[English] 日本語
Yorodumi
- PDB-5jvy: Crystal structure of S121P murine COX-2 mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jvy
TitleCrystal structure of S121P murine COX-2 mutant
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE / Cyclooxygenase / COX / NSAID
Function / homology
Function and homology information


Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / hair cycle / cellular response to homocysteine / Nicotinamide salvaging ...Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / hair cycle / cellular response to homocysteine / Nicotinamide salvaging / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / negative regulation of synaptic transmission, dopaminergic / cellular response to lead ion / response to nematode / positive regulation of transforming growth factor beta production / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / regulation of neuroinflammatory response / positive regulation of synaptic plasticity / positive regulation of smooth muscle contraction / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / response to fatty acid / response to fructose / positive regulation of fever generation / prostaglandin secretion / response to vitamin D / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / prostaglandin biosynthetic process / nuclear inner membrane / negative regulation of smooth muscle contraction / cellular response to ATP / positive regulation of cell migration involved in sprouting angiogenesis / maintenance of blood-brain barrier / bone mineralization / negative regulation of calcium ion transport / decidualization / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / response to tumor necrosis factor / brown fat cell differentiation / response to glucocorticoid / keratinocyte differentiation / positive regulation of vasoconstriction / positive regulation of brown fat cell differentiation / embryo implantation / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / memory / regulation of blood pressure / positive regulation of protein import into nucleus / peroxidase activity / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-serine phosphorylation / response to estradiol / cellular response to heat / regulation of cell population proliferation / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / response to xenobiotic stimulus / neuron projection / positive regulation of apoptotic process / negative regulation of cell population proliferation / heme binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily ...Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACRYLIC ACID / PROTOPORPHYRIN IX CONTAINING CO / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsOrlando, B.J. / Malkowski, M.G. / Dong, L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Fatty Acid Binding to the Allosteric Subunit of Cyclooxygenase-2 Relieves a Tonic Inhibition of the Catalytic Subunit.
Authors: Dong, L. / Yuan, C. / Orlando, B.J. / Malkowski, M.G. / Smith, W.L.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,39613
Polymers126,8252
Non-polymers3,57111
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-22 kcal/mol
Surface area42680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.098, 131.929, 180.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Prostaglandin G/H synthase 2 / Cyclooxygenase-2 / COX-2 / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / ...Cyclooxygenase-2 / COX-2 / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / Macrophage activation-associated marker protein P71/73 / PES-2 / PHS II / Prostaglandin H2 synthase 2 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


Mass: 63412.344 Da / Num. of mol.: 2 / Mutation: S122P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q05769, prostaglandin-endoperoxide synthase

-
Sugars , 4 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: prostaglandin-endoperoxide synthase
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: prostaglandin-endoperoxide synthase
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / References: prostaglandin-endoperoxide synthase
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, 494 molecules

#4: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32CoN4O4 / References: prostaglandin-endoperoxide synthase
#7: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 23-34% PAA 5100, 100mM HEPES, 20mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→30 Å / Num. obs: 59557 / % possible obs: 99.6 % / Redundancy: 4.2 % / Net I/σ(I): 16.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HS5

3hs5


Resolution: 2.36→19.99 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.17
RfactorNum. reflection% reflection
Rfree0.2143 3080 5.2 %
Rwork0.1691 --
obs0.1715 59215 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.36→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 10 490 9640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039442
X-RAY DIFFRACTIONf_angle_d0.71212837
X-RAY DIFFRACTIONf_dihedral_angle_d12.3633455
X-RAY DIFFRACTIONf_chiral_restr0.0271369
X-RAY DIFFRACTIONf_plane_restr0.0031646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3593-2.39610.28321170.24432438X-RAY DIFFRACTION97
2.3961-2.43530.2931450.23882478X-RAY DIFFRACTION99
2.4353-2.47720.29271170.23362555X-RAY DIFFRACTION99
2.4772-2.52220.28111430.21962518X-RAY DIFFRACTION100
2.5222-2.57060.28661210.22272555X-RAY DIFFRACTION100
2.5706-2.62290.24881410.21292530X-RAY DIFFRACTION100
2.6229-2.67990.25051230.21122544X-RAY DIFFRACTION99
2.6799-2.7420.27221610.20262508X-RAY DIFFRACTION100
2.742-2.81040.2361660.19752509X-RAY DIFFRACTION100
2.8104-2.88620.26251570.19422550X-RAY DIFFRACTION100
2.8862-2.97090.25121390.18852532X-RAY DIFFRACTION100
2.9709-3.06640.28371270.19352537X-RAY DIFFRACTION100
3.0664-3.17560.23851160.19242606X-RAY DIFFRACTION100
3.1756-3.30220.22681200.18562551X-RAY DIFFRACTION100
3.3022-3.45180.25151640.17312556X-RAY DIFFRACTION100
3.4518-3.63270.21061330.15472575X-RAY DIFFRACTION100
3.6327-3.85880.17481310.14072566X-RAY DIFFRACTION100
3.8588-4.15430.18021000.13232615X-RAY DIFFRACTION100
4.1543-4.56790.1511330.13342599X-RAY DIFFRACTION100
4.5679-5.21850.17441440.13122585X-RAY DIFFRACTION100
5.2185-6.53640.19181600.17262612X-RAY DIFFRACTION100
6.5364-19.99110.19462220.16042616X-RAY DIFFRACTION99
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)
12.2142-1.84180.38032.72040.15064.31220.22350.3023-0.6638-0.2464-0.12330.50991.0232-0.1727-0.07930.8112-0.028-0.01290.3297-0.06750.516630.75560.143433.0074
21.08450.144-0.82143.09940.96113.20120.28590.2291-0.52790.0321-0.13290.17390.5014-0.337-0.09130.6363-0.151-0.15980.6046-0.06760.70422.942515.656225.6664
30.7217-0.53960.47480.9656-0.76072.5360.09110.0803-0.0152-0.1554-0.0319-0.05380.18730.1333-0.05720.2704-0.03220.0250.254-0.0090.250531.068324.802126.5
40.7316-0.344-0.26370.930.05351.30440.05650.18150.0463-0.1720.00860.04010.0378-0.0841-0.06210.3059-0.0261-0.0110.34790.02540.321219.018535.678927.3069
53.4516-0.21220.45592.42340.3563.6528-0.0371-0.3191-0.44090.06720.19280.30370.1069-0.6891-0.12840.32310.00810.06470.59780.0820.4503-0.84432.416360.4588
63.97170.355-2.74931.48541.04997.6340.0411-0.115-0.39510.150.01870.54660.8172-0.831-0.02430.6564-0.2533-0.11120.65140.21930.69813.05433.691967.0517
71.2141-0.60840.34461.2527-0.70882.097-0.0286-0.1710.07860.10240.06-0.0054-0.1461-0.0812-0.03130.2173-0.02930.01330.2325-0.0340.256123.639731.617667.2507
81.0121-0.3413-0.14640.6555-0.0591.112-0.0057-0.1947-0.02320.06510.0399-0.03550.11780.0305-0.02710.2931-0.01140.01470.25680.02670.278133.211718.448466.4191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 33:78)
2X-RAY DIFFRACTION2(chain A and resid 79:121)
3X-RAY DIFFRACTION3(chain A and resid 122:226)
4X-RAY DIFFRACTION4(chain A and resid 227:582)
5X-RAY DIFFRACTION5(chain B and resid 33:83)
6X-RAY DIFFRACTION6(chain B and resid 84:121)
7X-RAY DIFFRACTION7(chain B and resid 122:226)
8X-RAY DIFFRACTION8(chain B and resid 227:582)

+
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://pdbjlvh1.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