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- PDB-5ew1: Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-... -

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Basic information

Entry
Database: PDB / ID: 5ew1
TitleHuman thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3
Components
  • HD1-deltaT3
  • 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


cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / 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. ...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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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: 2.95 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
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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-deltaT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7028
Polymers46,9814
Non-polymers7214
Water1,33374
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-20 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.548, 145.548, 145.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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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-deltaT3


Mass: 4618.955 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HD1 variant in which nucleobase of T3 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 / 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.: 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, 77 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.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 28% MPEG 2000, 0.1 M Bis/Tris pH 6.5

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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: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 10960 / % possible obs: 100 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.04 / Rrim(I) all: 0.189 / Χ2: 0.999 / Net I/av σ(I): 21.217 / Net I/σ(I): 4.6 / Num. measured all: 236610
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-3.0620.20.74910780.9190.170.7690.917100
3.06-3.18220.55110830.9570.120.5640.961100
3.18-3.3221.90.39910820.9790.0870.4090.942100
3.32-3.522.10.30710910.9860.0670.3140.965100
3.5-3.72220.21310830.9940.0460.2180.992100
3.72-4220.1710900.9950.0370.1740.997100
4-4.41220.12710910.9980.0280.131.1100
4.41-5.0421.80.11111040.9980.0240.1131.035100
5.04-6.3521.60.11711060.9980.0260.121.02100
6.35-5020.40.07211520.9990.0160.0741.05499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I7Y

4i7y


Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.1653 / WRfactor Rwork: 0.1261 / FOM work R set: 0.8568 / SU B: 26.779 / SU ML: 0.241 / SU R Cruickshank DPI: 0.2638 / SU Rfree: 0.3497 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 586 5.4 %RANDOM
Rwork0.1555 ---
obs0.1584 10317 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.09 Å2 / Biso mean: 50.954 Å2 / Biso min: 20.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 851 46 74 3214
Biso mean--38.47 39.64 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0173303
X-RAY DIFFRACTIONr_bond_other_d0.0030.022690
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.7234649
X-RAY DIFFRACTIONr_angle_other_deg1.29336236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27423.211109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68515413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9591520
X-RAY DIFFRACTIONr_chiral_restr0.1140.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213087
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02739
X-RAY DIFFRACTIONr_mcbond_it1.9593.5871108
X-RAY DIFFRACTIONr_mcbond_other1.9583.5871109
X-RAY DIFFRACTIONr_mcangle_it3.1165.3791378
LS refinement shellResolution: 2.951→3.028 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 48 -
Rwork0.264 741 -
all-789 -
obs--98.38 %
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)
14.374-1.52280.13422.9930.9134.67960.19450.26220.5636-0.1917-0.3274-0.3086-0.3636-0.00280.13290.13840.02270.05540.04010.04950.097155.06859.32589.1011
21.7022-0.26580.22881.6864-0.25291.03790.07110.03280.01550.0374-0.0379-0.076-0.0141-0.0013-0.03320.0240.01730.01450.02970.01690.017753.630342.229518.3733
30.6488-0.3415-0.14242.2311-0.7463.75810.04380.1065-0.3482-0.0078-0.1227-0.1520.52280.31070.07890.25580.0589-0.02720.1305-0.0530.249455.261820.15687.7815
41.53210.7541-1.2886.9759-2.64792.7403-0.0079-0.35750.1890.8412-0.0280.1066-0.18030.30960.0360.1490.020.02480.0903-0.03110.146240.7164.920334.0931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 14
2X-RAY DIFFRACTION2H16 - 246
3X-RAY DIFFRACTION3D2 - 27
4X-RAY DIFFRACTION4E1 - 15

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