[English] 日本語
Yorodumi
- PDB-4rrw: Crystal Structure of Apo Murine Cyclooxygenase-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rrw
TitleCrystal Structure of Apo Murine Cyclooxygenase-2
ComponentsProstaglandin G/H synthase 2Cyclooxygenase
KeywordsOXIDOREDUCTASE / prostaglandin-endoperoxide synthase / glycosylation / membrane
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 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / hair cycle / 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 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / hair cycle / Nicotinamide salvaging / 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 / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / response to fructose / positive regulation of smooth muscle contraction / response to fatty acid / cyclooxygenase pathway / positive regulation of fever generation / response to vitamin D / prostaglandin secretion / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / prostaglandin biosynthetic process / nuclear inner membrane / cellular response to ATP / negative regulation of smooth muscle contraction / maintenance of blood-brain barrier / positive regulation of cell migration involved in sprouting angiogenesis / 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 / positive regulation of vasoconstriction / response to glucocorticoid / keratinocyte differentiation / embryo implantation / positive regulation of brown fat cell differentiation / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / peroxidase activity / 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 / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / response to estradiol / cellular response to heat / positive regulation of peptidyl-serine phosphorylation / regulation of cell population proliferation / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / endoplasmic reticulum / 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
Chem-LUR / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.569 Å
AuthorsXu, S. / Blobaum, A.L. / Banerjee, S. / Marnett, L.J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Action at a Distance: MUTATIONS OF PERIPHERAL RESIDUES TRANSFORM RAPID REVERSIBLE INHIBITORS TO SLOW, TIGHT BINDERS OF CYCLOOXYGENASE-2.
Authors: Blobaum, A.L. / Xu, S. / Rowlinson, S.W. / Duggan, K.C. / Banerjee, S. / Kudalkar, S.N. / Birmingham, W.R. / Ghebreselasie, K. / Marnett, L.J.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
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.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,16520
Polymers269,5234
Non-polymers4,64216
Water9,728540
1
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,08310
Polymers134,7622
Non-polymers2,3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint11 kcal/mol
Surface area42810 Å2
MethodPISA
2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,08310
Polymers134,7622
Non-polymers2,3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint14 kcal/mol
Surface area42670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.711, 121.047, 135.111
Angle α, β, γ (deg.)90.00, 123.20, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Prostaglandin G/H synthase 2 / Cyclooxygenase / 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 / PGH synthase 2 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


Mass: 67380.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): baculovirus
References: UniProt: Q05769, prostaglandin-endoperoxide synthase
#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.: 4
Source method: isolated from a genetically manipulated source
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: 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.: 8
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
#4: Chemical
ChemComp-LUR / {2-[(2-chloro-6-fluorophenyl)amino]-5-methylphenyl}acetic acid / Lumiracoxib / Lumiracoxib


Mass: 293.721 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H13ClFNO2 / Comment: antiinflammatory, inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM EPPS pH 8.0, 20~25% PEG MME 550, 80~120 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.569→107.814 Å / Num. all: 28740 / Num. obs: 28734 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 38.9 Å2
Reflection shellResolution: 2.569→2.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 1.6 / % possible all: 96.12

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NT1

3nt1


Resolution: 2.569→45.123 Å / SU ML: 0.3 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 2746 3.01 %
Rwork0.1841 --
obs0.1851 -98.57 %
all-75618 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.569→45.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17912 0 304 540 18756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418768
X-RAY DIFFRACTIONf_angle_d0.70725456
X-RAY DIFFRACTIONf_dihedral_angle_d13.2456932
X-RAY DIFFRACTIONf_chiral_restr0.0312724
X-RAY DIFFRACTIONf_plane_restr0.0033284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.569-2.61370.28771410.26054362X-RAY DIFFRACTION98
2.6137-2.66120.30621340.2534429X-RAY DIFFRACTION99
2.6612-2.71240.28621400.24514426X-RAY DIFFRACTION99
2.7124-2.76770.28771370.23244370X-RAY DIFFRACTION98
2.7677-2.82790.27081310.23154274X-RAY DIFFRACTION96
2.8279-2.89370.29791320.23794470X-RAY DIFFRACTION99
2.8937-2.9660.25431330.23054421X-RAY DIFFRACTION99
2.966-3.04620.28861390.23054446X-RAY DIFFRACTION99
3.0462-3.13580.261390.21874439X-RAY DIFFRACTION99
3.1358-3.2370.22881470.20184485X-RAY DIFFRACTION100
3.237-3.35270.21141390.20724443X-RAY DIFFRACTION99
3.3527-3.48690.21711430.19554421X-RAY DIFFRACTION98
3.4869-3.64550.21691370.17414344X-RAY DIFFRACTION97
3.6455-3.83760.21691350.16814377X-RAY DIFFRACTION98
3.8376-4.07790.19051340.15814456X-RAY DIFFRACTION99
4.0779-4.39250.18271400.14914480X-RAY DIFFRACTION99
4.3925-4.83410.17751310.14214479X-RAY DIFFRACTION99
4.8341-5.53250.17851390.15024348X-RAY DIFFRACTION96
5.5325-6.96630.21111390.18094518X-RAY DIFFRACTION100
6.9663-45.13020.17971360.17614506X-RAY DIFFRACTION98
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)
10.9661-0.930.08980.92350.1680.7145-0.3995-0.5859-0.30010.84890.26960.26790.1935-0.210.11510.63770.02130.21150.74090.10880.5178-62.173212.934129.4847
20.8594-1.58470.3324.95510.38530.5654-0.0754-0.4169-0.25760.34410.02980.63890.1535-0.14510.04710.4165-0.04080.11310.58360.06920.418-60.250510.292316.5203
31.7501-0.65220.18361.1072-0.05970.6714-0.0493-0.16380.2125-0.02730.0456-0.1516-0.08250.1162-0.00070.2827-0.03080.05740.291-0.00520.2892-43.565919.11996.7974
42.39070.50820.37273.12570.27121.63420.17440.15340.0151-0.4286-0.0762-0.2375-0.21030.3197-0.09490.3380.0380.11640.3968-0.01970.3294-36.416411.252-6.3444
51.4578-0.41750.42971.0417-0.17241.36510.1022-0.1209-0.27010.0048-0.00110.21630.19230.0126-0.10110.279-0.00960.03820.29910.01020.3131-51.11684.50236.2401
61.97730.9271-0.07683.93491.00252.96430.1335-0.13660.26770.18250.031-0.6076-0.0090.3146-0.14680.3436-0.01380.06510.4826-0.00980.4755-23.73089.98635.2189
71.3426-0.55960.47951.33570.0050.5465-0.0827-0.4515-0.03790.25740.1178-0.0973-0.0176-0.0751-0.01690.29660.00080.07450.45030.01530.2595-44.389612.102918.5195
82.5497-1.3466-0.10511.64310.56470.24970.17950.2685-1.17070.1273-0.22920.81310.1923-0.09970.09090.5902-0.0518-0.11340.4243-0.03350.9955-79.2714-4.4923-5.5023
93.1795-0.8664-1.88071.08270.96452.3142-0.0716-0.0486-0.5144-0.0270.02230.46460.4777-0.0760.09040.3109-0.0675-0.04350.35240.01330.5185-75.73236.97870.369
101.4994-0.65930.32531.10820.04480.64150.19420.2922-0.1566-0.5013-0.16630.4206-0.07450.0074-0.01520.3830.0405-0.05380.3796-0.04840.3603-75.837824.7595-11.285
112.0858-0.36220.22452.3877-0.46262.8463-0.00410.0830.0132-0.3222-0.02230.3903-0.2915-0.16010.04820.3260.0705-0.01790.3007-0.04770.3412-78.56639.6871-3.7701
121.2955-0.50870.24751.33860.30630.87960.11870.122-0.2969-0.2548-0.1320.6084-0.0296-0.23010.01890.33250.0042-0.07530.4069-0.05030.5643-84.96220.268-6.2264
130.9809-0.14670.36662.33371.50241.46930.03530.35850.2717-0.18820.2071-0.7961-0.23020.4753-0.28510.4654-0.05810.12270.6378-0.02880.6729-63.8796-29.79941.6818
141.0456-0.22860.13254.97231.36190.79830.03390.290.2355-0.61840.05-0.3942-0.09010.358-0.0710.36360.00050.04710.5132-0.00210.3954-76.0808-27.27346.4974
150.69990.23730.4650.58530.24220.89520.29140.2451-0.25730.20640.0727-0.4040.55330.4801-0.33170.48320.1648-0.05040.5108-0.10440.4861-69.6819-47.169354.9055
161.1507-0.46540.4261.53540.47121.3221-0.1264-0.14370.03840.41360.1553-0.21220.08010.1082-0.01930.40120.0473-0.03260.3219-0.05650.3015-80.467-27.821966.5098
170.5458-0.51490.33841.67571.42982.5902-0.07370.01550.2762-0.5798-0.2453-0.2541-0.904-0.14370.28540.64940.0690.01550.38510.04930.575-101.7601-12.611332.7848
181.273-0.8502-1.39061.06651.65025.04330.03880.06290.246-0.2484-0.127-0.0594-0.535-0.10550.07150.39480.02650.01720.36410.020.3915-95.2415-24.067434.9308
191.02920.00170.57050.83760.29560.9098-0.0511-0.09070.04480.0065-0.09530.29910.0647-0.33250.14640.323-0.02830.06110.4037-0.0120.3051-106.5712-41.850137.45
202.48770.32440.20622.3329-0.24141.56060.04810.0473-0.1792-0.02860.05750.33390.1617-0.1676-0.06970.3854-0.05560.01910.3552-0.0170.298-99.8336-56.765433.1714
211.1701-0.22770.38761.24560.48681.1842-0.00270.14830.0634-0.256-0.09920.2434-0.0513-0.20270.10670.3636-0.0129-0.01130.38410.01630.278-103.6775-37.37327.4281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 105A)
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 269 )
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 319 )
5X-RAY DIFFRACTION5chain 'A' and (resid 320 through 390 )
6X-RAY DIFFRACTION6chain 'A' and (resid 391 through 428 )
7X-RAY DIFFRACTION7chain 'A' and (resid 429 through 583 )
8X-RAY DIFFRACTION8chain 'B' and (resid 33 through 105A)
9X-RAY DIFFRACTION9chain 'B' and (resid 106 through 138 )
10X-RAY DIFFRACTION10chain 'B' and (resid 139 through 269 )
11X-RAY DIFFRACTION11chain 'B' and (resid 270 through 319 )
12X-RAY DIFFRACTION12chain 'B' and (resid 320 through 583 )
13X-RAY DIFFRACTION13chain 'C' and (resid 33 through 105A)
14X-RAY DIFFRACTION14chain 'C' and (resid 106 through 138 )
15X-RAY DIFFRACTION15chain 'C' and (resid 139 through 181 )
16X-RAY DIFFRACTION16chain 'C' and (resid 182 through 583 )
17X-RAY DIFFRACTION17chain 'D' and (resid 33 through 105A)
18X-RAY DIFFRACTION18chain 'D' and (resid 106 through 138 )
19X-RAY DIFFRACTION19chain 'D' and (resid 139 through 269 )
20X-RAY DIFFRACTION20chain 'D' and (resid 270 through 319 )
21X-RAY DIFFRACTION21chain 'D' and (resid 320 through 583 )

+
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