[English] 日本語
Yorodumi
- PDB-4rrx: Crystal Structure of Apo Murine V89W Cyclooxygenase-2 Complexed w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rrx
TitleCrystal Structure of Apo Murine V89W Cyclooxygenase-2 Complexed with Lumiracoxib
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE / NSAID / protein-drug complex / 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 / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity ...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 / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / 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 fever generation / response to selenium ion / cellular response to fluid shear stress / prostaglandin secretion / response to nematode / nuclear inner membrane / prostaglandin biosynthetic process / dioxygenase activity / bone mineralization / decidualization / nuclear outer membrane / brown fat cell differentiation / keratinocyte differentiation / positive regulation of brown fat cell differentiation / embryo implantation / peroxidase activity / regulation of blood pressure / regulation of cell population proliferation / response to oxidative stress / cellular response to hypoxia / neuron projection / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / 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
Chem-LUR / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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 / Database references / 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_ref_seq_dif / 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_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 / _struct_ref_seq_dif.details
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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,74512
Polymers134,8402
Non-polymers2,90610
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint14 kcal/mol
Surface area42600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.985, 132.433, 120.354
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 / PGH synthase 2 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


Mass: 67419.789 Da / Num. of mol.: 2 / Mutation: V89W
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

-
Sugars , 3 types, 8 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.: 2
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.: 4
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: 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 , 2 types, 215 molecules

#5: Chemical ChemComp-LUR / {2-[(2-chloro-6-fluorophenyl)amino]-5-methylphenyl}acetic acid / Lumiracoxib


Mass: 293.721 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13ClFNO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.67 Å3/Da / Density % sol: 54 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.78→45.25 Å / Num. all: 36548 / Num. obs: 36512 / % possible obs: 98.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 49.6 Å2 / Rmerge(I) obs: 0.141
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3360 / % possible all: 92.59

-
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: 2.78→45.246 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 1091 3 %RANDOM
Rwork0.2486 ---
all0.2498 36512 --
obs0.2495 36346 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→45.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8962 0 192 213 9367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029488
X-RAY DIFFRACTIONf_angle_d0.65312872
X-RAY DIFFRACTIONf_dihedral_angle_d12.8913506
X-RAY DIFFRACTIONf_chiral_restr0.0271376
X-RAY DIFFRACTIONf_plane_restr0.0031660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7802-2.90670.36811280.33214129X-RAY DIFFRACTION94
2.9067-3.05990.37661350.31334388X-RAY DIFFRACTION100
3.0599-3.25160.29671380.29564423X-RAY DIFFRACTION100
3.2516-3.50260.31021360.27554391X-RAY DIFFRACTION100
3.5026-3.85490.25321360.24374441X-RAY DIFFRACTION100
3.8549-4.41230.28041370.22544435X-RAY DIFFRACTION100
4.4123-5.55740.21411390.21534472X-RAY DIFFRACTION100
5.5574-45.25220.27451420.22774576X-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)
13.06310.31621.96511.74791.01644.0928-0.49010.80030.29920.1550.14920.9492-1.0390.6712-0.16130.39760.0614-0.03760.5406-0.0011.046330.2647-61.4217-34.905
21.6242-0.9766-1.62840.82030.51092.5315-0.34710.779-0.50840.9341-0.53560.58641.109-0.8049-0.18040.7124-0.03750.07140.5331-0.15340.802436.2252-65.3348-40.4988
31.933-1.4572-1.43361.31270.75271.7211-0.6013-0.3317-0.0460.53460.16491.14680.70030.0109-0.04790.739-0.1518-0.15460.4970.04560.801934.5345-68.4595-24.5872
41.9092-1.4575-1.16661.32341.41431.3039-0.5457-0.1772-0.2835-0.460.93641.14060.15210.34090.02351.0697-0.21550.00520.72510.21830.998525.7512-62.4441-11.4683
53.31831.1916-0.22221.52131.24941.62780.4124-0.38920.20090.4671-0.21740.0707-0.725-0.1206-0.35850.7901-0.1050.06240.64690.22240.649724.7568-46.84931.0745
62.8181.12930.95552.10751.23443.25480.52520.466-0.92011.1394-0.0638-0.69810.1937-0.9721-0.4980.6721-0.12520.05480.5240.10491.325332.755-50.8012-12.5038
71.59120.1144-0.74060.7934-0.22261.3669-0.04080.1611-0.15110.3488-0.3749-0.02130.1433-0.20670.25060.3805-0.0381-0.01460.4147-0.03820.380238.5674-46.9436-33.3728
81.6696-0.4031-0.70731.4469-0.4581.0477-0.02210.6902-0.3733-0.57530.1836-0.0161-0.1560.0153-0.04670.61780.0057-0.12660.6019-0.07540.591315.5154-48.4167-40.3605
91.88930.1631.88081.54960.10032.0045-0.5752-0.2375-0.24810.1540.00430.496-0.037-0.69890.01180.46940.01810.06940.8304-0.03010.4527.0091-34.9403-19.3195
103.1033-1.02640.15230.25390.87892.4389-0.10350.48860.0663-0.3874-0.06760.0555-0.236-0.3885-0.09030.4340.0528-0.0210.41-0.02780.512532.0858-29.6776-25.4678
113.1552-0.83670.8081.5464-0.39881.50520.12430.2720.9201-0.0413-0.2198-0.2684-0.3216-0.1420.27390.5730.0857-0.03960.3841-0.04350.422837.8299-11.5091-19.9113
123.6146-0.03790.83252.1199-1.02212.104-0.38830.14590.5732-0.7386-0.14870.0575-0.5764-0.27070.25390.72390.0532-0.2480.51260.00820.694831.4466-12.8901-32.6296
134.0563-0.45541.10792.6614-0.53541.8323-0.4983-0.24441.0257-0.96131.0976-0.9865-0.2134-0.25090.21560.4894-0.032-0.03740.4643-0.10930.787128.9863-14.4206-28.2571
141.05220.0692-0.28211.8026-0.80350.1832-0.0374-0.21680.18940.02780.00420.1111-0.1194-0.07720.03020.42890.04820.00210.4397-0.02540.371136.8629-22.6721-11.5419
151.7770.31770.47251.0285-0.04861.4515-0.6485-1.8056-0.30480.260.198-0.03090.7220.01770.08370.68120.00750.10990.59620.04440.51930.8709-41.6043-4.2238
162.303-0.0929-1.0804-0.03480.73931.4636-0.1538-0.3645-0.01870.0530.01710.1140.2934-0.44080.09470.4493-0.01660.03840.27320.03380.552631.7078-41.3057-20.8858
172.36851.67040.74664.2411-1.60712.7159-0.0539-0.07950.5116-0.16410.31370.7792-0.1861-0.6843-0.24320.49220.1319-0.07980.7538-0.05040.655614.4691-17.1129-19.7454
182.48110.4925-0.55912.0867-0.5351.9315-0.10880.1068-0.2819-0.31220.08250.24340.1928-0.32540.00070.4547-0.0679-0.08590.52110.04210.576814.7936-47.1706-29.2357
192.38770.63150.34791.12660.48951.59130.0042-0.32590.0368-0.0081-0.03420.1590.0066-0.06090.06010.43390.0579-0.02150.39640.02210.385132.2701-33.5199-9.8037
203.91071.39640.41531.5107-0.78020.90770.099-1.49050.03141.09520.66950.279-0.0967-1.33940.64040.50940.47650.20910.9096-0.20740.753116.1541-29.3241-7.2389
210.91130.8374-0.53781.2631-0.29831.41230.1651-0.76710.453-0.6267-0.0127-0.4173-0.05850.2460.18610.47560.0003-0.03560.7087-0.12360.676460.9248-25.8608-3.4929
221.89130.2887-0.31493.6906-0.25271.230.1186-0.77770.7910.2306-0.47250.57180.05930.37890.22880.57310.0959-0.05510.85920.00660.490658.3172-31.77432.4488
236.3434-1.282-1.6212.58341.39290.9301-1.2672-1.8045-2.56691.52530.3713-0.63841.0242-0.62360.14691.12960.00530.0490.75390.12710.826261.658-46.87596.7284
241.02230.0204-0.62862.7425-1.5011.1465-0.504-0.34520.29650.81160.7292-0.37230.64580.15170.13581.0059-0.0628-0.10410.67960.14010.676472.2678-54.957-6.5358
251.30490.39780.19561.7208-0.2320.58020.52910.1749-0.5530.3509-0.0284-0.14330.6555-0.25650.04711.05020.0411-0.17050.51620.12720.772568.2365-67.7878-14.7203
262.70030.33041.89422.00320.12131.75-0.2343-1.35270.09391.66740.4783-0.1726-0.5150.1647-0.03320.7458-0.1024-0.10750.92420.09470.518360.0143-55.2019-12.5321
272.545-0.4366-0.19461.984-0.97513.020.2173-0.02380.30610.2462-0.1906-0.3757-0.04020.2791-0.11470.37490.02060.00330.3459-0.00650.483356.8709-29.8988-17.5749
281.1228-0.33530.27861.4365-1.01632.29570.3230.03720.1846-0.3374-0.1996-0.1303-0.84740.45640.2070.4066-0.1160.07820.5473-0.02870.718782.5104-28.1068-19.3905
291.3473-0.5986-0.67231.23860.13032.0103-0.19760.1252-0.26330.10550.2217-0.0792-0.10740.3023-0.11380.4630.02060.00010.5078-0.09640.48672.6349-47.3461-31.8995
305.44061.2905-0.35985.89354.15059.73050.6211.880.6988-1.5935-0.2057-0.015-1.66011.1413-0.19730.4519-0.02350.11610.6453-0.02860.827461.0172-28.5924-32.0243
311.9951-0.67630.38180.5694-0.32642.120.13370.0443-0.0337-0.24610.0110.0432-0.13140.1776-0.19910.39640.0434-0.06430.4296-0.10690.491256.4066-45.9141-46.878
323.2114-1.11461.61283.0814-1.66351.4274-0.05151.57131.85190.2839-0.66060.341-0.7052-0.57160.05060.8394-0.05950.01980.96220.05890.623564.2695-35.744-51.2187
331.1853-0.06641.2370.9851-0.23932.78760.14310.1093-0.20790.0532-0.02970.04960.17720.3470.17610.45860.1106-0.00170.4355-0.05840.455559.5631-53.8915-38.6902
340.9982-1.6558-0.13291.67610.28511.21920.0729-0.2054-0.0038-0.1381-0.1158-0.07720.17330.3522-0.07750.46130.0107-0.03440.5076-0.05680.390463.6096-45.0576-23.2645
353.28591.18480.81722.1742-1.02564.3869-0.04582.1293-0.6893-0.7558-0.1308-0.517-0.00450.95080.46120.63570.13770.03561.15770.09850.839684.0281-46.1928-45.2841
360.9361-0.11360.71861.8502-1.06123.30130.02030.2387-0.2009-0.37380.11640.08790.11960.92810.35210.53480.1796-0.00450.9739-0.07160.548377.3305-51.0882-46.0411
371.3804-0.4325-0.63023.227-0.00732.39760.1097-0.04720.1816-0.06110.24550.0925-0.3060.06150.09370.3784-0.0221-0.02210.5170.03220.514476.7818-36.1532-17.907
380.79750.5870.52091.8041-0.06251.75031.02480.7518-1.06780.4089-0.5473-1.1710.14310.44860.24150.5045-0.0551-0.08191.3013-0.18430.861190.0593-35.6473-13.2182
392.25091.13120.3580.86260.71942.36560.1869-0.2304-0.33750.18420.027-0.06940.30020.3567-0.03620.44070.1361-0.0290.34080.02470.531565.5283-51.1533-25.5923
402.2399-2.5484-0.96347.0978-4.76498.5887-0.43050.006-1.8569-0.5165-0.9871-1.0822-0.48961.4216-0.50540.38240.023-0.11750.7332-0.08261.049977.5597-59.724-31.9512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 33:45)
2X-RAY DIFFRACTION2(chain A and resid 46:56)
3X-RAY DIFFRACTION3(chain A and resid 57:74)
4X-RAY DIFFRACTION4(chain A and resid 75:89)
5X-RAY DIFFRACTION5(chain A and resid 90:114)
6X-RAY DIFFRACTION6(chain A and resid 115:123)
7X-RAY DIFFRACTION7(chain A and resid 124:156)
8X-RAY DIFFRACTION8(chain A and resid 157:183)
9X-RAY DIFFRACTION9(chain A and resid 184:193)
10X-RAY DIFFRACTION10(chain A and resid 194:239)
11X-RAY DIFFRACTION11(chain A and resid 240:266)
12X-RAY DIFFRACTION12(chain A and resid 267:278)
13X-RAY DIFFRACTION13(chain A and resid 279:292)
14X-RAY DIFFRACTION14(chain A and resid 293:352)
15X-RAY DIFFRACTION15(chain A and resid 353:366)
16X-RAY DIFFRACTION16(chain A and resid 367:391)
17X-RAY DIFFRACTION17(chain A and resid 392:429)
18X-RAY DIFFRACTION18(chain A and resid 430:511)
19X-RAY DIFFRACTION19(chain A and resid 512:578)
20X-RAY DIFFRACTION20(chain A and resid 579:583)
21X-RAY DIFFRACTION21(chain B and resid 33:52)
22X-RAY DIFFRACTION22(chain B and resid 53:70)
23X-RAY DIFFRACTION23(chain B and resid 71:81)
24X-RAY DIFFRACTION24(chain B and resid 82:92)
25X-RAY DIFFRACTION25(chain B and resid 93:110)
26X-RAY DIFFRACTION26(chain B and resid 111:122)
27X-RAY DIFFRACTION27(chain B and resid 123:160)
28X-RAY DIFFRACTION28(chain B and resid 161:186)
29X-RAY DIFFRACTION29(chain B and resid 187:212)
30X-RAY DIFFRACTION30(chain B and resid 213:222)
31X-RAY DIFFRACTION31(chain B and resid 223:267)
32X-RAY DIFFRACTION32(chain B and resid 268:278)
33X-RAY DIFFRACTION33(chain B and resid 279:364)
34X-RAY DIFFRACTION34(chain B and resid 365:394)
35X-RAY DIFFRACTION35(chain B and resid 395:407)
36X-RAY DIFFRACTION36(chain B and resid 408:430)
37X-RAY DIFFRACTION37(chain B and resid 431:482)
38X-RAY DIFFRACTION38(chain B and resid 483:493)
39X-RAY DIFFRACTION39(chain B and resid 494:578)
40X-RAY DIFFRACTION40(chain B and resid 579:583)

+
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