[English] 日本語
Yorodumi
- PDB-4z0l: The murine cyclooxygenase-2 complexed with a nido-dicarbaborate-c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z0l
TitleThe murine cyclooxygenase-2 complexed with a nido-dicarbaborate-containing indomethacin derivative
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / cyclooxygenase / indomethacin / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / positive regulation of synaptic plasticity / regulation of neuroinflammatory response / response to fructose / cyclooxygenase pathway / positive regulation of smooth muscle contraction / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / response to fatty acid / positive regulation of fever generation / response to vitamin D / cellular response to fluid shear stress / prostaglandin secretion / nuclear outer membrane / response to angiotensin / nuclear inner membrane / response to manganese ion / negative regulation of smooth muscle contraction / prostaglandin biosynthetic process / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to ATP / 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 / positive regulation of vasoconstriction / keratinocyte differentiation / positive regulation of brown fat cell differentiation / embryo implantation / positive regulation of synaptic transmission, glutamatergic / : / learning / response to cytokine / positive regulation of smooth muscle cell proliferation / peroxidase activity / caveola / memory / regulation of blood pressure / positive regulation of protein import into nucleus / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-serine phosphorylation / response to estradiol / regulation of cell population proliferation / cellular response to heat / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / neuron projection / positive regulation of apoptotic process / response to xenobiotic stimulus / 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 ...: / 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-4LA / PROTOPORPHYRIN IX CONTAINING FE / Chem-N1B / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsXu, S. / Neumann, W. / Banerjee, S. / Hey-Hawkins, E. / Marnett, L.J.
Funding support United States, Germany, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA89450 United States
German Research Foundation (DFG) Germany
the Fonds der Chemischen Industrie Germany
the Free State of SaxonyESF-NFG 100148835 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: Chemmedchem / Year: 2016
Title: nido-Dicarbaborate Induces Potent and Selective Inhibition of Cyclooxygenase-2.
Authors: Neumann, W. / Xu, S. / Sarosi, M.B. / Scholz, M.S. / Crews, B.C. / Ghebreselasie, K. / Banerjee, S. / Marnett, L.J. / Hey-Hawkins, E.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_detector / pdbx_struct_oper_list / software
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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)279,77933
Polymers269,3314
Non-polymers10,44829
Water11,746652
1
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,74316
Polymers134,6652
Non-polymers5,07814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-22 kcal/mol
Surface area42350 Å2
MethodPISA
2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,03517
Polymers134,6652
Non-polymers5,37015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-18 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.944, 135.011, 124.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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


Mass: 67332.711 Da / Num. of mol.: 4 / Fragment: UNP residues 18-604
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 / Cell line (production host): sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q05769, prostaglandin-endoperoxide synthase

-
Sugars , 3 types, 17 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
#4: 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
#7: 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.: 5 / Source method: isolated from a natural source / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 664 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-4LA / (R)-7-{[5-methoxy-2-methyl-3-(methoxycarbonylmethyl)-1H-indolyl]carbonyl}-7,8-dicarba-nido-dodeca-hydroundecaborate


Mass: 381.586 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H14B9NO4
#6: Chemical
ChemComp-N1B / (S)-7-{[5-methoxy-2-methyl-3-(methoxycarbonylmethyl)-1H-indolyl]carbonyl}-7,8-dicarba-nido-dodeca-hydroundecaborate


Mass: 381.586 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H14B9NO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM ...Details: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM DMSO stocks were added to protein samples. Mixing 3 uL of the protein-inhibitor complex with 3 uL crystallization solution containing 50 mM EPPS, pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550 against reservoir solutions comprised of 50 mM EPPS pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 135815 / % possible obs: 98.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.0609 / Net I/σ(I): 17.7
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.1949 / Mean I/σ(I) obs: 5.7 / % possible all: 91

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NT1

3nt1


Resolution: 2.29→49.6 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4042 2.99 %Random selection
Rwork0.21 ---
obs0.212 135407 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17860 0 736 652 19248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819332
X-RAY DIFFRACTIONf_angle_d0.94626757
X-RAY DIFFRACTIONf_dihedral_angle_d11.6847091
X-RAY DIFFRACTIONf_chiral_restr0.0292749
X-RAY DIFFRACTIONf_plane_restr0.0043312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.31320.4107980.33683373X-RAY DIFFRACTION74
2.3132-2.34140.35961430.32114538X-RAY DIFFRACTION100
2.3414-2.3710.33631280.31214537X-RAY DIFFRACTION100
2.371-2.40220.32711300.29994551X-RAY DIFFRACTION100
2.4022-2.43510.3261540.28914543X-RAY DIFFRACTION99
2.4351-2.46990.36681360.27934485X-RAY DIFFRACTION99
2.4699-2.50680.31861500.27184556X-RAY DIFFRACTION99
2.5068-2.5460.30141360.25824537X-RAY DIFFRACTION99
2.546-2.58770.32661350.2614548X-RAY DIFFRACTION99
2.5877-2.63230.35681380.26544479X-RAY DIFFRACTION99
2.6323-2.68020.27031450.25114499X-RAY DIFFRACTION99
2.6802-2.73170.27321410.24614544X-RAY DIFFRACTION99
2.7317-2.78750.2451250.24234579X-RAY DIFFRACTION100
2.7875-2.84810.31611600.24954524X-RAY DIFFRACTION100
2.8481-2.91430.31961340.25444583X-RAY DIFFRACTION100
2.9143-2.98720.28571460.24954555X-RAY DIFFRACTION100
2.9872-3.0680.30531320.24454594X-RAY DIFFRACTION99
3.068-3.15820.26691420.24214546X-RAY DIFFRACTION100
3.1582-3.26010.27771400.23264587X-RAY DIFFRACTION100
3.2601-3.37660.25031460.2364577X-RAY DIFFRACTION99
3.3766-3.51180.26531310.22014523X-RAY DIFFRACTION99
3.5118-3.67160.29421440.20414609X-RAY DIFFRACTION100
3.6716-3.86510.20451330.1794616X-RAY DIFFRACTION99
3.8651-4.10710.19461510.16984598X-RAY DIFFRACTION99
4.1071-4.42410.17551490.16154604X-RAY DIFFRACTION100
4.4241-4.86890.19661360.1584610X-RAY DIFFRACTION99
4.8689-5.57270.20231460.16544606X-RAY DIFFRACTION98
5.5727-7.01780.2461480.19234720X-RAY DIFFRACTION100
7.0178-49.61350.20821450.18074744X-RAY DIFFRACTION96
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)
12.1553-0.82030.76780.96220.26441.3963-0.0224-0.56360.10660.4175-0.08480.2002-0.22-0.20.10350.4935-0.02020.06860.79330.02290.3456118.157937.157692.3182
24.09070.593-2.34052.7342-0.68282.39430.4466-0.1480.8175-0.0203-0.05910.3985-0.3914-0.1043-0.34320.59510.03230.1950.5051-0.11490.5786111.327764.371475.8878
33.2583-0.2104-0.10330.6607-0.51481.05650.0970.1726-0.0327-0.0635-0.10520.01250.0154-0.18420.00260.2897-0.00530.00770.43360.01450.2365113.389635.934866.5657
42.7080.61780.38930.90410.84281.1657-0.01120.40030.1612-0.2020.14880.09030.0132-0.2546-0.12560.35350.04780.02490.64970.15310.3037119.883246.058441.564
52.35520.444-0.881.1508-0.42211.36530.21760.3480.57120.1285-0.03890.0627-0.2698-0.1687-0.19780.36480.06830.04820.41930.11540.3567120.717353.282662.2392
63.28143.3764-1.05465.26810.13393.3463-0.26850.57480.1138-0.5990.30880.5373-0.0323-0.994-0.02810.42570.0994-0.02811.070.18010.522999.997147.581644.2181
72.83220.16410.07231.38040.60761.59380.1219-0.25830.02840.1703-0.0850.3112-0.0847-0.5194-0.03310.30470.00180.05280.58810.08620.2736102.016739.394573.147
86.7475-0.06272.38821.1894-0.23932.2470.17540.10570.7935-0.0572-0.16420.0374-0.1376-0.20110.03070.38490.08380.10730.3460.03280.4177121.277560.324455.5835
94.0145-1.10662.24122.306-0.44342.2565-0.25140.23120.90140.29140.0011-0.1209-0.44150.52090.23040.5416-0.09980.14960.38580.05420.7775146.399766.658462.8102
102.2807-0.04610.37490.79330.13093.17910.1233-0.39760.41880.2921-0.09230.0095-0.0441-0.2054-0.06610.4106-0.11090.04470.362-0.04980.4046147.67550.490478.728
112.41120.6737-0.41221.578-0.66621.3194-0.00450.0071-0.1752-0.1358-0.0653-0.16430.13140.13320.07250.27380.0080.0040.31720.02660.2036150.649728.114767.5353
121.4850.073-0.35960.3436-0.24010.83160.0702-0.23830.06660.0468-0.1166-0.1266-0.06550.29310.03890.3179-0.0568-0.01850.46220.04410.3286154.571837.409373.9823
133.1853-2.1854-0.63093.55490.99351.1463-0.23-0.96350.0360.46950.2789-0.25950.07560.1827-0.03720.42420.0224-0.02360.91280.01180.3834158.681929.821630.2529
142.7559-0.94051.55173.18990.28771.9777-0.044-0.312-0.80470.17460.01280.13660.30520.02540.05980.5020.06830.05360.42290.23090.5852165.36162.791413.5456
152.8972-0.6254-0.35190.98570.67650.8613-0.0384-0.23560.2004-0.03430.0216-0.0075-0.08910.27080.03060.2847-0.00720.00520.35710.07580.3033163.598831.30994.5525
164.48170.6123-1.02882.1269-0.83993.4148-0.060.43840.0222-0.19820.0765-0.0282-0.13790.1263-0.010.2561-0.00970.00290.3298-0.03810.2139157.125521.5885-20.6162
172.55310.4110.79510.44030.20071.16750.0306-0.022-0.27460.0535-0.01070.11920.19720.0622-0.03330.32010.02180.01280.29170.0410.385156.134414.1154-0.0383
184.36754.16022.74385.69330.04355.9224-0.12290.8404-0.3773-0.52130.3308-0.5382-0.08570.8621-0.18950.3480.01250.07020.6673-0.07490.413176.921619.8757-17.909
192.2006-0.0005-0.3171.0916-0.14611.81-0.0122-0.4692-0.01730.14860.0562-0.1410.02870.4255-0.04260.26330.0225-0.00930.49310.0210.3301174.9127.67511.1428
205.4717-0.4374-1.47071.17470.79211.8934-0.21760.0829-0.95570.0227-0.03870.13930.2990.25080.27390.38670.0670.03840.25720.0590.4466155.55517.1983-6.7971
213.7531-1.2198-1.59972.78610.05451.2352-0.38520.2011-0.87890.30060.08510.27820.4756-0.29340.24120.4257-0.04780.07440.2856-0.01380.6978130.24091.02030.2157
221.68080.1012-0.84790.022-0.10582.4974-0.0726-0.2118-0.40770.2008-0.17180.0739-0.1142-0.11830.30040.3848-0.01110.05760.33480.10340.4348129.03616.971716.388
233.7784-0.9394-0.49041.44210.52171.16440.04320.7109-0.4998-0.1877-0.11140.35920.0403-0.31080.0660.3569-0.01710.0210.4385-0.05670.4522119.57519.3904-8.9089
242.26820.69640.44080.85490.87660.97410.0474-0.02070.1219-0.0338-0.02780.0903-0.1866-0.0699-0.00210.26910.04390.01920.23130.00390.3644127.778141.95888.1037
255.7460.99911.88941.7161-0.13527.563-0.217-0.00520.5393-0.11170.00990.1805-0.4392-0.13220.2650.29030.03570.00720.1864-0.03440.4252128.932949.477610.8407
261.88770.10860.16210.70560.31491.0814-0.0352-0.16170.02360.034-0.04140.1967-0.0049-0.17970.07830.23960.00060.03710.29730.00970.3114121.578531.455411.1727
271.34060.1435-0.13980.81740.43151.4631-0.0154-0.2183-0.10060.0789-0.11380.19720.0953-0.22250.09740.2550.01660.01460.24460.05220.3429123.621228.123412.6907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 33:85 )A33 - 85
2X-RAY DIFFRACTION2( CHAIN A AND RESID 86:120 )A86 - 120
3X-RAY DIFFRACTION3( CHAIN A AND RESID 121:237 )A121 - 237
4X-RAY DIFFRACTION4( CHAIN A AND RESID 238:319 )A238 - 319
5X-RAY DIFFRACTION5( CHAIN A AND RESID 320:390 )A320 - 390
6X-RAY DIFFRACTION6( CHAIN A AND RESID 391:428 )A391 - 428
7X-RAY DIFFRACTION7( CHAIN A AND RESID 429:534 )A429 - 534
8X-RAY DIFFRACTION8( CHAIN A AND RESID 535:582 )A535 - 582
9X-RAY DIFFRACTION9( CHAIN B AND RESID 33:85 )B33 - 85
10X-RAY DIFFRACTION10( CHAIN B AND RESID 86:143 )B86 - 143
11X-RAY DIFFRACTION11( CHAIN B AND RESID 144:319 )B144 - 319
12X-RAY DIFFRACTION12( CHAIN B AND RESID 320:582 )B320 - 582
13X-RAY DIFFRACTION13( CHAIN C AND RESID 33:85 )C33 - 85
14X-RAY DIFFRACTION14( CHAIN C AND RESID 86:120 )C86 - 120
15X-RAY DIFFRACTION15( CHAIN C AND RESID 121:237 )C121 - 237
16X-RAY DIFFRACTION16( CHAIN C AND RESID 238:319 )C238 - 319
17X-RAY DIFFRACTION17( CHAIN C AND RESID 320:390 )C320 - 390
18X-RAY DIFFRACTION18( CHAIN C AND RESID 391:428 )C391 - 428
19X-RAY DIFFRACTION19( CHAIN C AND RESID 429:534 )C429 - 534
20X-RAY DIFFRACTION20( CHAIN C AND RESID 535:582 )C535 - 582
21X-RAY DIFFRACTION21( CHAIN D AND RESID 33:85 )D33 - 85
22X-RAY DIFFRACTION22( CHAIN D AND RESID 86:143 )D86 - 143
23X-RAY DIFFRACTION23( CHAIN D AND RESID 144:181 )D144 - 181
24X-RAY DIFFRACTION24( CHAIN D AND RESID 182:269 )D182 - 269
25X-RAY DIFFRACTION25( CHAIN D AND RESID 270:319 )D270 - 319
26X-RAY DIFFRACTION26( CHAIN D AND RESID 320:485 )D320 - 485
27X-RAY DIFFRACTION27( CHAIN D AND RESID 486:582 )D486 - 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://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