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- PDB-5nb8: Structure of vWC domain from CCN3 -

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Basic information

Entry
Database: PDB / ID: 5nb8
TitleStructure of vWC domain from CCN3
ComponentsProtein NOV homolog
KeywordsSIGNALING PROTEIN / CCN3 / vWC / domains / signalling / BMP
Function / homology
Function and homology information


endothelial cell-cell adhesion / bone regeneration / smooth muscle cell proliferation / negative regulation of monocyte chemotaxis / negative regulation of chondrocyte proliferation / : / negative regulation of sensory perception of pain / hematopoietic stem cell homeostasis / negative regulation of myotube differentiation / endothelial cell chemotaxis ...endothelial cell-cell adhesion / bone regeneration / smooth muscle cell proliferation / negative regulation of monocyte chemotaxis / negative regulation of chondrocyte proliferation / : / negative regulation of sensory perception of pain / hematopoietic stem cell homeostasis / negative regulation of myotube differentiation / endothelial cell chemotaxis / fibroblast migration / type B pancreatic cell proliferation / gap junction / negative regulation of non-canonical NF-kappaB signal transduction / Notch binding / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of Notch signaling pathway / negative regulation of SMAD protein signal transduction / negative regulation of insulin secretion / chondrocyte differentiation / extracellular matrix / cell chemotaxis / growth factor activity / negative regulation of cell growth / negative regulation of inflammatory response / integrin binding / heparin binding / regulation of gene expression / angiogenesis / collagen-containing extracellular matrix / cell adhesion / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / signal transduction / extracellular region / cytoplasm
Similarity search - Function
IGFBP-related, CNN / CCN, TSP1 domain / CCN3 Nov like TSP1 domain / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Glycoprotein hormone subunit beta / Cystine-knot domain / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. ...IGFBP-related, CNN / CCN, TSP1 domain / CCN3 Nov like TSP1 domain / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Glycoprotein hormone subunit beta / Cystine-knot domain / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Growth factor receptor cysteine-rich domain superfamily
Similarity search - Domain/homology
IMIDAZOLE / CCN family member 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXu, E.-R. / Hyvonen, M.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of von Willebrand factor C domains of collagen 2A and CCN3 reveal an alternative mode of binding to bone morphogenetic protein-2.
Authors: Xu, E.R. / Blythe, E.E. / Fischer, G. / Hyvonen, M.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein NOV homolog
B: Protein NOV homolog
C: Protein NOV homolog
D: Protein NOV homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,22510
Polymers41,7874
Non-polymers4386
Water2,792155
1
A: Protein NOV homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5853
Polymers10,4471
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein NOV homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6083
Polymers10,4471
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein NOV homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5162
Polymers10,4471
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein NOV homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5162
Polymers10,4471
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.400, 43.100, 72.300
Angle α, β, γ (deg.)75.30, 82.00, 89.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein NOV homolog / NovH / CCN family member 3 / Nephroblastoma-overexpressed gene protein homolog


Mass: 10446.865 Da / Num. of mol.: 4 / Fragment: UNP residues 100-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nov, Ccn3 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9QZQ5
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.8 M Na/K Tartrate, 0.4M NaCl, 0.1 M Imidazole, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.1→28.58 Å / Num. obs: 25475 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.92
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3237 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.58 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1298 5.1 %
Rwork0.1889 --
obs0.1903 25446 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 31 155 2303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072255
X-RAY DIFFRACTIONf_angle_d0.8723063
X-RAY DIFFRACTIONf_dihedral_angle_d17.1841403
X-RAY DIFFRACTIONf_chiral_restr0.055303
X-RAY DIFFRACTIONf_plane_restr0.007418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.30191450.2532614X-RAY DIFFRACTION95
2.1841-2.28340.28271370.24072667X-RAY DIFFRACTION97
2.2834-2.40380.22571470.22432744X-RAY DIFFRACTION99
2.4038-2.55430.27531400.21792661X-RAY DIFFRACTION98
2.5543-2.75130.24441430.21172703X-RAY DIFFRACTION99
2.7513-3.02790.23351380.20642696X-RAY DIFFRACTION99
3.0279-3.46540.21151440.18652691X-RAY DIFFRACTION99
3.4654-4.36360.19461560.16462694X-RAY DIFFRACTION99
4.3636-28.58310.19121480.17092678X-RAY DIFFRACTION98
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)
11.45050.8293-0.96461.8572-1.44952.48720.01640.1593-0.05610.0651-0.0015-0.0251-0.04830.0377-0.04930.2730.0224-0.03930.32230.01910.32481.6965-4.346.9438
24.35412.4487-2.0063.0654-1.85523.8229-0.00130.35830.0749-0.06540.00570.0532-0.11420.1547-0.03880.27710.0344-0.0290.33680.00460.2647-1.88535.0488-7.2081
32.8627-1.7187-1.50962.17972.12353.06770.0361-0.08140.0166-0.030.0006-0.0336-0.062-0.0571-0.05430.2626-0.017-0.03580.2538-0.00390.3005-8.250317.338815.8033
44.35-1.3416-1.74962.06381.72424.25630.0864-0.3208-0.00080.06340.01040.07-0.2251-0.0227-0.10660.3172-0.0083-0.02470.32910.00180.2709-4.606326.675629.9002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain D
4X-RAY DIFFRACTION4chain C

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