[English] 日本語
Yorodumi
- PDB-4nhy: Crystal structure of human OGFOD1, 2-oxoglutarate and iron-depend... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nhy
TitleCrystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)
Components2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
KeywordsOxidoreductase/Oxidoreductase inhibitor / Jelly-roll fold / translation / ribosome / double-stranded beta helix / oxygen sensing / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


peptidyl-proline 3-dioxygenase activity / peptidyl-proline hydroxylation / protein hydroxylation / peptidyl-proline dioxygenase activity / regulation of translational termination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / L-ascorbic acid binding / Protein hydroxylation / stress granule assembly / cytoplasmic stress granule ...peptidyl-proline 3-dioxygenase activity / peptidyl-proline hydroxylation / protein hydroxylation / peptidyl-proline dioxygenase activity / regulation of translational termination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / L-ascorbic acid binding / Protein hydroxylation / stress granule assembly / cytoplasmic stress granule / cell population proliferation / iron ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls ...Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / PYRIDINE-2,4-DICARBOXYLIC ACID / Prolyl 3-hydroxylase OGFOD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsHorita, S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Structure / Year: 2015
Title: Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases.
Authors: Horita, S. / Scotti, J.S. / Thinnes, C. / Mottaghi-Taromsari, Y.S. / Thalhammer, A. / Ge, W. / Aik, W. / Loenarz, C. / Schofield, C.J. / McDonough, M.A.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
B: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
C: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
D: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,16215
Polymers261,9984
Non-polymers1,16511
Water1,49583
1
A: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8144
Polymers65,4991
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8144
Polymers65,4991
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7213
Polymers65,4991
Non-polymers2222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8144
Polymers65,4991
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules

B: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6278
Polymers130,9992
Non-polymers6286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area3100 Å2
ΔGint-41 kcal/mol
Surface area41150 Å2
MethodPISA
6
D: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules

C: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5357
Polymers130,9992
Non-polymers5365
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1/2,y+1/2,-z-11
Buried area2740 Å2
ΔGint-37 kcal/mol
Surface area41390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.680, 130.473, 175.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1 / Termination and polyadenylation 1 homolog


Mass: 65499.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGFOD1, KIAA1612, TPA1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N543, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID / Lutidinic acid


Mass: 167.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 mM MnCl2, 2.0 mM PD2, 20% (w/v) PEG 6000, 100 mM HEPES buffer and 200 mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 77000 / Num. obs: 76983 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.6-2.695.50.9131.921100
2.69-2.85.50.6752.721100
2.8-2.935.30.4724.051100
2.93-3.085.50.3185.511100
3.08-3.285.60.2168.041100
3.28-3.535.40.13610.41100
3.53-3.885.70.094141100
3.88-4.455.40.07118.61100
4.45-5.65.40.0621.51100
5.6-505.20.04921.3199.9

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
HKL-3000data scaling
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KT7

3kt7


Resolution: 2.603→48.238 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 2000 2.6 %Random
Rwork0.1904 ---
obs0.1913 76901 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.7747 Å2
Refinement stepCycle: LAST / Resolution: 2.603→48.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15066 0 70 83 15219
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.1
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shellResolution: 2.6→2.67 Å
RfactorNum. reflection% reflection
Rfree0.2867 133 -
Rwork0.2672 --
obs--94 %
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)
13.1492-0.5618-1.39037.7867-1.7461.99030.1590.97840.6979-1.3234-0.10320.4294-0.8545-0.0710.0020.59860.1037-0.01260.560.19290.5071-15.119959.2286-74.789
22.4835-0.35171.98356.19931.50576.60990.36840.2507-0.1084-0.4928-0.2729-0.02211.0894-0.1674-0.05780.31810.02060.07840.38670.02550.3001-11.788733.6015-68.4736
31.53170.1381-0.41452.9105-1.25186.46850.11630.32640.1128-0.4006-0.1036-0.26510.01980.4429-0.02510.27060.0497-0.01450.3860.05330.3042-7.348244.368-71.3009
44.0081.48531.80944.20880.73027.6716-0.0314-0.08460.5910.0942-0.11560.3998-0.6487-0.26920.11270.2440.05070.040.19610.04670.353-13.974751.634-58.8548
5-0.06210.0277-0.0165-0.5987-1.52226.95650.10590.20.11420.2268-0.08670.0234-0.56730.93240.11660.44350.0884-0.01750.2637-0.02850.4561-5.528946.5978-53.1881
69.3848-2.8495-0.31144.7412-1.19354.5432-0.0787-0.4526-0.22320.44440.15460.12680.30130.1306-0.09980.3131-0.0584-0.06430.1852-0.01920.2132-6.339226.892-21.7814
71.1045-0.56440.13592.1122-1.82528.2885-0.0816-0.19080.22350.32720.12730.1599-0.97370.0267-0.10930.3381-0.0603-0.0240.2354-0.05590.3332-13.158345.005-29.1116
87.8488-2.89644.67932.10786.71912.1729-0.22910.37920.204-0.11140.4295-0.6372-0.19270.7935-0.30710.4138-0.03130.01070.3380.06010.25646.707633.057-20.0858
94.2042-1.85233.60811.27580.04468.51120.03320.26580.14540.064-0.0472-0.07680.05520.39840.01360.3050.00840.01460.15170.00650.2435-7.669137.4193-38.1173
102.23742.30392.36582.9295-7.27822.3486-0.27341.1518-0.1273-0.63880.1465-0.41571.1212-0.0410.87970.47-0.04050.08780.394-0.09880.4247-2.538630.2646-42.3047
117.0622-2.28894.92571.92150.21938.05070.1305-0.1605-0.396-0.1124-0.04160.17770.0582-0.3937-0.10120.4121-0.03910.02020.06440.04310.2682-10.009634.569-37.7342
125.5002-1.6354-0.13291.39433.00612.5052-0.18121.38410.4618-1.14810.37770.1345-0.0025-0.4832-0.23760.8031-0.15070.02010.70480.14190.4335-29.720458.6118-52.3651
131.6454-0.1829-0.63173.4813-1.66397.27170.12270.57320.8217-0.29420.43250.5485-1.4036-1.0235-0.5130.62250.07960.05410.61550.26880.8019-37.407471.1542-38.1823
142.24970.7629-0.68854.8373-0.58687.0254-0.17240.2820.1963-0.29450.27120.1088-0.06130.1264-0.09420.2741-0.02790.05460.31910.05280.2887-31.251856.5561-34.7252
150.27321.493-1.56063.8564-4.73837.618-0.19190.31290.1339-0.50810.49840.31420.4836-0.9015-0.36960.35050.11570.09820.4879-0.01580.4269-37.864552.7169-27.6215
163.5342-1.687-2.94183.61740.6985.30980.0269-0.4942-0.02490.28940.047-0.12860.20780.6856-0.07080.3634-0.0334-0.0530.3882-0.00180.2807-35.262544.53888.1963
171.52171.1003-1.34952.021-3.26388.1393-0.0823-0.0121-0.2501-0.2476-0.1816-0.36681.03150.7570.21020.4050.08660.04930.343-0.01910.3389-29.14337.5191-9.7708
189.4258-0.3509-5.44132.1197-3.42125.2534-0.01530.0695-0.13-0.3244-0.01370.56780.4696-0.44120.04890.3828-0.03920.01080.2956-0.01760.2009-48.350838.16065.4825
194.5781.5455-3.67536.0766-3.6847.31130.2280.21260.39750.07250.14570.2559-0.4073-0.2596-0.32540.35120.02960.06240.2898-0.02280.2396-36.495651.1038-9.8531
205.16923.2-4.14767.1367-2.40266.5870.2999-0.34440.00040.103-0.296-0.5205-0.42170.591-0.00030.35860.0273-0.02850.3213-0.03630.2066-32.664350.8331-8.4515
215.1654-2.3684-3.54055.19651.63882.7855-0.1584-0.8730.38640.8808-0.20110.8205-0.5069-1.90190.37410.72230.14360.15360.8708-0.14110.5308-33.183514.9085-19.5603
221.09380.05370.00351.19061.03075.6186-0.0764-0.1164-0.2110.3575-0.1720.20210.5905-0.79710.21120.4603-0.10350.09570.3309-0.04080.3547-22.70473.2421-29.8815
231.8336-0.2514-1.18473.16991.39154.10690.03140.3149-0.1137-0.35250.004-0.03480.2245-0.0212-0.06730.2419-0.0219-0.02820.3631-0.05050.2998-8.2001-7.3669-72.8256
241.6943-0.8593-0.57355.18654.07285.39120.22260.1440.338-0.5533-0.54190.287-0.6257-0.6240.31430.22230.0305-0.02680.4107-0.04470.3112-20.34721.9924-66.9876
252.35910.40130.96024.17132.33274.8420.1402-0.1849-0.27870.3537-0.27510.28310.4901-0.54710.11990.2928-0.05940.0520.3277-0.03340.2637-15.699-5.868-58.2291
262.27091.23391.19644.87082.79455.12170.03260.130.00050.3755-0.03430.15320.1108-0.06480.01110.1860.06010.03980.2431-0.01080.2206-13.0982-0.5508-56.809
272.7534-0.09693.47184.53632.38085.57920.3686-1.1205-0.01371.5603-0.4329-0.3622-0.69970.71750.10180.9935-0.4223-0.12231.42320.23880.6041-54.750723.7447-29.424
283.18341.3721-2.00352.6779-1.42635.07090.3844-0.65440.13320.319-0.4186-0.0074-0.61150.62090.04090.5188-0.2578-0.04250.69640.1340.4376-60.822425.3952-45.6506
293.58342.4068-5.24640.5023-2.40595.76321.0116-0.70970.40.5753-0.5636-0.0025-0.94820.9038-0.52510.6336-0.1383-0.06290.92470.22680.5793-51.227132.2614-54.5054
308.5413-3.4110.79216.7526-1.49424.8218-0.2580.1226-0.4337-0.5609-0.0764-0.50350.82450.79830.31250.54090.05930.11860.46120.08880.4012-43.236932.5283-90.3812
311.50281.48820.39192.4455-1.89083.65540.1836-0.6513-0.71230.1226-0.5663-0.67350.43581.12120.30730.52720.11240.05820.91470.36720.6248-35.593831.4663-76.2121
324.33792.6313-1.85067.4298-4.67176.0148-0.0342-0.5364-0.44330.1397-0.2851-0.14590.38090.10940.29330.3254-0.01080.02270.52850.10720.3011-47.867831.5906-73.9384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 72 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 101 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 175 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 220 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 258 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 259 through 312 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 313 through 349 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 350 through 433 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 434 through 478 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 479 through 499 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 500 through 542 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 24 through 72 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 73 through 146 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 147 through 220 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 221 through 258 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 259 through 313 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 314 through 349 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 350 through 433 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 434 through 499 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 500 through 542 )B0
21X-RAY DIFFRACTION21chain 'C' and (resid 24 through 72 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 73 through 258 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 259 through 311 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 312 through 361 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 362 through 499 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 500 through 542 )C0
27X-RAY DIFFRACTION27chain 'D' and (resid 24 through 72 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 73 through 220 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 221 through 258 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 259 through 312 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 313 through 361 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 362 through 542 )D0

+
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