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- PDB-3bk3: Crystal structure of the complex of BMP-2 and the first Von Wille... -

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Basic information

Entry
Database: PDB / ID: 3bk3
TitleCrystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2
Components
  • Bone morphogenetic protein 2
  • Crossveinless 2
KeywordsHormone/growth Factor / TGF-beta superfamily / BMP modulator proteins / Chordin / BMP inhibitor / Chondrogenesis / Cleavage on pair of basic residues / Cytokine / Developmental protein / Differentiation / Glycoprotein / Growth factor / Osteogenesis / Polymorphism / Secreted / Hormone-growth Factor COMPLEX
Function / homology
Function and homology information


otic placode formation / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development ...otic placode formation / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / ameloblast differentiation / positive regulation of extracellular matrix constituent secretion / negative regulation of cardiac muscle cell differentiation / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / aortic valve development / telencephalon regionalization / neural crest formation / positive regulation of odontogenesis / BMP binding / positive regulation of phosphatase activity / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / pericardium development / lung vasculature development / regulation of BMP signaling pathway / BMP receptor complex / co-receptor binding / telencephalon development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / positive regulation of odontoblast differentiation / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / phosphatase activator activity / Transcriptional regulation by RUNX2 / positive regulation of astrocyte differentiation / Signaling by BMP / cellular response to BMP stimulus / cardiac muscle cell differentiation / cardiac muscle tissue morphogenesis / positive regulation of BMP signaling pathway / positive regulation of ossification / astrocyte differentiation / dorsal/ventral pattern formation / extracellular matrix binding / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / endocardial cushion morphogenesis / branching involved in ureteric bud morphogenesis / negative regulation of fat cell differentiation / blood vessel development / bone mineralization / positive regulation of osteoblast proliferation / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / inner ear development / hemopoiesis / cellular response to organic cyclic compound / negative regulation of cell cycle / positive regulation of Wnt signaling pathway / epithelial to mesenchymal transition / positive regulation of fat cell differentiation / cell fate commitment / regulation of angiogenesis / chondrocyte differentiation / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / positive regulation of neuron differentiation / protein serine/threonine kinase activator activity / osteoclast differentiation / extracellular matrix / negative regulation of MAP kinase activity / skeletal system development / cytokine activity / animal organ morphogenesis / negative regulation of smooth muscle cell proliferation / response to bacterium / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / protein destabilization / bone development / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / osteoblast differentiation / Regulation of RUNX2 expression and activity / positive regulation of protein binding
Similarity search - Function
Defensin A-like - #20 / Defensin A-like / : / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / Trypsin Inhibitor-like, cysteine rich domain ...Defensin A-like - #20 / Defensin A-like / : / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / von Willebrand factor type C domain / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Other non-globular / Cystine-knot cytokine / Special / Ribbon / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein 2 / Crossveinless 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsMueller, T.D. / Sebald, W. / Zhang, J.-L.
CitationJournal: Dev.Cell / Year: 2008
Title: Crystal structure analysis reveals how the Chordin family member crossveinless 2 blocks BMP-2 receptor binding
Authors: Zhang, J.-L. / Qiu, L.-Y. / Kotzsch, A. / Weidauer, S. / Patterson, L. / Hammerschmidt, M. / Sebald, W. / Mueller, T.D.
History
DepositionDec 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone morphogenetic protein 2
B: Bone morphogenetic protein 2
C: Crossveinless 2
D: Crossveinless 2


Theoretical massNumber of molelcules
Total (without water)40,1364
Polymers40,1364
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-57 kcal/mol
Surface area19510 Å2
MethodPISA
2
A: Bone morphogenetic protein 2
C: Crossveinless 2

B: Bone morphogenetic protein 2
D: Crossveinless 2


Theoretical massNumber of molelcules
Total (without water)40,1364
Polymers40,1364
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-y,x-1/2,z+1/41
Buried area4170 Å2
ΔGint-37 kcal/mol
Surface area21140 Å2
MethodPISA
3
A: Bone morphogenetic protein 2
C: Crossveinless 2


Theoretical massNumber of molelcules
Total (without water)20,0682
Polymers20,0682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-13 kcal/mol
Surface area11180 Å2
MethodPISA
4
B: Bone morphogenetic protein 2
D: Crossveinless 2


Theoretical massNumber of molelcules
Total (without water)20,0682
Polymers20,0682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-14 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.750, 83.750, 139.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Bone morphogenetic protein 2 / BMP-2 / BMP-2A


Mass: 12875.898 Da / Num. of mol.: 2 / Mutation: F41M, Y91M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Plasmid: pN25C109 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12643
#2: Protein Crossveinless 2


Mass: 7192.293 Da / Num. of mol.: 2 / Fragment: VWC1 CV-2, VWC domain 1, UNP residues 28-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: crossveinless-2 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5D734
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS COORDINATES IN CHAINS C AND D ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. SINCE RESIDUE -1 IS A ...THIS COORDINATES IN CHAINS C AND D ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. SINCE RESIDUE -1 IS A EXPRESSION TAG, IT HAS BEEN GIVEN A NEGATIVE NUMBER. 0(ZERO) WAS SIMPLY SKIPPED IN THE NUMBERING.

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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: 3.05 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9799, 0.9796, 0.9079
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2006 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.97961
30.90791
ReflectionResolution: 2.7→40.7 Å / Num. all: 13231 / Num. obs: 13191 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 40 Å2 / Rsym value: 0.09 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1303 / Rsym value: 0.342 / % possible all: 99.7

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Processing

Software
NameClassification
MAR345dtbdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 652 -Random
Rwork0.203 ---
all0.205 13230 --
obs0.205 13191 5 %-
Displacement parametersBiso mean: 56.2 Å2
Refine analyzeLuzzati coordinate error free: 0.313 Å
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 0 47 2635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.829
LS refinement shellResolution: 2.7→2.77 Å
RfactorNum. reflection% reflection
Rfree0.359 45 -
Rwork0.29 --
obs-755 100 %

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