[English] 日本語
Yorodumi
- PDB-4f49: 2.25A resolution structure of Transmissible Gastroenteritis Virus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f49
Title2.25A resolution structure of Transmissible Gastroenteritis Virus Protease containing a covalently bound Dipeptidyl Inhibitor
Components3C-like proteinase
KeywordsHYDROLASE/Hydrolase INHIBITOR / PROTEASE / ANTIVIRAL INHIBITORS / DIPEPTIDYL INHIBITOR / HYDROLASE-Hydrolase INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / viral genome replication / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm ...host cell membrane / viral genome replication / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Coronavirus 3Ecto domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus ...Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Coronavirus 3Ecto domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Trypsin-like serine proteases / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Thrombin, subunit H / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-K36 / Replicase polyprotein 1a
Similarity search - Component
Biological speciesPorcine transmissible gastroenteritis coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLovell, S. / Battaile, K.P. / Kim, Y. / Tiew, K.-C. / Mandadapu, S.R. / Alliston, K.R. / Groutas, W.C. / Chang, K.-O.
CitationJournal: J.Virol. / Year: 2012
Title: Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses.
Authors: Kim, Y. / Lovell, S. / Tiew, K.C. / Mandadapu, S.R. / Alliston, K.R. / Battaile, K.P. / Groutas, W.C. / Chang, K.O.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3May 20, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3C-like proteinase
B: 3C-like proteinase
C: 3C-like proteinase
D: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,7559
Polymers136,6184
Non-polymers2,1365
Water5,350297
1
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6402
Polymers34,1551
Non-polymers4861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6402
Polymers34,1551
Non-polymers4861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6402
Polymers34,1551
Non-polymers4861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8343
Polymers34,1551
Non-polymers6802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.662, 170.140, 66.130
Angle α, β, γ (deg.)90.000, 113.320, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3C-like proteinase / 3CL-PRO / 3CLp / M-PRO / nsp5 / p34


Mass: 34154.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine transmissible gastroenteritis coronavirus
Strain: Purdue / Gene: 1a / Plasmid: pET28(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0C6V2, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-K36 / (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid / GC376 / GC376


Type: peptide-like / Mass: 485.551 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H31N3O8S / Comment: medication, antivirus*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsWHEN THE K36 LIGAND IS MIXED WITH THE TGEV PROTEASE, IT FORMS A COVALENT COMPLEX WITH A LINKAGE ...WHEN THE K36 LIGAND IS MIXED WITH THE TGEV PROTEASE, IT FORMS A COVALENT COMPLEX WITH A LINKAGE BETWEEN C21 OF THE LIGAND AND THE SULFUR ATOM (SG) OF CYS144. THE BISULFITE FUNCTIONAL GROUP OF K36 IS REMOVED DURING THIS REACTION

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 20% PEG 3350, 100 mM MES, 200 mM sodium acetate, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→170.14 Å / Num. all: 57334 / Num. obs: 57334 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.56 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.0574
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.25-2.373.480.61.9828686823297.71
2.37-2.523.690.422.7429082788197.93
2.52-2.693.640.33.726900738498.21
2.69-2.93.550.234.6824680695698.56
2.9-3.183.40.176.3321666637498.89
3.18-3.563.480.119.4120105577498.96
3.56-4.113.710.0813.3819019513399.21
4.11-5.033.580.0615.515578434799.27
5.03-7.123.350.0613.311268336199.7
7.12-170.143.720.0516.67032189299.77

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å34.87 Å
Translation2.5 Å34.87 Å

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
PHASER2.4.0phasing
PHENIXdev_961refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AMP
Resolution: 2.25→55.708 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 2907 5.08 %RANDOM
Rwork0.1813 ---
obs0.1844 57275 98.48 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.987 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 94.6 Å2 / Biso mean: 31.8543 Å2 / Biso min: 11.94 Å2
Baniso -1Baniso -2Baniso -3
1--4.7032 Å20 Å21.6393 Å2
2---1.3206 Å20 Å2
3---6.0238 Å2
Refinement stepCycle: LAST / Resolution: 2.25→55.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9087 0 129 297 9513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019407
X-RAY DIFFRACTIONf_angle_d1.30512735
X-RAY DIFFRACTIONf_chiral_restr0.0861422
X-RAY DIFFRACTIONf_plane_restr0.0051635
X-RAY DIFFRACTIONf_dihedral_angle_d17.2853356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.28690.30911280.262522265097
2.2869-2.32630.3091620.22412544270698
2.3263-2.36860.26241120.21482567267998
2.3686-2.41420.27271360.19692605274198
2.4142-2.46350.28681140.19912564267898
2.4635-2.5170.26621500.2022561271198
2.517-2.57560.26841620.1922562272498
2.5756-2.640.28941320.19972587271998
2.64-2.71140.31661070.19382592269998
2.7114-2.79110.27891280.19382615274398
2.7911-2.88120.25731460.1912575272198
2.8812-2.98420.27661260.1892564269099
2.9842-3.10370.24711660.19012583274999
3.1037-3.24490.25191540.19032570272499
3.2449-3.4160.25661410.18852625276699
3.416-3.630.23161350.18632597273299
3.63-3.91020.24541540.17332606276099
3.9102-4.30350.18791560.14462593274999
4.3035-4.92590.17211280.12982620274899
4.9259-6.20490.20031300.168526482778100
6.2049-55.7080.2171400.19112668280899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.4746-0.55620.44910.9069-0.5092.3133-0.1877-0.52690.10070.27220.1032-0.0531-0.01450.14840.04320.26610.0673-0.0310.279-0.0490.202922.25272.323619.2022
21.86540.22391.15490.8134-0.79711.81960.1968-0.83230.33410.6036-0.1112-0.0902-0.52410.0783-0.01270.4190.0072-0.11640.4584-0.10430.274124.694411.028224.0552
33.34080.53730.30050.9489-0.03113.2473-0.0229-0.07190.2120.05480.08760.1470.1303-0.2621-0.04830.16720.0101-0.04080.2109-0.04570.146311.67626.14639.0266
42.6237-0.46641.92670.7908-0.45291.9718-0.0512-0.43260.09490.1460.11580.1056-0.0861-0.2362-0.07050.21170.03230.01150.2609-0.02810.15837.27994.744311.1657
52.4844-0.6167-0.57542.3118-0.22233.96670.0503-0.2512-0.01410.0989-0.0980.0242-0.3787-0.45010.02430.16290.0092-0.08340.20320.01330.1784-13.02178.4413-2.6791
65.04034.1344-1.2396.3936-3.12675.1916-0.15610.27370.5258-0.25590.1483-0.21-0.1879-0.31150.0230.21150.01420.01760.17360.02930.3351-9.577412.9787-7.6543
74.39632.7745-0.52995.16121.13972.4019-0.1124-0.25730.0688-0.42380.014-0.1128-0.0470.24880.07640.19010.0312-0.02130.15780.04580.33540.48996.5843-7.0182
80.79410.41960.01481.7214-0.10761.96040.07450.14350.40440.03720.0005-0.0741-0.3092-0.0087-0.02530.15420.0198-0.00960.20780.08220.34424.84716.9717-13.3181
91.20990.5810.79483.2391.13072.20910.06650.17830.754-0.26940.16670.0809-1.13920.02330.15450.37670.01950.07890.18470.12930.559831.062427.8478-18.832
102.27961.50821.71634.293.94764.189-0.38940.46480.3675-0.72590.5318-0.8887-0.53340.3043-0.26170.28470.01480.14660.27520.10290.432935.19419.637-21.2905
113.51190.90771.26651.72372.1793.03290.0585-0.0091-0.09250.30730.2887-0.3760.1520.4211-0.27750.1712-0.0129-0.01490.1530.05660.240434.42159.7273-9.4735
122.90420.14030.03024.72492.88334.2013-0.02870.20310.2805-0.00560.2354-0.19470.2132-0.2199-0.11680.1349-0.0480.01280.20950.07240.165618.48738.2247-11.7684
131.37760.9389-0.21323.338-0.30440.0507-0.03380.31740.0693-0.19850.0151-0.1516-0.03470.0046-0.00850.21310.0056-0.02960.29430.03660.173319.89544.1831-17.0609
143.44650.7137-0.51143.2234-0.07421.0955-0.27380.4571-0.2337-0.26360.1441-0.19650.0279-0.14780.11720.2688-0.032-0.00840.1975-0.00310.14879.8972-19.0014-16.393
153.1863-1.38770.28414.79790.05753.6244-0.09790.0863-0.04770.09870.05050.3191-0.087-0.04180.04970.1661-0.01960.02290.20040.04050.17388.5494-17.7012-9.5288
167.6531.60112.26712.52341.18783.9239-0.54140.02380.15840.20840.4093-0.1963-0.54020.39960.11210.25560.0223-0.01580.1724-0.03680.198414.9758-8.1688-5.6954
173.11551.1125-2.27561.3823-2.01722.7585-0.14840.1423-0.2344-0.18850.0917-0.10290.0330.03470.0420.2006-0.00550.00910.1748-0.0570.167551.3169-33.3226-8.4799
182.0879-0.08-0.01381.1579-0.34652.1034-0.10830.4009-0.2869-0.14020.0276-0.03860.0336-0.02040.08610.1935-0.02440.04850.2478-0.06540.178548.442-32.6434-17.3832
192.6730.931-3.0330.8428-1.0244.055-0.04330.4566-0.1195-0.01810.1405-0.0405-0.0528-0.4947-0.11810.1707-0.0038-0.01250.2954-0.01080.203331.9637-31.85-10.1045
203.00041.661.54471.9780.16794.8130.0343-0.0905-0.00980.0232-0.15610.10870.4921-0.21780.06120.19710.03060.06630.24980.02960.216717.5437-36.33163.5569
215.6139-3.75531.40236.8474-2.92513.2203-0.1282-0.1156-0.51310.36060.22050.05560.025-0.0889-0.0590.23380.0098-0.01150.18420.02230.333720.7292-40.89917.8561
222.433-1.48091.11093.09450.4851.53250.0510.1051-0.25040.1737-0.21480.1388-0.08590.19870.110.1398-0.0540.04950.21780.05790.237430.6175-34.56487.368
230.9888-0.39850.14231.9335-0.43951.06780.1078-0.2397-0.31250.0944-0.02-0.00690.128-0.0124-0.08090.2022-0.01030.0170.23460.09050.333854.8439-44.827713.5568
241.6126-0.4646-0.89243.49810.06292.7193-0.155-0.3359-0.61580.54940.0970.06530.65340.17560.04570.39810.03750.07220.28510.17040.614461.5288-55.792719.7804
252.2117-2.4935-1.89383.95573.74743.8732-0.1732-0.253-0.12580.69290.1077-1.01280.35430.202-0.05860.27880.0593-0.09320.38180.13890.524665.5929-47.762421.3083
263.367-0.6332-1.17030.96651.22832.7867-0.0490.00860.1191-0.05190.1368-0.3433-0.1860.281-0.11880.2096-0.00260.01510.13980.03540.249664.7368-37.61559.624
273.7368-0.19760.72874.51531.88683.6742-0.2062-0.042-0.07920.06920.2741-0.1273-0.1155-0.0563-0.0170.16780.03510.01570.23520.0610.229548.7928-36.252212.1005
281.3049-1.1895-0.31812.9751-0.1790.0247-0.1362-0.3469-0.21240.33250.15540.1312-0.06370.1218-0.03930.26720.04150.02660.27780.04410.204950.1619-32.411217.4661
291.62630.20450.63862.1673-1.02960.8906-0.2546-0.22550.25680.34610.07460.10940.0910.24350.03330.30810.1021-0.03250.3305-0.00810.104340.5413-8.848916.8693
306.86440.2466-2.74754.5025-0.23986.66650.0005-0.2760.23140.12540.0075-0.3421-0.2960.0290.04120.16420.0162-0.04230.18290.01820.194142.2643-7.702510.0306
317.5195-0.596-1.16922.88710.76423.7875-0.00440.2249-0.2253-0.31770.07780.19070.21990.1156-0.04780.25850.0110.01240.15490.01050.229640.2822-19.14226.908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 75 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 100 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 138 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 212 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 244 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 270 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 271 through 299 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 52 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 75 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 90 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 109 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 138 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 139 through 212 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 213 through 244 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 245 through 280 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 281 through 298 )B0
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 32 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 33 through 174 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 175 through 212 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 213 through 244 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 245 through 270 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 271 through 299 )C0
23X-RAY DIFFRACTION23chain 'D' and (resid 0 through 52 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 53 through 75 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 76 through 90 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 91 through 109 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 110 through 138 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 139 through 212 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 213 through 244 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 245 through 270 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 271 through 299 )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