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- PDB-4gyx: The von Willebrand Factor A3 domain binding region of type III co... -

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Basic information

Entry
Database: PDB / ID: 4gyx
TitleThe von Willebrand Factor A3 domain binding region of type III collagen stabilized by the cysteine knot
ComponentsType III collagen fragment in a host peptide stabilized by the cysteine knot
KeywordsSTRUCTURAL PROTEIN / BLOOD CLOTTING / collagen triple helix / type III collagen cysteine knot / von Willebrand factor A3 domain / 4-hydroxylation / extracellular matrix
Function / homology
Function and homology information


collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength ...collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / basement membrane organization / Extracellular matrix organization / layer formation in cerebral cortex / Collagen biosynthesis and modifying enzymes / peptide cross-linking / tissue homeostasis / Signaling by PDGF / negative regulation of immune response / digestive tract development / NCAM1 interactions / response to angiotensin / collagen fibril organization / Scavenging by Class A Receptors / skin development / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Syndecan interactions / positive regulation of Rho protein signal transduction / SMAD binding / Collagen degradation / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / supramolecular fiber organization / transforming growth factor beta receptor signaling pathway / extracellular matrix organization / cell-matrix adhesion / response to cytokine / integrin-mediated signaling pathway / cellular response to amino acid stimulus / lung development / neuron migration / wound healing / response to radiation / multicellular organism growth / platelet activation / cerebral cortex development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / heart development / fibroblast proliferation / protease binding / collagen-containing extracellular matrix / in utero embryonic development / endoplasmic reticulum lumen / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Collagen alpha-1(III) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsBoudko, S.P. / Bachinger, H.P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The NC2 Domain of Type IX Collagen Determines the Chain Register of the Triple Helix.
Authors: Boudko, S.P. / Bachinger, H.P.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III collagen fragment in a host peptide stabilized by the cysteine knot
B: Type III collagen fragment in a host peptide stabilized by the cysteine knot
C: Type III collagen fragment in a host peptide stabilized by the cysteine knot


Theoretical massNumber of molelcules
Total (without water)8,6263
Polymers8,6263
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-29 kcal/mol
Surface area4890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)19.070, 26.990, 64.120
Angle α, β, γ (deg.)90.00, 92.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Type III collagen fragment in a host peptide stabilized by the cysteine knot


Mass: 2875.201 Da / Num. of mol.: 3 / Fragment: Von Willebrand Factor binding fragment / Source method: obtained synthetically
Details: This sequence contains two fragments of human type III collagen: the von Willebrand factor A3 domain binding region and the cysteine knot
Source: (synth.) Homo sapiens (human) / References: UniProt: P02461*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.91 Å3/Da / Density % sol: 35.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 28% PEG 3350, 0.1M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 29, 2011
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→19.05 Å / Num. all: 10872 / Num. obs: 10752 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.49-1.573.10.3833.2193.1
4.71-19.053.40.06814.5198.4

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Processing

Software
NameVersionClassification
AMoREphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DMT

4dmt


Resolution: 1.49→19.05 Å / SU ML: 0.12 / σ(F): 1.38 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1059 9.88 %
Rwork0.176 --
obs0.1805 10716 98.7 %
all-10857 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms530 0 0 122 652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006567
X-RAY DIFFRACTIONf_angle_d2.146781
X-RAY DIFFRACTIONf_dihedral_angle_d18.938262
X-RAY DIFFRACTIONf_chiral_restr0.10975
X-RAY DIFFRACTIONf_plane_restr0.005104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.5580.28291200.26721083X-RAY DIFFRACTION90
1.558-1.64010.20341330.19031199X-RAY DIFFRACTION100
1.6401-1.74270.21061330.18321247X-RAY DIFFRACTION100
1.7427-1.87720.25281320.17641195X-RAY DIFFRACTION100
1.8772-2.06590.21251350.16451224X-RAY DIFFRACTION100
2.0659-2.36440.21021390.16021217X-RAY DIFFRACTION100
2.3644-2.9770.21931290.18121221X-RAY DIFFRACTION100
2.977-19.05370.22111380.16951271X-RAY DIFFRACTION100
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)
11.1144-0.5008-1.53040.49490.10533.35830.0466-0.74230.02410.9908-0.01320.6103-0.0004-0.16-0.09380.6618-0.010.3241.05890.02090.4224-9.64910.34232.2667
25.26290.0539-2.4952.4301-0.26383.7772-0.0051-0.1402-0.0883-0.0618-0.0109-0.0826-0.0032-0.05420.01710.05820.0055-0.04360.05840.0030.08616.01640.31064.6527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 1:9) OR (CHAIN B AND RESSEQ 1:9) OR (CHAIN C AND RESSEQ 1:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 10:28) OR (CHAIN B AND RESSEQ 10:28) OR (CHAIN C AND RESSEQ 10:26)

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