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- PDB-3qb4: Crystal structure of a TGF-beta ligand-receptor complex -

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Basic information

Entry
Database: PDB / ID: 3qb4
TitleCrystal structure of a TGF-beta ligand-receptor complex
Components
  • Bone morphogenetic protein receptor type-1A
  • Growth/differentiation factor 5
KeywordsCYTOKINE/TRANSFERASE RECEPTOR / CYSTINE-KNOT / Ligand-receptor complex / Protein / Membrane/Extracellular / CYTOKINE-TRANSFERASE RECEPTOR complex
Function / homology
Function and homology information


neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / positive regulation of transforming growth factor beta2 production / ossification involved in bone remodeling / Mullerian duct regression / heart formation / atrioventricular node cell development / mesendoderm development ...neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / positive regulation of transforming growth factor beta2 production / ossification involved in bone remodeling / Mullerian duct regression / heart formation / atrioventricular node cell development / mesendoderm development / forelimb morphogenesis / dorsal aorta morphogenesis / tricuspid valve morphogenesis / atrioventricular valve development / cardiac right ventricle morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of muscle cell differentiation / regulation of cardiac muscle cell proliferation / pharyngeal arch artery morphogenesis / negative regulation of mesenchymal cell apoptotic process / regulation of lateral mesodermal cell fate specification / lateral mesoderm development / pituitary gland development / positive regulation of chondrocyte differentiation / mitral valve morphogenesis / negative regulation of smooth muscle cell migration / BMP receptor activity / regulation of cellular senescence / ventricular compact myocardium morphogenesis / dorsal/ventral axis specification / mesenchymal cell apoptotic process / neural crest cell development / ectoderm development / transforming growth factor beta receptor activity, type I / cardiac conduction system development / endocardial cushion formation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / cellular response to BMP stimulus / Signaling by BMP / ventricular trabecula myocardium morphogenesis / central nervous system neuron differentiation / positive regulation of BMP signaling pathway / outflow tract septum morphogenesis / dorsal/ventral pattern formation / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / positive regulation of dendrite development / positive regulation of mesenchymal cell proliferation / endocardial cushion morphogenesis / Molecules associated with elastic fibres / embryonic digit morphogenesis / ventricular septum morphogenesis / SMAD binding / odontogenesis of dentin-containing tooth / outflow tract morphogenesis / roof of mouth development / mesoderm formation / positive regulation of SMAD protein signal transduction / developmental growth / somatic stem cell population maintenance / regulation of multicellular organism growth / response to mechanical stimulus / chondrocyte differentiation / embryonic organ development / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / somitogenesis / positive regulation of cardiac muscle cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / positive regulation of epithelial cell proliferation / epithelial cell proliferation / cytokine activity / stem cell differentiation / growth factor activity / lung development / HFE-transferrin receptor complex / cellular response to growth factor stimulus / negative regulation of neurogenesis / positive regulation of miRNA transcription / negative regulation of epithelial cell proliferation / osteoblast differentiation / cell-cell signaling / angiogenesis / in utero embryonic development / negative regulation of neuron apoptotic process / cell differentiation / receptor complex / immune response / external side of plasma membrane / negative regulation of gene expression / neuronal cell body / protein serine/threonine kinase activity / dendrite / positive regulation of gene expression
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein receptor type-1A / Growth/differentiation factor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMueller, T.D. / Nickel, J. / Sebald, W.
CitationJournal: Bmc Biol. / Year: 2015
Title: GDF-5 can act as a context-dependent BMP-2 antagonist.
Authors: Klammert, U. / Mueller, T.D. / Hellmann, T.V. / Wuerzler, K.K. / Kotzsch, A. / Schliermann, A. / Schmitz, W. / Kuebler, A.C. / Sebald, W. / Nickel, J.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 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: Growth/differentiation factor 5
B: Bone morphogenetic protein receptor type-1A
C: Growth/differentiation factor 5
D: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)55,9884
Polymers55,9884
Non-polymers00
Water1,67593
1
A: Growth/differentiation factor 5
B: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)27,9942
Polymers27,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-8 kcal/mol
Surface area11260 Å2
MethodPISA
2
C: Growth/differentiation factor 5
D: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)27,9942
Polymers27,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-8 kcal/mol
Surface area11460 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-50 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.810, 62.850, 124.991
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Growth/differentiation factor 5 / GDF-5 / Cartilage-derived morphogenetic protein 1 / CDMP-1 / Radotermin


Mass: 13319.365 Da / Num. of mol.: 2 / Fragment: GDF-5, residues 387-501 / Mutation: R57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDMP1, GDF5 / Plasmid: RBSIIN25x/o / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43026
#2: Protein Bone morphogenetic protein receptor type-1A / BMP type-1A receptor / BMPR-1A / Activin receptor-like kinase 3 / ALK-3 / Serine/threonine-protein ...BMP type-1A receptor / BMPR-1A / Activin receptor-like kinase 3 / ALK-3 / Serine/threonine-protein kinase receptor R5 / SKR5


Mass: 14674.451 Da / Num. of mol.: 2 / Fragment: BMP receptor BMPR-IA, residues 24-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVRLK3, ALK3, BMPR1A / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3)
References: UniProt: P36894, receptor protein serine/threonine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2005
RadiationMonochromator: Vari-Max HighRes Cu mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→24 Å / Num. all: 22540 / Num. obs: 22044 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WAQ and chain C of 1REW

1waq

1rew


Resolution: 2.28→24 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 16.399 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24135 1128 5.1 %RANDOM
Rwork0.19748 ---
all0.19983 21466 --
obs0.19983 20852 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 75.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0.1 Å2
2---0.22 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.28→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 0 93 3108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223102
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9614229
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3455384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.3325.035141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.83915506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2571514
X-RAY DIFFRACTIONr_chiral_restr0.1270.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212372
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5951.51950
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.63123169
X-RAY DIFFRACTIONr_scbond_it4.23831152
X-RAY DIFFRACTIONr_scangle_it6.0914.51060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 92 -
Rwork0.258 1496 -
obs--96.24 %
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)
14.6584-3.59240.06317.0296-0.09781.350.23390.3791-0.6682-0.2715-0.23710.43280.2173-0.00350.00320.1006-0.0353-0.12490.1441-0.05940.3717-0.519-14.97315.823
23.419-2.5304-0.18366.08071.76251.77970.0780.16930.3915-0.0769-0.2294-0.0744-0.114-0.16490.15140.057-0.0216-0.09950.07040.0580.30010.3421.73420.356
38.3962-2.84360.254511.5365-1.42675.23190.25770.7208-0.0698-0.8137-0.21542.2734-0.2125-0.5192-0.04230.10230.0189-0.30160.37310.0640.8489-21.561.33512.384
45.31360.25270.72974.31740.44072.70450.04790.2786-0.0708-0.11730.0066-0.34610.0240.1855-0.05450.03330.0082-0.09170.04470.00870.369121.995-13.81619.818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 120
2X-RAY DIFFRACTION2C15 - 120
3X-RAY DIFFRACTION3B31 - 118
4X-RAY DIFFRACTION4D31 - 119

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