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- PDB-7ntu: X-ray structure of the complex between human alpha thrombin and t... -

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Basic information

Entry
Database: PDB / ID: 7ntu
TitleX-ray structure of the complex between human alpha thrombin and two duplex/quadruplex aptamers: NU172 and HD22_27mer
Components
  • (Prothrombin) x 2
  • HD22_27mer
  • NU172
KeywordsHYDROLASE / Ternary complex / Anticoagulant aptamers / Duplex/quadruplex / Coagulation factor
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / 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 / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. ...Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle 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. / Kringle-like fold / 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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / DNA / DNA (> 10) / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTroisi, R. / Santamaria, A. / Sica, F.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human alpha-thrombin.
Authors: Troisi, R. / Balasco, N. / Santamaria, A. / Vitagliano, L. / Sica, F.
History
DepositionMar 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prothrombin
B: Prothrombin
C: Prothrombin
D: Prothrombin
E: NU172
F: HD22_27mer
G: NU172
I: HD22_27mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,51116
Polymers101,0698
Non-polymers1,4428
Water95553
1
A: Prothrombin
B: Prothrombin
E: NU172
F: HD22_27mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2568
Polymers50,5344
Non-polymers7214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Prothrombin
D: Prothrombin
G: NU172
I: HD22_27mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2568
Polymers50,5344
Non-polymers7214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.927, 77.616, 95.408
Angle α, β, γ (deg.)90.000, 103.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23G
14F
24I

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A6 - 33
2010C6 - 33
1020B37 - 293
2020D37 - 293
1030E1 - 26
2030G1 - 26
1040F1 - 27
2040I1 - 27

NCS ensembles :
ID
1
2
3
4

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Components

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DNA chain , 2 types, 4 molecules EGFI

#3: DNA chain NU172


Mass: 8172.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain HD22_27mer


Mass: 8485.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide / Protein / Sugars , 3 types, 6 molecules ACBD

#1: Protein/peptide Prothrombin / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#2: Protein Prothrombin / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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 , 3 types, 59 molecules

#5: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% w/v PEG 3350, 0.2 M ammonium acetate and 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 14, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→60 Å / Num. obs: 22065 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 1 / Net I/σ(I): 6.6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2150 / CC1/2: 0.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PPB

1ppb


Resolution: 3.1→26.77 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.84 / SU B: 22.771 / SU ML: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1089 4.9 %RANDOM
Rwork0.1999 ---
obs0.2027 20946 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.71 Å2 / Biso mean: 36.82 Å2 / Biso min: 1.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å2-0 Å2-1.67 Å2
2---4.28 Å20 Å2
3---2.1 Å2
Refinement stepCycle: final / Resolution: 3.1→26.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4462 2214 92 53 6821
Biso mean--36.37 18.27 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127243
X-RAY DIFFRACTIONr_bond_other_d00.0185628
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.47410305
X-RAY DIFFRACTIONr_angle_other_deg1.1381.92513057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5895548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.39321.284257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.05615807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9191539
X-RAY DIFFRACTIONr_chiral_restr0.050.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026581
X-RAY DIFFRACTIONr_gen_planes_other00.021677
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A7570.14
12C7570.14
21B74500.14
22D74500.14
31E26020.1
32G26020.1
41F26400.1
42I26400.1
LS refinement shellResolution: 3.1→3.178 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.354 72 -
Rwork0.341 1463 -
obs--94.69 %

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