[English] 日本語
Yorodumi
- PDB-7vph: Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vph
TitleCrystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98
Components
  • Isoform 3 of Nuclear pore complex protein Nup98-Nup96
  • ORF6 protein
  • mRNA export factor
KeywordsVIRAL PROTEIN / Complex / Coronavirus / RNA nuclear export / Protein binding
Function / homology
Function and homology information


transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket ...transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / mitotic spindle pole / Vpr-mediated nuclear import of PICs / host cell Golgi membrane / SUMOylation of DNA replication proteins / cellular response to organic cyclic compound / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / molecular condensate scaffold activity / ubiquitin binding / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / fibrillar center / HCMV Early Events / Separation of Sister Chromatids / protein import into nucleus / nuclear envelope / snRNP Assembly / microtubule binding / nuclear membrane / transcription coactivator activity / host cell endoplasmic reticulum membrane / nuclear body / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / cell cycle / cell division / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Non-structural protein NS6, betacoronavirus / Betacoronavirus NS6 protein / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like ...Non-structural protein NS6, betacoronavirus / Betacoronavirus NS6 protein / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ORF6 protein / Nuclear pore complex protein Nup98-Nup96 / mRNA export factor RAE1
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, T. / Guo, H. / Yang, T. / Wen, Y. / Ji, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81871639 China
CitationJournal: Front Mol Biosci / Year: 2021
Title: Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export.
Authors: Li, T. / Wen, Y. / Guo, H. / Yang, T. / Yang, H. / Ji, X.
History
DepositionOct 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mRNA export factor
B: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
C: mRNA export factor
D: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
E: mRNA export factor
F: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
G: mRNA export factor
H: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
I: ORF6 protein
J: ORF6 protein
K: ORF6 protein
X: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)210,68412
Polymers210,68412
Non-polymers00
Water1,00956
1
A: mRNA export factor
B: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
X: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)52,6713
Polymers52,6713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-15 kcal/mol
Surface area17070 Å2
MethodPISA
2
C: mRNA export factor
D: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
I: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)52,6713
Polymers52,6713
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-17 kcal/mol
Surface area16430 Å2
MethodPISA
3
E: mRNA export factor
F: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
J: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)52,6713
Polymers52,6713
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-15 kcal/mol
Surface area17140 Å2
MethodPISA
4
G: mRNA export factor
H: Isoform 3 of Nuclear pore complex protein Nup98-Nup96
K: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)52,6713
Polymers52,6713
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-18 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.657, 103.319, 136.588
Angle α, β, γ (deg.)90.00, 97.45, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
mRNA export factor / Rae1 protein homolog / mRNA-associated protein mrnp 41


Mass: 42398.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAE1, MRNP41 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P78406
#2: Protein
Isoform 3 of Nuclear pore complex protein Nup98-Nup96


Mass: 7785.728 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98, ADAR2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P52948, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Protein/peptide
ORF6 protein / ORF6 / Accessory protein 6 / Non-structural protein 6 / ns6 / Protein X3


Mass: 2486.661 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Sodium citrate pH 5.5, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.796→41.065 Å / Num. obs: 51228 / % possible obs: 99.32 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 1
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 5087 / CC1/2: 0.58

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMY

3mmy


Resolution: 2.8→41.06 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 1992 3.89 %
Rwork0.1924 --
obs0.1945 51064 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12503 0 0 56 12559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112839
X-RAY DIFFRACTIONf_angle_d1.3817416
X-RAY DIFFRACTIONf_dihedral_angle_d7.7661672
X-RAY DIFFRACTIONf_chiral_restr0.0711855
X-RAY DIFFRACTIONf_plane_restr0.0112278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.41351390.34553441X-RAY DIFFRACTION97
2.87-2.940.37831420.32113505X-RAY DIFFRACTION100
2.94-3.030.32681410.28963490X-RAY DIFFRACTION100
3.03-3.130.32921440.26913543X-RAY DIFFRACTION100
3.13-3.240.31921390.26063462X-RAY DIFFRACTION99
3.24-3.370.29611440.2453528X-RAY DIFFRACTION100
3.37-3.520.29471430.22783527X-RAY DIFFRACTION100
3.52-3.710.25021410.20093474X-RAY DIFFRACTION100
3.71-3.940.26181420.18173527X-RAY DIFFRACTION100
3.94-4.240.23211440.16293528X-RAY DIFFRACTION100
4.24-4.670.18211430.13163535X-RAY DIFFRACTION100
4.67-5.350.15941450.13223557X-RAY DIFFRACTION100
5.35-6.730.28071430.16713547X-RAY DIFFRACTION100
6.73-41.060.18521420.17563520X-RAY DIFFRACTION97
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)
12.93151.831.8852.38381.34881.3058-0.38230.4791-0.0174-0.48740.2797-0.1191-0.25240.92130.03560.4542-0.05990.15530.7646-0.02190.7499-15.939626.3828-1.2791
22.88820.18150.13923.6622-1.20112.87350.02320.0134-0.1052-0.0983-0.017-0.5559-0.19960.4026-0.02310.27730.04730.06770.4675-0.04660.4262-22.239813.33346.5938
32.0341-1.264-1.11194.90691.34392.8492-0.07460.0651-0.24870.08540.02470.39920.3822-0.06430.10210.3421-0.0338-0.02210.3988-0.01760.3033-38.771912.33712.2218
41.8882-0.0613-0.73155.1342-1.30182.92620.1045-0.28190.03530.35270.05620.2151-0.1175-0.1429-0.14910.3056-0.0196-0.03310.3954-0.01320.2966-38.536930.014420.6294
53.14391.28820.16993.55042.14961.58430.09650.32270.3755-0.6301-0.1888-0.1554-0.3989-0.02660.01840.4471-0.03160.09910.34420.00340.4333-28.557937.94999.1268
63.1610.45080.51274.0344-0.31093.92110.0572-0.16480.45760.3554-0.1822-0.4549-0.52960.196-0.05310.4929-0.10680.0460.4019-0.03160.5256-24.830738.256113.9097
73.24110.8280.83963.38090.85862.76730.20320.3118-0.0469-0.65620.0618-0.8277-0.06390.5329-0.25590.48670.00480.15360.4878-0.02790.5528-22.281629.22543.3081
83.09210.4572-1.5885.51793.75883.75030.2919-0.3183-0.17270.22940.30690.5371-0.3372-0.6216-0.56150.78640.0708-0.0510.64850.17120.4956-41.781338.7644-5.5791
97.94993.02023.50897.37422.0112.26720.2348-0.57840.16920.23390.6872-2.0329-2.3681-1.2966-0.68381.35610.18840.0520.5728-0.03110.8737-38.409350.33554.5794
105.32961.74710.63018.4014-1.70621.65470.04450.27530.1317-0.25590.1920.11770.2472-0.1788-0.16030.57220.0691-0.10230.50460.01830.2314-41.0427.1914-6.1004
112.4664-0.82830.96721.59730.46561.8408-0.20110.2935-0.46830.2492-0.10290.78290.3982-0.79080.26060.5505-0.2920.04840.86420.04111.2859-2.625844.681925.1695
125.17290.6425-0.42940.13150.16290.9491-0.01120.4903-0.312-0.53850.06411.04310.2637-0.66240.11270.5435-0.1931-0.16860.67530.03481.12423.262349.173215.6113
133.86170.76871.31382.8980.89224.8938-0.08880.1219-0.1488-0.09240.13010.4511-0.06440.1029-0.00660.363-0.09130.00840.3675-0.0060.440419.340957.596923.6392
142.8798-1.8286-1.43122.13981.64991.24770.30260.43780.0890.7651-0.5786-0.14810.0217-0.36580.29880.7425-0.10350.29140.47440.03590.743113.373957.661937.9935
152.43051.7046-0.12912.4633-0.21973.08040.1529-0.4558-0.1430.9257-0.12250.68940.4682-0.2021-0.07760.8959-0.14520.37560.55080.0151.00578.193252.045344.9032
161.3176-0.6899-0.99270.62060.72332.9781-0.00070.2342-0.19510.4762-0.20650.84380.9832-0.91030.1690.7317-0.30650.23170.8093-0.03091.413-0.036142.524234.7729
170.08610.0789-0.01750.2535-0.15030.10020.1753-0.35620.65971.0479-0.44061.70470.68630.2317-0.21591.1052-0.03140.08920.8460.03360.939421.964928.086331.2805
181.93521.3736-0.07021.6744-0.70560.49390.1597-0.4319-0.23670.71790.1508-0.05810.96910.2248-0.20321.38010.06930.22160.57580.08721.10819.834834.28942.2349
197.1389-0.5921-1.47754.4099-4.70175.6837-0.29790.936-1.04730.08490.12220.80961.8933-0.44730.13191.142-0.14320.10870.4708-0.10040.957216.122932.481125.4768
205.8036-0.23530.12640.97840.10412.68220.24650.47481.2756-0.02610.1550.4291-1.0913-0.201-0.60690.61560.23310.27780.70750.02350.9853-0.08589.744632.7782
210.87321.2164-0.1191.9257-0.97872.87690.2497-0.18550.22940.7336-0.09180.6821-0.1588-0.5424-0.12130.90750.06230.46460.6304-0.02770.9393.1465-1.56244.3045
221.9172-0.3606-0.02561.25510.87923.71970.1399-0.29260.08120.99340.00120.46090.1811-0.16210.00170.8533-0.00760.21750.4681-0.0130.45717.368-10.059946.7585
234.3722-0.572-0.97884.8414-0.96267.23720.1155-0.0595-0.0795-0.0186-0.24670.12440.2873-0.03840.04670.45220.01450.14070.4301-0.04640.396520.1572-14.867530.6501
243.2397-1.2878-0.4656.132-0.45264.13990.2460.42390.0997-0.7066-0.1290.1988-0.0251-0.3583-0.11020.43470.03830.02970.45150.04080.459712.9733-6.188320.0868
255.191-0.22580.37514.39981.21296.4670.35570.0142-0.36950.3169-0.34061.15450.0752-0.4988-0.05110.58050.11450.20720.5831-0.03830.80463.33461.060829.4228
264.041-0.62531.02323.31660.82123.72660.1065-0.30410.92740.2449-0.07540.6278-0.8612-0.8135-0.01350.64240.17770.17560.57340.09570.65817.28887.168929.6299
272.7712-0.56751.53333.24591.5095.70290.0733-0.14250.06630.7419-0.1710.041-0.4135-0.27830.00410.7478-0.15070.22130.50990.07690.484727.897114.138127.2851
285.67455.4613-0.44976.166-3.46129.9188-0.7656-0.06690.0727-0.77230.8879-0.47910.9656-0.6857-0.43020.69170.02-0.11940.8138-0.05190.95721.07732.07576.3896
293.4825-0.0957-0.58391.0125-1.99074.56650.1931-0.02120.05420.2773-0.1719-0.1758-0.2822-0.0193-0.11290.7655-0.07510.17310.4260.01630.587225.17169.558733.3267
304.181-0.90270.81251.5285-0.79670.4254-0.1639-0.89110.03880.63390.4205-0.17610.71150.576-0.06751.29390.0345-0.421.02980.16620.5389-21.350518.382863.9724
311.73490.33820.59071.52060.36012.7437-0.0090.00840.24251.11020.0205-0.4440.01130.63290.01921.1125-0.155-0.32671.00530.05220.4322-24.741226.968563.723
322.03030.02280.79792.3981.55061.6501-0.116-0.39240.1820.6891-0.02330.0613-0.29860.18220.12961.0012-0.0721-0.0630.66990.01830.3548-38.719130.33255.443
333.1405-1.00961.00483.8463-0.6573.83850.0885-0.1877-0.3620.89880.09530.58090.3161-0.1563-0.07260.7985-0.0308-0.00690.42750.10650.3482-41.810714.56947.7858
343.3233-0.08260.56761.3186-1.21741.06440.3831-0.4893-0.78670.8473-0.2050.26461.16410.53480.04511.44480.0563-0.08040.6160.17410.7503-39.94140.355152.922
351.82070.3058-0.14530.19220.55362.1777-0.2369-0.3652-0.61161.7681-0.248-0.98010.68040.87930.09761.42430.0847-0.40280.82540.28560.4168-27.1657.477156.7986
362.9519-0.1977-0.56390.1671-0.27952.28430.1123-0.596-1.05521.2662-0.2322-0.1770.62420.3337-0.07461.50120.0587-0.26731.14470.34920.656-27.89969.605767.4783
377.5706-1.62830.39852.613-2.69373.1919-0.6078-0.8224-2.04780.05250.11990.11240.1779-0.7090.23822.0694-0.30440.3340.85310.31981.006-47.70061.209471.6874
381.2355-1.26640.89155.6059-4.46083.7733-0.2995-1.0412-0.73420.2866-0.30620.43190.75570.62770.80081.6836-0.02340.11051.02140.15380.7089-48.27346.619368.9911
396.794-0.9124-0.62093.5579-2.98226.6322-0.5952-1.27630.27392.26850.57670.23770.1770.72380.231.59580.0450.05521.05890.1410.5599-42.669819.534275.4788
400.2137-0.97510.20594.6143-1.45842.7817-0.1097-0.3727-0.52340.12160.60751.23680.3222-0.15620.2621.7174-0.16580.86740.65930.35780.93443.783552.136253.0377
417.0673-2.48846.762.4335-1.36877.1328-0.06551.82781.5273-0.29850.19170.3412-0.6903-0.9548-0.27260.54640.0841-0.22190.83320.26080.796110.1644-6.16411.0032
425.7562-1.69522.30798.06822.47533.11340.79-0.5353-0.75620.21720.29781.2162-0.71120.4331-1.26261.21080.07820.07640.74720.1760.9512-31.094-5.247351.7349
430.042-0.2586-0.42113.57432.52094.37580.00170.9951.6901-0.52970.01060.0048-1.16140.3697-0.18440.9448-0.21590.04640.66770.04930.7444-26.217745.235515.9534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 196 )
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 258 )
5X-RAY DIFFRACTION5chain 'A' and (resid 259 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 310 )
7X-RAY DIFFRACTION7chain 'A' and (resid 311 through 365 )
8X-RAY DIFFRACTION8chain 'B' and (resid 158 through 172 )
9X-RAY DIFFRACTION9chain 'B' and (resid 173 through 186 )
10X-RAY DIFFRACTION10chain 'B' and (resid 187 through 213 )
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 69 )
12X-RAY DIFFRACTION12chain 'C' and (resid 70 through 125 )
13X-RAY DIFFRACTION13chain 'C' and (resid 126 through 208 )
14X-RAY DIFFRACTION14chain 'C' and (resid 209 through 235 )
15X-RAY DIFFRACTION15chain 'C' and (resid 236 through 310 )
16X-RAY DIFFRACTION16chain 'C' and (resid 311 through 365 )
17X-RAY DIFFRACTION17chain 'D' and (resid 158 through 162 )
18X-RAY DIFFRACTION18chain 'D' and (resid 163 through 199 )
19X-RAY DIFFRACTION19chain 'D' and (resid 200 through 213 )
20X-RAY DIFFRACTION20chain 'E' and (resid 25 through 41 )
21X-RAY DIFFRACTION21chain 'E' and (resid 42 through 105 )
22X-RAY DIFFRACTION22chain 'E' and (resid 106 through 187 )
23X-RAY DIFFRACTION23chain 'E' and (resid 188 through 235 )
24X-RAY DIFFRACTION24chain 'E' and (resid 236 through 310 )
25X-RAY DIFFRACTION25chain 'E' and (resid 311 through 334 )
26X-RAY DIFFRACTION26chain 'E' and (resid 335 through 365 )
27X-RAY DIFFRACTION27chain 'F' and (resid 158 through 169 )
28X-RAY DIFFRACTION28chain 'F' and (resid 170 through 183 )
29X-RAY DIFFRACTION29chain 'F' and (resid 184 through 213 )
30X-RAY DIFFRACTION30chain 'G' and (resid 26 through 61 )
31X-RAY DIFFRACTION31chain 'G' and (resid 62 through 105 )
32X-RAY DIFFRACTION32chain 'G' and (resid 106 through 187 )
33X-RAY DIFFRACTION33chain 'G' and (resid 188 through 244 )
34X-RAY DIFFRACTION34chain 'G' and (resid 245 through 275 )
35X-RAY DIFFRACTION35chain 'G' and (resid 276 through 334 )
36X-RAY DIFFRACTION36chain 'G' and (resid 335 through 366 )
37X-RAY DIFFRACTION37chain 'H' and (resid 158 through 183 )
38X-RAY DIFFRACTION38chain 'H' and (resid 184 through 199 )
39X-RAY DIFFRACTION39chain 'H' and (resid 200 through 213 )
40X-RAY DIFFRACTION40chain 'I' and (resid 53 through 61 )
41X-RAY DIFFRACTION41chain 'J' and (resid 54 through 61 )
42X-RAY DIFFRACTION42chain 'K' and (resid 53 through 61 )
43X-RAY DIFFRACTION43chain 'X' and (resid 53 through 61 )

+
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://pdbjlvh1.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