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- PDB-1z6c: Solution structure of an EGF pair (EGF34) from vitamin K-dependen... -

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Basic information

Entry
Database: PDB / ID: 1z6c
TitleSolution structure of an EGF pair (EGF34) from vitamin K-dependent protein S
ComponentsVitamin K-dependent protein S
KeywordsBLOOD CLOTTING / EGF module
Function / homology
Function and homology information


endopeptidase inhibitor activity / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen / Regulation of Complement cascade / Cell surface interactions at the vascular wall ...endopeptidase inhibitor activity / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen / Regulation of Complement cascade / Cell surface interactions at the vascular wall / Golgi lumen / blood coagulation / Platelet degranulation / blood microparticle / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Laminin G domain / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Laminin G domain / Laminin G domain / : / Calcium-binding EGF domain ...: / Laminin G domain / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Laminin G domain / Laminin G domain / : / Calcium-binding EGF domain / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Vitamin K-dependent protein S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Simulated annealing Torsion angle dynamics
AuthorsDrakenberg, T. / Ghasriani, H. / Thulin, E. / Thamlitz, A.M. / Muranyi, A. / Annila, A. / Stenflo, J.
CitationJournal: Biochemistry / Year: 2005
Title: Solution Structure of the Ca(2+)-Binding EGF3-4 Pair from Vitamin K-Dependent Protein S: Identification of an Unusual Fold in EGF3.
Authors: Drakenberg, T. / Ghasriani, H. / Thulin, E. / Muranyi, A. / Annila, A. / Stenflo, J.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin K-dependent protein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6773
Polymers9,5971
Non-polymers802
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Vitamin K-dependent protein S


Mass: 9596.842 Da / Num. of mol.: 1 / Fragment: EGF modules 3 and 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PROS1, PROS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07225
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
232IPAP
3432D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM EGF34 U-15N; pH 6.0; 0.1mM NaN3; 1mM DSS; 10mM CaCl290% H2O/10% D2O
20.5 mM EGF34 U-15N; phage Pf1 16 mg/ml; pH 6.0; 10mM CaCl290% H2O/10% D2O
31mM EGF34; pH 6.0; 0.1 mM NaN3; 1mM Dss; 10 mM CaCl2100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1low 6ambient 309 K
2low 6ambient 309 K
3low 6ambient 309 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
VNMR5.1processing
Sparky3.1Goddard and Kellerdata analysis
Felix97processing
CNS1.1refinement
RefinementMethod: Simulated annealing Torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 912 restraints, 756 NOE restraints, 76 torsion angle restraints, 46 residual dipolar couplings and 30 restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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