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- PDB-1lx5: Crystal Structure of the BMP7/ActRII Extracellular Domain Complex -

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Basic information

Entry
Database: PDB / ID: 1lx5
TitleCrystal Structure of the BMP7/ActRII Extracellular Domain Complex
Components
  • Activin Type II Receptor
  • bone morphogenetic protein 7
KeywordsGROWTH FACTOR/GROWTH FACTOR RECEPTOR / LIGAND-RECEPTOR COMPLEX / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / TGFBR3 regulates activin signaling / positive regulation of hyaluranon cable assembly / Signaling by Activin / inhibin-betaglycan-ActRII complex / chorio-allantoic fusion ...negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / TGFBR3 regulates activin signaling / positive regulation of hyaluranon cable assembly / Signaling by Activin / inhibin-betaglycan-ActRII complex / chorio-allantoic fusion / inhibin binding / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / Signaling by BMP / penile erection / negative regulation of striated muscle cell apoptotic process / embryonic skeletal joint morphogenesis / neural fold elevation formation / positive regulation of activin receptor signaling pathway / activin receptor activity / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of epithelial cell differentiation / embryonic camera-type eye morphogenesis / mesenchyme development / ameloblast differentiation / cellular response to oxygen-glucose deprivation / positive regulation of follicle-stimulating hormone secretion / Sertoli cell proliferation / monocyte aggregation / allantois development / sperm ejaculation / mesonephros development / BMP receptor activity / embryonic skeletal system development / regulation of removal of superoxide radicals / BMP receptor binding / activin receptor complex / mesenchymal cell differentiation / hindbrain development / pericardium morphogenesis / endocardial cushion formation / receptor protein serine/threonine kinase / pharyngeal system development / activin binding / cellular response to BMP stimulus / heart trabecula morphogenesis / activin receptor signaling pathway / embryonic pattern specification / SMAD protein signal transduction / branching involved in salivary gland morphogenesis / response to vitamin D / metanephros development / regulation of phosphorylation / negative regulation of mitotic nuclear division / gastrulation with mouth forming second / regulation of nitric oxide biosynthetic process / positive regulation of heterotypic cell-cell adhesion / negative regulation of non-canonical NF-kappaB signal transduction / determination of left/right symmetry / cartilage development / embryonic limb morphogenesis / cardiac muscle tissue development / positive regulation of dendrite development / Molecules associated with elastic fibres / anterior/posterior pattern specification / ureteric bud development / negative regulation of NF-kappaB transcription factor activity / regulation of branching involved in prostate gland morphogenesis / branching morphogenesis of an epithelial tube / negative regulation of Notch signaling pathway / cardiac septum morphogenesis / dendrite development / growth factor binding / odontogenesis of dentin-containing tooth / mesoderm development / positive regulation of SMAD protein signal transduction / negative regulation of cell cycle / mesoderm formation / negative regulation of neuron differentiation / regulation of signal transduction / epithelial to mesenchymal transition / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / coreceptor activity / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of epithelial to mesenchymal transition / positive regulation of neuron differentiation / positive regulation of brown fat cell differentiation / ossification / neuron projection morphogenesis / positive regulation of erythrocyte differentiation / axon guidance / skeletal system development / cytokine activity / PDZ domain binding / growth factor activity / cellular response to growth factor stimulus / response to peptide hormone / negative regulation of neurogenesis
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / 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 / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein 7 / Activin receptor type-2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.3 Å
AuthorsGreenwald, J. / Groppe, J. / Kwiatkowski, W. / Choe, S.
CitationJournal: Mol.Cell / Year: 2003
Title: The BMP7/ActRII Extracellular Domain Complex Provides New Insights into the Cooperative Nature of Receptor Assembly
Authors: Greenwald, J. / Groppe, J. / Gray, P. / Wiater, E. / Kwiatkowski, W. / Vale, W. / Choe, S.
History
DepositionJun 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 21, 2015Group: Refinement description
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE SEQEUNCE FOR ACVR2 IS TRUNCATED. THE PROTEIN IN THE CRYSTAL ENDS AT GLU 102.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bone morphogenetic protein 7
B: Activin Type II Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2355
Polymers27,7192
Non-polymers1,5153
Water00
1
A: bone morphogenetic protein 7
B: Activin Type II Receptor
hetero molecules

A: bone morphogenetic protein 7
B: Activin Type II Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,46910
Polymers55,4384
Non-polymers3,0316
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area9240 Å2
ΔGint19 kcal/mol
Surface area23220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.920, 140.920, 90.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThe second part of the biological assembly is generated by the two fold axis: y-x+1, y, -z+1

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Components

#1: Protein bone morphogenetic protein 7 / BMP7 / Osteogenic protein 1 / OP-1


Mass: 15699.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DHFR- / Gene: BMP7 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P18075
#2: Protein Activin Type II Receptor / ACTR-II


Mass: 12019.440 Da / Num. of mol.: 1
Fragment: Extracellular Ligand Binding Domain, C-terminal truncation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ACVR2 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168 / References: UniProt: P27038
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-4][DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-2-3/a4-b1_b4-c1_c3-d1_c4-e1_c6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(4+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 2
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
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: 4.69 Å3/Da / Density % sol: 73.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M sodium acetate, 0.1M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
21 Msodium acetate1reservoir
3100 mMimidazole1reservoirpH7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 8320 / Num. obs: 8320 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 145 Å2 / Rsym value: 0.055 / Net I/σ(I): 16.5
Reflection shellResolution: 3.3→3.42 Å / Rsym value: 0.332 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 31531 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.332

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
REFMAC5refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MIR / Resolution: 3.3→27.12 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.858 / SU B: 8.619 / SU ML: 0.151 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.949 / ESU R Free: 0.435 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 410 5 %RANDOM
Rwork0.238 ---
all0.24 8150 --
obs0.24 8150 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 69.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å2-0.93 Å20 Å2
2---1.86 Å20 Å2
3---2.78 Å2
Refinement stepCycle: LAST / Resolution: 3.3→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 100 0 1695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0211696
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9781.9932326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0883196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.94915248
X-RAY DIFFRACTIONr_chiral_restr0.1620.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021262
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3420.3901
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.5190
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3720.351
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3570.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2791.5988
X-RAY DIFFRACTIONr_mcangle_it2.51221582
X-RAY DIFFRACTIONr_scbond_it3.1243708
X-RAY DIFFRACTIONr_scangle_it5.2784.5744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 22
Rwork0.228 566
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)
111.17532.9765-4.26993.0318-1.37454.33490.1544-0.6758-0.07410.65230.0301-0.21110.00530.5906-0.18450.3536-0.0136-0.05160.203-0.07710.176579.605835.741946.6469
210.9636-2.8195-2.154911.80783.03946.36310.27720.7131-0.1724-1.0754-0.37080.3208-0.1584-0.18210.09360.36580.3626-0.11330.49550.09710.35739.712751.471248.1483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA36 - 13936 - 139
2X-RAY DIFFRACTION2BB9 - 1009 - 100
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 100 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.032
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.978
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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