[English] 日本語
Yorodumi
- PDB-5ew1: Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway ...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-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / 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 / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / growth factor activity / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / response to wounding / 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 / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of protein phosphorylation / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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-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)

-
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, 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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
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