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- PDB-5ew2: Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-... -

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Basic information

Entry
Database: PDB / ID: 5ew2
TitleHuman thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT12
Components
  • HD1-deltaT12
  • HD22 (27mer)
  • Thrombin heavy chain
  • thrombin light chain
Keywordsprotein/dna / PROTEIN-DNA COMPLEX / BLOOD COAGULATION / DNA APTAMER / DNA-INHIBITOR / G-QUADRUPLEX / DUPLEX-QUADRUPLEX JUNCTION / SERINE PROTEASE / HYDROLASE / ABASIC FURAN / HYDROLASE-DNA COMPLEX
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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / DNA / DNA (> 10) / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.59 Å
AuthorsPica, A. / Russo Krauss, I. / Parente, V. / Sica, F.
Citation
Journal: Nucleic Acids Res. / Year: 2017
Title: Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers.
Authors: Pica, A. / Russo Krauss, I. / Parente, V. / Tateishi-Karimata, H. / Nagatoishi, S. / Tsumoto, K. / Sugimoto, N. / Sica, F.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer.
Authors: Russo Krauss, I. / Pica, A. / Merlino, A. / Mazzarella, L. / Sica, F.
#2: Journal: FEBS J. / Year: 2013
Title: Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer.
Authors: Pica, A. / Russo Krauss, I. / Merlino, A. / Nagatoishi, S. / Sugimoto, N. / Sica, F.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Non-polymer description
Revision 1.3Jan 18, 2017Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
L: thrombin light chain
H: Thrombin heavy chain
D: HD22 (27mer)
E: HD1-deltaT12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7259
Polymers46,9814
Non-polymers7445
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-31 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.089, 41.296, 104.923
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 2 types, 2 molecules DE

#3: DNA chain HD22 (27mer)


Mass: 8485.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain HD1-deltaT12


Mass: 4618.955 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HD1 variant in which nucleobase of T12 has been deleted
Source: (synth.) Homo sapiens (human)

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Protein/peptide / Protein / Sugars , 3 types, 3 molecules LH

#1: Protein/peptide thrombin light chain / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#2: Protein Thrombin heavy chain / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 3 types, 11 molecules

#6: 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.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 0.2 M Sodium Formate, 2% acetonitrile

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.58→50 Å / Num. obs: 5755 / % possible obs: 96.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.084 / Rrim(I) all: 0.147 / Χ2: 0.811 / Net I/av σ(I): 7.51 / Net I/σ(I): 5.9 / Num. measured all: 16010
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.58-3.712.60.4665760.6610.3290.5730.97495.7
3.71-3.862.60.3755440.7720.2680.4630.92192.8
3.86-4.032.60.3745590.8370.2670.4620.92394.9
4.03-4.242.60.2955290.8910.210.3640.9391.7
4.24-4.512.70.1965610.9010.1370.24194.6
4.51-4.862.80.1515670.9530.1050.1850.78897.6
4.86-5.3530.1045980.9710.0690.1260.69199.7
5.35-6.1230.1056010.9650.0710.1270.71399.5
6.12-7.730.0636020.9890.0420.0760.61999
7.7-502.80.0266180.9710.0180.0310.71498.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.59 Å37.25 Å
Translation3.59 Å37.25 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.59→50 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.859 / SU ML: 0.57 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26772 271 5 %RANDOM
Rwork0.20849 ---
obs0.2115 5167 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0.47 Å2
2--1.49 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 3.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 832 47 7 3146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0173299
X-RAY DIFFRACTIONr_bond_other_d0.0030.022695
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.7244640
X-RAY DIFFRACTIONr_angle_other_deg1.23736247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37523.273110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48315417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.741520
X-RAY DIFFRACTIONr_chiral_restr0.1180.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213096
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02737
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5693.8361116
X-RAY DIFFRACTIONr_mcbond_other1.5683.8361117
X-RAY DIFFRACTIONr_mcangle_it2.7345.7521388
X-RAY DIFFRACTIONr_mcangle_other2.7335.7511389
X-RAY DIFFRACTIONr_scbond_it2.0734.3322183
X-RAY DIFFRACTIONr_scbond_other2.0744.3322182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6036.4783253
X-RAY DIFFRACTIONr_long_range_B_refined7.59539.90714184
X-RAY DIFFRACTIONr_long_range_B_other7.5939.90814183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.589→3.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 9 -
Rwork0.285 219 -
obs--49.89 %
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)
15.92651.2961-0.68862.2683-1.18443.8518-0.2949-0.22691.6795-0.11980.3894-0.6251-0.15240.0437-0.09450.1401-0.1408-0.05190.2637-0.28871.0309-12.551729.644926.5447
25.71490.02460.58183.32660.38582.5072-0.2540.01620.11010.15650.40060.04250.01910.0472-0.14660.0549-0.01890.01110.095-0.02620.0489-25.185415.594123.987
34.7521-0.53790.18152.6528-1.19335.7599-0.48090.3790.6995-0.1250.42010.6893-0.1411-0.74630.06070.1083-0.1085-0.090.29090.15980.6444-48.268119.769916.2639
44.60852.78050.42333.9519-0.5020.65210.3555-0.9524-0.85020.5931-0.2629-0.83180.28290.282-0.09260.69830.3153-0.22010.9732-0.0430.2971-4.03376.127444.8645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 14
2X-RAY DIFFRACTION2H16 - 246
3X-RAY DIFFRACTION3D2 - 26
4X-RAY DIFFRACTION4E1 - 15

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