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- PDB-1a2c: Structure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-G... -

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Basic information

Entry
Database: PDB / ID: 1a2c
TitleStructure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-GREEN ALGA
Components
  • Aeruginosin 298-A
  • Hirudin variant-2
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHydrolase/Hydrolase Inhibitor / HYDROLASE / SERINE PROTEASE / Hydrolase-Hydrolase Inhibitor 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 / 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 / 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 / serine-type endopeptidase inhibitor 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 / 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
Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain ...Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / 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
AERUGINOSIN 298-A / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRios-Steiner, J.L. / Murakami, M. / Tulinsky, A.
Citation
Journal: J.Am.Chem.Soc. / Year: 1998
Title: Structure of Thrombin Inhibited by Aeruginosin 298-A from a Blue-Green Alga
Authors: Steiner, J.L.R. / Murakami, M. / Tulinsky, A.
#1: Journal: Tetrahedron Lett. / Year: 1994
Title: Aeruginosin 298-A, a Thrombin and Trypsin Inhibitor from the Blue-Green Alga Microcystis Aeruginosa (Nies-298)
Authors: Murakami, M. / Okita, Y. / Matsuda, H. / Okino, T. / Yamaguchi, K.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Structure of the Hirudin-Thrombin Complex
Authors: Rydel, T.J. / Tulinsky, A. / Bode, W. / Huber, R.
#3: Journal: Science / Year: 1990
Title: The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin
Authors: Rydel, T.J. / Ravichandran, K.G. / Tulinsky, A. / Bode, W. / Huber, R. / Roitsch, C. / Fenton II, J.W.
History
DepositionDec 26, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jun 5, 2013Group: Atomic model
Revision 1.5Aug 2, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_polymer_linkage / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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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
I: Hirudin variant-2
J: Aeruginosin 298-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0395
Polymers36,0164
Non-polymers231
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.970, 72.480, 72.240
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 3 types, 3 molecules LIJ

#1: Protein/peptide Thrombin light chain


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide Hirudin variant-2


Mass: 1534.554 Da / Num. of mol.: 1 / Fragment: UNP residues 60-71
Source method: isolated from a genetically manipulated source
Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945
#4: Protein/peptide Aeruginosin 298-A


Type: Oligopeptide / Class: Thrombin inhibitor, Trypsin inhibitor / Mass: 604.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Microcystis aeruginosa (bacteria) / References: AERUGINOSIN 298-A

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Protein , 1 types, 1 molecules H

#2: Protein Thrombin heavy chain


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin

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Non-polymers , 2 types, 177 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN IDENTIFIER *H* IS USED FOR RESIDUES 16 - 247. RESIDUES 355 - 364 REPRESENT THE HIRUGEN AND HAVE BEEN ASSIGNED CHAIN IDENTIFIER *I*. THE HIRUGEN RESIDUE NUMBERING CORRESPONDS TO THE C-TERMINAL RESIDUES OF HIRUDIN.

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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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growpH: 7.3 / Details: pH 7.3
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.75 mg/mlthrombin1drop
20.05 Msodium phosphate1drop
30.5 mMsodium azide1drop
412.5 %(w/v)PEG80001drop
50.1 Msodium phosphate1reservoir
61 mMsodium azide1reservoir
725 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1995 / Details: NO MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 15999 / % possible obs: 70 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.25 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.4 / % possible all: 47

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Processing

Software
NameClassification
RIGAKUdata collection
RIGAKUdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
RIGAKUdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HGT

1hgt


Resolution: 2.1→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.15 --
obs-15999 70 %
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 1 176 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.040.044
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.068
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.31.5
X-RAY DIFFRACTIONp_mcangle_it2.142
X-RAY DIFFRACTIONp_scbond_it2.662.5
X-RAY DIFFRACTIONp_scangle_it3.83
X-RAY DIFFRACTIONp_plane_restr0.0360.04
X-RAY DIFFRACTIONp_chiral_restr0.1970.15
X-RAY DIFFRACTIONp_singtor_nbd0.250.6
X-RAY DIFFRACTIONp_multtor_nbd0.3450.6
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.3230.6
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor2415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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