[English] 日本語
Yorodumi
- PDB-3nxp: Crystal structure of human prethrombin-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nxp
TitleCrystal structure of human prethrombin-1
ComponentsPrethrombin-1
KeywordsHYDROLASE / Thrombin / prethrombin-1 / allostery / blood coagulation / kringle / serine protease / zymogen
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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / 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 / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Plasminogen Kringle 4 / Plasminogen Kringle 4 / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, Z. / Bush-Pelc, L.A. / Di Cera, E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of prethrombin-1.
Authors: Chen, Z. / Pelc, L.A. / Di Cera, E.
#1: Journal: CELL.MOL.LIFE SCI. / Year: 2008
Title: NA(+) binding to meizothrombin DESF1.
Authors: Papaconstantinou, M.E. / Gandhi, P.S. / Chen, Z. / Bah, A. / Di Cera, E.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prethrombin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4866
Polymers47,8371
Non-polymers6505
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.893, 81.006, 88.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Prethrombin-1 / Coagulation factor II


Mass: 47836.688 Da / Num. of mol.: 1 / Fragment: UNP residues 199-622 / Mutation: R271A, R284A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): BHK / References: UniProt: P00734, thrombin
#2: 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 / N-Acetylglucosamine


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
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl, pH 8.5 and 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2010
RadiationMonochromator: NE-CAT, 24-ID-E / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 25400 / Num. obs: 24257 / % possible obs: 95.5 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2351 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPfrom ccp4phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E6P

3e6p


Resolution: 2.2→59.74 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU ML: 0.138 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -0.5 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1244 5.1 %RANDOM
Rwork0.1975 ---
obs0.19895 22995 95.5 %-
all-24078 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å20 Å2
2---2.75 Å2-0 Å2
3---2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 42 197 3351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223236
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.964378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79523.875160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8815540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0291524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212490
X-RAY DIFFRACTIONr_mcbond_it0.4651.51934
X-RAY DIFFRACTIONr_mcangle_it0.88723106
X-RAY DIFFRACTIONr_scbond_it1.59431302
X-RAY DIFFRACTIONr_scangle_it2.4984.51272
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 83 -
Rwork0.272 1643 -
obs-1643 92.95 %
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)
19.2247-0.5155-0.17381.43180.59023.10070.0151-0.69320.05510.65290.1243-0.13350.15780.0948-0.13940.3150.0132-0.04660.2109-0.02030.05568.491-14.53931.883
22.15350.4599-0.27762.7152-0.0611.69220.0231-0.0574-0.1386-0.09-0.00260.37250.2238-0.232-0.02050.09760.01930.00090.14840.00280.107-10.139-18.84417.621
31.8744-0.3383-0.61881.21340.15691.3360.08620.00640.1803-0.02750.00210.0036-0.1538-0.0039-0.08830.0948-0.0198-0.00720.0872-0.01730.07645.083-7.96315.551
41.1355-0.54350.15623.4951-0.45490.43690.00630.0776-0.1664-0.2338-0.02160.23370.139-0.06010.01530.0789-0.00830.0010.0926-0.00310.0614-2.352-24.37814.175
53.0826-0.3316-1.44993.0260.51842.66070.05940.3037-0.0253-0.2956-0.0306-0.2633-0.18580.1139-0.02880.1371-0.0134-0.07290.1716-0.01150.1221-0.784-21.4563.266
65.8357-0.51882.8530.5211-0.92312.66470.0890.3586-0.2282-0.06590.0333-0.09580.13530.1207-0.12220.13510.0063-0.01080.1263-0.04360.1329-2.505-26.6362.093
72.23020.12610.28761.1861-0.06980.74270.0091-0.02-0.01910.03340.0249-0.0312-0.02760.1624-0.0340.08770.00750.00510.0746-0.00950.08235.605-20.21815.059
812.39333.58138.20195.8139-1.314417.7197-0.1901-0.339-1.4063-0.10820.237-0.2251.2320.2084-0.04690.30.10960.08160.16210.07170.361624.156-34.0715.165
94.9697-0.88130.97093.0484-0.55643.37620.1049-0.243-0.11350.0041-0.0707-0.46120.05170.5426-0.03420.06060.02120.01430.2624-0.00350.15732.433-21.08814.173
100.0161-0.01130.00590.03120.03360.0652-0.00590.07480.17180.1993-0.1476-0.05580.3406-0.0970.15352.1838-0.17860.0841.55110.08842.263930.614-16.09329.455
112.3065-0.89951.498814.06442.92761.88570.1527-0.5989-0.7760.59580.35480.2910.3027-0.2741-0.50750.21170.1725-0.05470.73990.20240.308334.152-26.48922.101
124.571.3618-0.37823.30530.29023.30220.0023-0.16530.0108-0.01760.01690.12690.05890.3459-0.01920.0820.0246-0.01930.18410.01660.080224.735-21.77417.179
1381.574716.178544.87773.312710.496163.56710.27452.8187-4.76410.04420.6888-0.9948-0.422-2.1573-0.96340.67320.0510.32961.3016-0.84841.2258.177-37.47611.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 3
2X-RAY DIFFRACTION2A4 - 37
3X-RAY DIFFRACTION3A38 - 126
4X-RAY DIFFRACTION4A127 - 145
5X-RAY DIFFRACTION5A146 - 175
6X-RAY DIFFRACTION6A176 - 192
7X-RAY DIFFRACTION7A193 - 247
8X-RAY DIFFRACTION8F7 - 15
9X-RAY DIFFRACTION9F16 - 33
10X-RAY DIFFRACTION10F34 - 46
11X-RAY DIFFRACTION11F47 - 57
12X-RAY DIFFRACTION12F58 - 87
13X-RAY DIFFRACTION13F88 - 95

+
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