[English] 日本語
Yorodumi
- PDB-5ew2: Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-... -

+
Open data


ID or keywords:

Loading...

-
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 / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / 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 / 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 / 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 / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / 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 / 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 / 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
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more