[English] 日本語
Yorodumi
- PDB-4rut: crystal structure of murine cyclooxygenase-2 with 13-methyl-arach... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rut
Titlecrystal structure of murine cyclooxygenase-2 with 13-methyl-arachidonic Acid
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE / PROTEIN-LIGAND COMPLEX / PROSTAGLANDIN-ENDOPEROXIDE SYNTHASE / FATTY ACID ANALOG / 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) / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / positive regulation of fibroblast growth factor production ...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) / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / negative regulation of synaptic transmission, dopaminergic / positive regulation of transforming growth factor beta production / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / prostanoid biosynthetic process / regulation of neuroinflammatory response / cyclooxygenase pathway / positive regulation of fever generation / positive regulation of prostaglandin biosynthetic process / positive regulation of smooth muscle contraction / response to selenium ion / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin secretion / positive regulation of synaptic plasticity / cellular response to fluid shear stress / response to nematode / prostaglandin biosynthetic process / negative regulation of smooth muscle contraction / nuclear inner membrane / positive regulation of cell migration involved in sprouting angiogenesis / bone mineralization / maintenance of blood-brain barrier / decidualization / negative regulation of calcium ion transport / negative regulation of cell cycle / nuclear outer membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / positive regulation of vasoconstriction / positive regulation of vascular endothelial growth factor production / keratinocyte differentiation / positive regulation of synaptic transmission, glutamatergic / positive regulation of brown fat cell differentiation / response to cytokine / embryo implantation / positive regulation of smooth muscle cell proliferation / brown fat cell differentiation / learning / peroxidase activity / positive regulation of protein import into nucleus / caveola / regulation of blood pressure / memory / positive regulation of nitric oxide biosynthetic process / regulation of cell population proliferation / response to oxidative stress / angiogenesis / response to lipopolysaccharide / cellular response to hypoxia / neuron projection / positive regulation of apoptotic process / endoplasmic reticulum lumen / negative regulation of cell population proliferation / heme binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm / cytosol
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 ...: / 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
PROTOPORPHYRIN IX CONTAINING CO / Chem-LM8 / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsXu, S. / Kudalkar, S.N. / Banerjee, S. / Makriyannis, A. / Nikas, S.P. / Marnett, L.J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: 13-methylarachidonic Acid is a positive allosteric modulator of endocannabinoid oxygenation by cyclooxygenase.
Authors: Kudalkar, S.N. / Nikas, S.P. / Kingsley, P.J. / Xu, S. / Galligan, J.J. / Rouzer, C.A. / Banerjee, S. / Ji, L. / Eno, M.R. / Makriyannis, A. / Marnett, L.J.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
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 / pdbx_struct_conn_angle / 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_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
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
Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.pdbx_aromatic_flag

-
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)277,13526
Polymers269,3314
Non-polymers7,80422
Water20,5011138
1
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,56813
Polymers134,6652
Non-polymers3,90211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-19 kcal/mol
Surface area42040 Å2
MethodPISA
2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,56813
Polymers134,6652
Non-polymers3,90211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-17 kcal/mol
Surface area41900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.796, 121.539, 134.943
Angle α, β, γ (deg.)90.00, 123.60, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#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 / PGH synthase 2 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


Mass: 67332.711 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: PLV1393 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q05769, prostaglandin-endoperoxide synthase

-
Sugars , 3 types, 14 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.: 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


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
#6: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 3 types, 1146 molecules

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


Mass: 619.575 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#5: Chemical
ChemComp-LM8 / (5Z,8Z,11Z,13S,14Z)-13-methylicosa-5,8,11,14-tetraenoic acid / (5Z,8Z,11Z,14Z)-13S-methyl-5,8,11,14-eicosatetraenoic acid


Mass: 318.493 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H34O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1138 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
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-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.16→112.4 Å / Num. all: 152423 / Num. obs: 152390 / % possible obs: 98.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 39.46 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.12
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.48 / Num. unique all: 15303 / % possible all: 95.94

-
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: PDB entry 3NT1 chain A

3nt1


Resolution: 2.16→112.393 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 4542 2.98 %RANDOM
Rwork0.176 ---
all0.1782 152390 --
obs0.1775 152330 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→112.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17896 0 528 1138 19562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01318996
X-RAY DIFFRACTIONf_angle_d1.45325778
X-RAY DIFFRACTIONf_dihedral_angle_d13.6397066
X-RAY DIFFRACTIONf_chiral_restr0.0512738
X-RAY DIFFRACTIONf_plane_restr0.0063316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1596-2.18420.33571310.30024644X-RAY DIFFRACTION93
2.1842-2.20990.3121710.28784920X-RAY DIFFRACTION98
2.2099-2.23680.31241430.27914849X-RAY DIFFRACTION97
2.2368-2.26510.30341510.27254807X-RAY DIFFRACTION97
2.2651-2.2950.33781410.27634869X-RAY DIFFRACTION96
2.295-2.32640.35041480.2614816X-RAY DIFFRACTION97
2.3264-2.35960.30081580.23644933X-RAY DIFFRACTION99
2.3596-2.39490.27711580.21364959X-RAY DIFFRACTION99
2.3949-2.43230.26821500.21434946X-RAY DIFFRACTION99
2.4323-2.47220.24181380.20564966X-RAY DIFFRACTION99
2.4722-2.51480.26511670.20494944X-RAY DIFFRACTION99
2.5148-2.56050.25071490.20494967X-RAY DIFFRACTION99
2.5605-2.60980.25441560.20344940X-RAY DIFFRACTION99
2.6098-2.66310.26481500.20454957X-RAY DIFFRACTION99
2.6631-2.7210.27091540.18974944X-RAY DIFFRACTION98
2.721-2.78430.28041490.19324887X-RAY DIFFRACTION97
2.7843-2.85390.28221540.19614841X-RAY DIFFRACTION97
2.8539-2.93110.24781530.18975020X-RAY DIFFRACTION99
2.9311-3.01730.24461490.19324972X-RAY DIFFRACTION99
3.0173-3.11470.23621590.18884963X-RAY DIFFRACTION99
3.1147-3.22610.24251460.1844988X-RAY DIFFRACTION99
3.2261-3.35520.25781510.18824973X-RAY DIFFRACTION99
3.3552-3.50790.22141580.16974942X-RAY DIFFRACTION99
3.5079-3.69290.24011430.15814846X-RAY DIFFRACTION96
3.6929-3.92430.18871570.14664981X-RAY DIFFRACTION99
3.9243-4.22730.1921520.14214982X-RAY DIFFRACTION99
4.2273-4.65270.16081500.13314991X-RAY DIFFRACTION99
4.6527-5.3260.16081420.13084941X-RAY DIFFRACTION98
5.326-6.710.19971610.15894947X-RAY DIFFRACTION98
6.71-112.54540.17071530.16055053X-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)
11.5215-0.20210.81342.7526-2.20392.75470.0968-0.37270.08490.1260.17810.3714-0.2561-0.6759-0.29510.33380.05790.12780.58330.05230.4701-81.5015-26.557318.5293
24.0332-0.60951.87213.36510.86771.5298-0.2705-0.24890.81670.36780.34040.3608-0.4875-0.00490.04140.43120.1160.06540.482-0.00820.558-74.5376-1.90085.049
31.6156-0.06660.68721.5258-0.64091.44530.0772-0.1995-0.2014-0.10340.1120.27270.3109-0.3656-0.15550.339-0.089-0.00950.36230.09070.3327-72.8147-36.82514.1322
41.08760.46170.28211.645-0.37841.368-0.05140.13920.1264-0.38380.2040.3650.0549-0.1133-0.05530.3816-0.0672-0.09320.33360.05780.2816-69.9769-22.7318-12.8525
530.875-0.02752.35-0.66981.7588-0.1820.4203-0.1722-0.54070.0285-0.21720.14440.23530.15460.3664-0.01380.05930.31430.03540.2254-49.8956-20.359-15.9213
61.8239-0.01630.58670.9128-0.36211.1354-0.0370.03610.1824-0.04040.04390.1152-0.0568-0.05860.0080.3088-0.0067-0.01930.27890.05220.2895-60.7574-12.4959-1.2627
72.41561.2443-0.54824.0832.63682.776-0.19370.26640.0833-1.02570.1780.5230.2631-0.2257-0.00010.6989-0.1172-0.14190.460.09240.3574-65.9225-17.8378-28.2246
81.7740.62720.22851.6513-0.29031.50250.0174-0.00440.0403-0.23940.1630.50080.1762-0.4635-0.19060.296-0.0671-0.0840.43340.11570.4258-81.9853-26.4657-4.1428
91.67980.7160.57531.7-0.48161.8619-0.21980.18960.3088-0.20410.01320.0978-0.2964-0.02470.12320.3530.0041-0.03590.24950.01610.306-56.6161-5.0794-6.7422
100.44730.59510.12472.0482-2.06693.7796-0.17820.00850.18170.3979-0.12670.0835-0.71290.15160.2320.4662-0.0134-0.07110.2824-0.02570.4897-42.9556-3.638423.5828
113.2511.8221-3.1461.1125-1.96383.26120.1451-0.11410.55150.2614-0.11070.1896-0.7817-0.1052-0.22910.41130.0602-0.02620.3612-0.01680.4119-49.6766-15.164421.7904
121.2879-0.01620.77721.1775-0.22041.4981-0.20090.27380.2679-0.0002-0.0338-0.369-0.15870.52180.20970.3001-0.0529-0.00250.44070.10430.3695-29.1046-17.494212.3582
131.26490.13020.4121.1628-0.13650.95270.03710.0094-0.08460.0385-0.034-0.13510.17490.0914-0.02410.2710.03420.00750.21980.0210.224-42.6634-40.185421.9615
142.5492-0.13211.02232.4165-0.08121.29650.1094-0.031-0.16790.0762-0.0657-0.12730.1360.013-0.02590.318-0.00370.02210.27160.03120.2092-50.2937-44.957923.4192
151.41640.02650.38660.8846-0.49231.69840.0448-0.28810.16670.3146-0.0167-0.0938-0.1251-0.05770.05550.32350.0023-0.01180.2079-0.03920.2306-48.1997-22.995227.8278
162.69730.4878-0.00162.3515-0.10611.3409-0.0046-0.3021-0.3380.2568-0.1098-0.31310.21110.27650.05510.43910.0319-0.12310.42920.06870.426-32.595-46.6235.2233
171.4686-0.02110.1731.1933-0.37021.4389-0.0391-0.15320.2810.2944-0.1084-0.3276-0.20720.33660.18380.3441-0.0564-0.1070.36490.02490.4062-29.5169-17.844426.9718
181.8589-0.12190.33611.7433-0.57321.50220.0432-0.37630.03710.14270.02140.11670.1287-0.2242-0.0430.27850.0040.06160.2941-0.01010.1738-56.8891-35.962732.2294
192.8653-2.5176-0.04552.39490.29311.1671-0.4058-0.6844-0.26430.54380.26590.04720.0265-0.26450.06940.40730.04920.08190.63960.05430.3389-102.3698-33.409286.9815
201.4371-0.2781.51074.4759-1.71652.4029-0.085-0.1367-0.45630.22780.50620.83530.4169-0.5215-0.35830.5448-0.06960.06560.58670.20390.4651-91.8954-57.629376.9844
212.0651-0.9691.3290.7733-0.12751.764-0.1448-0.44030.16310.1020.10970.08530.0126-0.17950.06750.25690.04680.02160.3603-0.06640.2636-97.5496-24.928569.2772
221.2025-0.30.26821.34190.37291.16370.04930.00250.074-0.15660.0244-0.1743-0.0510.0999-0.08050.2105-0.0010.03850.22180.00060.2416-78.2499-37.953356.9759
231.9431-0.62960.74131.40750.13610.95460.0698-0.1709-0.21780.0830.04680.04260.19240.0044-0.09290.24370.02040.03140.31530.04620.2256-88.7835-45.407469.794
241.71320.1005-0.00711.62110.56651.54280.1276-0.14990.0192-0.02760.193-0.57340.04460.2094-0.21210.32440.00670.04170.4017-0.06630.4437-60.9404-41.759861.4762
251.68-0.24030.20731.50470.3640.8524-0.1073-0.56160.15040.36910.1384-0.14480.0453-0.0955-0.05690.34240.0523-0.02480.4595-0.05360.2523-80.8336-32.93782.3847
262.4007-0.41090.60871.53090.44440.84510.15250.0008-0.4545-0.03680.0047-0.00910.10410.0744-0.17550.29880.0146-0.03960.2230.01940.3506-83.9984-54.440657.1864
273.098-0.8729-0.53630.82650.19620.29570.0899-0.0413-0.7357-0.0439-0.05090.4460.1663-0.0236-0.01150.5021-0.0444-0.14420.39070.03720.6292-115.5223-52.268452.5787
281.3767-0.31240.38680.6496-0.16560.81190.1770.571-0.2982-0.5575-0.13490.42070.2080.0973-0.06520.49260.0741-0.17140.399-0.08850.4244-108.7424-42.043534.5299
291.0709-0.18030.30821.02170.08840.82290.05750.0871-0.0748-0.2907-0.06270.3912-0.0262-0.18340.01950.31420.0234-0.09180.3107-0.010.409-119.5491-26.354848.4005
301.8307-0.69260.51291.75620.02411.7187-0.0057-0.4415-0.0292-0.05660.09470.4728-0.0312-0.42420.00510.2145-0.00180.03050.40710.030.3988-122.028-23.456166.1546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 218 )
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 319 )
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 390 )
7X-RAY DIFFRACTION7chain 'A' and (resid 391 through 428 )
8X-RAY DIFFRACTION8chain 'A' and (resid 429 through 535 )
9X-RAY DIFFRACTION9chain 'A' and (resid 536 through 583 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 105A)
11X-RAY DIFFRACTION11chain 'B' and (resid 106 through 138 )
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 181 )
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 269 )
14X-RAY DIFFRACTION14chain 'B' and (resid 270 through 346 )
15X-RAY DIFFRACTION15chain 'B' and (resid 347 through 390 )
16X-RAY DIFFRACTION16chain 'B' and (resid 391 through 428 )
17X-RAY DIFFRACTION17chain 'B' and (resid 429 through 535 )
18X-RAY DIFFRACTION18chain 'B' and (resid 536 through 583 )
19X-RAY DIFFRACTION19chain 'C' and (resid 33 through 94 )
20X-RAY DIFFRACTION20chain 'C' and (resid 95 through 123 )
21X-RAY DIFFRACTION21chain 'C' and (resid 124 through 158 )
22X-RAY DIFFRACTION22chain 'C' and (resid 159 through 346 )
23X-RAY DIFFRACTION23chain 'C' and (resid 347 through 390 )
24X-RAY DIFFRACTION24chain 'C' and (resid 391 through 428 )
25X-RAY DIFFRACTION25chain 'C' and (resid 429 through 535 )
26X-RAY DIFFRACTION26chain 'C' and (resid 536 through 583 )
27X-RAY DIFFRACTION27chain 'D' and (resid 33 through 138 )
28X-RAY DIFFRACTION28chain 'D' and (resid 139 through 181 )
29X-RAY DIFFRACTION29chain 'D' and (resid 182 through 536 )
30X-RAY DIFFRACTION30chain 'D' and (resid 537 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