Å2-0.344603059271 Å2-0.0650614258133 Å2--0.303413851476 Å2
L0.573082213808 °2-0.0987500037487 °20.0911256803157 °2-2.56634336805 °2-0.471947350331 °2--0.58004998369 °2
S0.0043702101192 Å °0.108757785784 Å °-0.0254052622361 Å °-0.354211613713 Å °-0.00403543454805 Å °-0.112158250877 Å °-0.00468512335351 Å °0.0451772871278 Å °0.00821688766491 Å °
Refinement TLS groupSelection details: all

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