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- PDB-3jtc: Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Car... -

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Basic information

Entry
Database: PDB / ID: 3jtc
TitleImportance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins
Components
  • Endothelial protein C receptor
  • Vitamin K-dependent protein C
KeywordsBLOOD CLOTTING / GLA (gamma-carboxyglutamic acid) residues / phospholipid binding groove / Ca ion binding / Blood coagulation / Disulfide bond / Glycoprotein / Membrane / Receptor / Transmembrane / Cleavage on pair of basic residues / Disease mutation / EGF-like domain / Gamma-carboxyglutamic acid / Hydrolase / Hydroxylation / Protease / Serine protease / Thrombophilia / Zymogen
Function / homology
Function and homology information


protein C (activated) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / 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 / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation ...protein C (activated) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / 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 / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / Cell surface interactions at the vascular wall / negative regulation of inflammatory response / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / signaling receptor activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / focal adhesion / centrosome / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Endothelial protein C receptor / MHC-I family domain / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / 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. ...Endothelial protein C receptor / MHC-I family domain / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / 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. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Vitamin K-dependent protein C / Endothelial protein C receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBajaj, S.P. / Vadivel, K. / Agah, S. / Cascio, D. / Krishnaswamy, S. / Esmon, C. / Padmanabhan, K.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural and Functional Studies of gamma-Carboxyglutamic Acid Domains of Factor VIIa and Activated Protein C: Role of Magnesium at Physiological Calcium.
Authors: Vadivel, K. / Agah, S. / Messer, A.S. / Cascio, D. / Bajaj, M.S. / Krishnaswamy, S. / Esmon, C.T. / Padmanabhan, K. / Bajaj, S.P.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3Jul 3, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothelial protein C receptor
B: Endothelial protein C receptor
C: Vitamin K-dependent protein C
D: Vitamin K-dependent protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,10526
Polymers52,8124
Non-polymers3,29322
Water7,332407
1
A: Endothelial protein C receptor
C: Vitamin K-dependent protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,05313
Polymers26,4062
Non-polymers1,64711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-86 kcal/mol
Surface area11410 Å2
MethodPISA
2
B: Endothelial protein C receptor
D: Vitamin K-dependent protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,05313
Polymers26,4062
Non-polymers1,64711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-79 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.220, 62.360, 71.030
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide / Sugars , 3 types, 10 molecules ABCD

#1: Protein Endothelial protein C receptor / Endothelial cell protein C receptor / Activated protein C receptor / APC receptor


Mass: 22046.562 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 18-210) / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UNN8
#2: Protein/peptide Vitamin K-dependent protein C / Autoprothrombin IIA / Anticoagulant protein C / Blood coagulation factor XIV / Vitamin K-dependent ...Autoprothrombin IIA / Anticoagulant protein C / Blood coagulation factor XIV / Vitamin K-dependent protein C light chain / Vitamin K-dependent protein C heavy chain / Activation peptide


Mass: 4359.409 Da / Num. of mol.: 2 / Fragment: GLA domain (UNP residues 43-75) / Source method: isolated from a natural source
Details: CLEAVAGE HAPPENED DURING CRYSTALLIZATION AND THE CRYSTAL CONTAINS ONLY THE N-TERMINAL DOMAIN (GLA DOMAIN) OF PROTEIN C.
Source: (natural) HOMO SAPIENS (human) / References: UniProt: P04070, protein C (activated)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 423 molecules

#4: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCLEAVAGE HAPPENED DURING CRYSTALLIZATION AND THE CRYSTAL CONTAINS ONLY THE N-TERMINAL DOMAIN (GLA ...CLEAVAGE HAPPENED DURING CRYSTALLIZATION AND THE CRYSTAL CONTAINS ONLY THE N-TERMINAL DOMAIN (GLA DOMAIN) OF PROTEIN C.

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growMethod: vapor diffusion / pH: 7
Details: PEG 400, potassium chloride, magnesium chloride, calcium chloride, HEPES, PH 7.0, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 66375 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.041 / Net I/σ(I): 27
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 27 / Rsym value: 0.043 / % possible all: 91

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→23.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22648 3024 5.1 %RANDOM
Rwork0.19066 ---
obs0.19246 56575 89.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å21.12 Å2
2--0.87 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 198 407 4027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d1.450.0213695
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5662.0335012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98223.064173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45715530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4721528
X-RAY DIFFRACTIONr_chiral_restr0.1730.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0320.0252841
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.21724
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22505
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2322
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1550.235
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.611.52050
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.62323315
X-RAY DIFFRACTIONr_scbond_it3.61231645
X-RAY DIFFRACTIONr_scangle_it5.3714.51697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 139 -
Rwork0.414 2850 -
obs--61.09 %

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