[English] 日本語
Yorodumi
- PDB-7vpg: Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vpg
TitleCrystal structure of the C-terminal tail of SARS-CoV-1 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
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 organization / nuclear pore outer ring / nuclear pore complex assembly / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / 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 organization / nuclear pore outer ring / nuclear pore complex assembly / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / 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 / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / positive regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / mitotic spindle pole / host cell Golgi membrane / Vpr-mediated nuclear import of PICs / 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 / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / ubiquitin binding / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / fibrillar center / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / microtubule binding / nuclear membrane / transcription coactivator activity / host cell endoplasmic reticulum membrane / nuclear body / cell cycle / ribonucleoprotein complex / cell division / mRNA binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96 / ORF6 protein / mRNA export factor RAE1
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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
X: ORF6 protein
I: ORF6 protein
J: ORF6 protein
K: ORF6 protein


Theoretical massNumber of molelcules
Total (without water)211,36912
Polymers211,36912
Non-polymers00
Water7,332407
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)52,8423
Polymers52,8423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)52,8423
Polymers52,8423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)52,8423
Polymers52,8423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)52,8423
Polymers52,8423
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.614, 103.299, 134.936
Angle α, β, γ (deg.)90.000, 95.958, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 25 through 183 or resid 185...
d_2ens_1(chain "C" and (resid 25 through 183 or resid 185 through 205 or resid 207 through 365))
d_3ens_1(chain "E" and (resid 25 through 183 or resid 185 through 205 or resid 207 through 365))
d_4ens_1(chain "G" and (resid 25 through 183 or resid 185 through 205 or resid 207 through 365))
d_1ens_2(chain "B" and (resid 158 through 172 or resid 181 through 213))
d_2ens_2chain "D"
d_3ens_2(chain "F" and (resid 158 through 172 or resid 181 through 213))
d_4ens_2(chain "H" and (resid 158 through 172 or resid 181 through 213))
d_1ens_3chain "I"
d_2ens_3chain "J"
d_3ens_3chain "K"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNALAA1 - 159
d_12ens_1VALARGA161 - 181
d_13ens_1ILEASNA183 - 239
d_14ens_1SERARGA243 - 340
d_21ens_1ASNALAC1 - 159
d_22ens_1VALARGC161 - 181
d_23ens_1ILEARGC183 - 337
d_31ens_1ASNALAE2 - 160
d_32ens_1VALARGE162 - 182
d_33ens_1ILEARGE184 - 338
d_41ens_1ASNALAG2 - 160
d_42ens_1VALARGG162 - 182
d_43ens_1ILEARGG184 - 338
d_11ens_2THRTHRB1 - 15
d_12ens_2ASNLYSB20 - 52
d_21ens_2THRLYSD1 - 48
d_31ens_2THRTHRF1 - 15
d_32ens_2ASNLYSF22 - 54
d_41ens_2THRTHRH1 - 15
d_42ens_2ASNLYSH19 - 51
d_11ens_3ASPTYRJ1 - 10
d_21ens_3ASPTYRK1 - 10
d_31ens_3ASPTYRL1 - 10

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.999848051541, 0.00845764318596, 0.015242772087), (0.0134396523175, -0.182876651157, 0.983044000138), (0.0111017825029, 0.983099485674, 0.182735195548)-21.6664027973, 45.2902717295, 6.58008830063
2given(-0.984868600223, 0.0862822289477, -0.150297096654), (0.164150841714, 0.186341545041, -0.968675038264), (-0.0555728482216, -0.978689023929, -0.197685237135)-17.8201859947, 5.60411583934, 58.0787830831
3given(0.990456267532, -0.125930634688, 0.0560165810625), (-0.126045541194, -0.992023335343, -0.00149120088429), (0.055757543454, -0.00558367101385, -0.99842872503)0.675979474443, 36.8286945954, 69.1768832526
4given(-0.999978304543, 0.00410122807653, -0.00515464554073), (-0.00587621651607, -0.201784974615, 0.97941221868), (0.00297666287017, 0.979421259698, 0.201804696502)-21.6356221596, 45.1067653216, 6.58176732448
5given(-0.980531158201, 0.0762813652884, -0.180941430042), (0.19311970195, 0.207816274706, -0.958914582581), (-0.0355447396229, -0.975188981315, -0.218501767059)-17.5264384871, 6.10390557411, 58.6428322407
6given(0.990618149058, -0.118971953833, 0.0672410362665), (-0.118465416972, -0.992891753481, -0.0114852448886), (0.0681294924292, 0.00341175463405, -0.997670653167)0.466546540485, 37.0873922609, 69.3706949521
7given(0.969106832499, -0.242825495504, 0.0432171949157), (-0.245408934121, -0.966840792571, 0.070663546997), (0.0246252361714, -0.0790864119434, -0.996563564049)14.3944037119, 42.0912344446, 69.5648366901
8given(-0.981769219424, 0.165513178712, -0.0934590148872), (0.119169764076, 0.152927359093, -0.981025886596), (-0.148080272559, -0.974278507673, -0.169863540424)-28.3084177376, 39.2235038249, 112.219015277

-
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 / / Accessory protein 6 / Non-structural protein 6 / ns6 / Protein X3


Mass: 2657.919 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome-related coronavirus
References: UniProt: P59634
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / 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: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→47.44 Å / Num. obs: 317454 / % possible obs: 99.74 % / Redundancy: 4.4 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 7.6
Reflection shellResolution: 2.49→2.57 Å / Num. unique obs: 7090 / CC1/2: 0.62

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMY

3mmy


Resolution: 2.49→47.44 Å / SU ML: 0.3955 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0609
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 3856 2.78 %
Rwork0.1855 134659 -
obs0.1867 138515 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.21 Å2
Refinement stepCycle: LAST / Resolution: 2.49→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12717 0 0 407 13124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008713059
X-RAY DIFFRACTIONf_angle_d1.094717722
X-RAY DIFFRACTIONf_chiral_restr0.06181887
X-RAY DIFFRACTIONf_plane_restr0.00842322
X-RAY DIFFRACTIONf_dihedral_angle_d7.47621705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.709941832532
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.750587761874
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.759771965431
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.990063141655
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.936683736954
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.705373716682
ens_3d_2JX-RAY DIFFRACTIONTorsion NCS1.74663103221
ens_3d_3JX-RAY DIFFRACTIONTorsion NCS1.90682059469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.520.45271330.35854622X-RAY DIFFRACTION93.62
2.52-2.550.35891390.33884823X-RAY DIFFRACTION98.86
2.55-2.580.37531370.29954866X-RAY DIFFRACTION98.5
2.58-2.620.28471390.29594857X-RAY DIFFRACTION98.62
2.62-2.650.36361390.29224848X-RAY DIFFRACTION98.11
2.65-2.690.32061390.27664788X-RAY DIFFRACTION97.93
2.69-2.740.32511410.28314786X-RAY DIFFRACTION97.72
2.74-2.780.34141390.28154812X-RAY DIFFRACTION97.46
2.78-2.830.32691400.26854795X-RAY DIFFRACTION97.76
2.83-2.880.33551370.25434809X-RAY DIFFRACTION98.8
2.88-2.930.30991410.25894943X-RAY DIFFRACTION98.76
2.93-2.990.3151340.22754770X-RAY DIFFRACTION98.83
2.99-3.060.29481380.22814877X-RAY DIFFRACTION98.47
3.06-3.130.28291430.20364884X-RAY DIFFRACTION98.67
3.13-3.210.24051370.20944780X-RAY DIFFRACTION98.79
3.21-3.30.23751390.19264839X-RAY DIFFRACTION98.5
3.3-3.390.25941410.19464899X-RAY DIFFRACTION98.5
3.39-3.50.24631380.18764740X-RAY DIFFRACTION97.27
3.5-3.630.19961340.174769X-RAY DIFFRACTION96.74
3.63-3.770.21831410.15914781X-RAY DIFFRACTION97.52
3.77-3.940.23791410.15814854X-RAY DIFFRACTION98.27
3.94-4.150.15861350.15024780X-RAY DIFFRACTION98.34
4.15-4.410.15591370.13564847X-RAY DIFFRACTION98.54
4.41-4.750.15131390.12094821X-RAY DIFFRACTION98.08
4.75-5.230.2011350.12534760X-RAY DIFFRACTION96.7
5.23-5.990.20991330.15044781X-RAY DIFFRACTION97.19
5.99-7.540.19991350.15354809X-RAY DIFFRACTION97.55
7.54-47.440.13761320.15174719X-RAY DIFFRACTION95.95
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)
12.2137191530.4612237210821.057563139892.191703065121.18723395260.927265165325-0.06548940422410.0183820555934-0.144947165655-0.75290985070.00905034831666-0.674349409792-0.2458850179480.6985034751270.1086494541990.366207568984-0.09705333231620.1653340538110.567572661225-0.05572578651010.472177986878-15.650051309526.431432236-1.74673978392
22.3187088975-0.5182891557280.5195993567112.648218634820.2078275720152.12569776717-0.07992177389390.0746389949862-0.2950054414180.03368902811070.0375121905361-0.2230095678020.2080131130630.2148227879980.04191507958190.3202211898610.02353387648390.04629083172450.251018487646-0.02291745704560.294166880297-26.59397798711.28873708457.88555648873
31.7385748439-0.2152361327680.07601338171583.48826549071-0.03754493990192.60086441317-0.00610707123224-0.00046514480082-0.03131186923390.135035538403-0.1067976517310.155099524934-0.0206964010129-0.01757095921810.1028352792690.231207426555-0.0139564778780.02769799278970.2436968383550.002271788424710.209878123859-39.837296598823.92175461617.7693407373
42.6841097653-3.288391260111.734305279254.07330481912-2.559517140424.34323829651-0.1304004166910.02627647045690.397684258217-0.135808174314-0.213633718302-0.637878904562-0.7906098332780.07859931602760.3246871446710.560925905363-0.0568610757036-0.02317973458040.2475487122270.04878885151450.325684494455-30.475036731241.99865631184.85104310755
51.709496158730.120813681778-0.09824125422382.758362687660.5239146458271.801200044430.0979178555301-0.0519468628010.0459795022308-0.0374283894331-0.0319166072668-0.538149438678-0.2870060764160.379587996045-0.1104579270370.239057466342-0.05296423051940.01644255254270.265463987265-0.02033950509190.302324249702-22.157027786532.518216815211.1598465015
62.497235515770.04902828778750.1119336413662.990393912690.04603882420452.431022174880.003973241738940.2681290936180.0555292982562-0.4434589645870.0820664862943-0.379338218898-0.1889596681320.364884232219-0.1226954696430.367547789983-0.0138663670220.09950081559820.3004463982990.008639393831170.382617869963-22.80794948530.15183658061.12730959184
72.94063015557-0.861543956902-1.778436389772.05995475916-0.7547015735981.445253077660.0331199105444-0.09029582284890.143583313624-0.1430759312720.0326355461217-0.1631486131080.0321753154771-0.0312421518459-0.1028784485790.5885465324250.0800496675854-0.07692715453520.4022384552860.06136052085990.294572739956-40.966612242239.7636381812-4.54997044568
89.04940118257-2.806376918720.09330479244228.436945933051.965322286539.960851218-0.302999458553-0.7023569317020.3469234467480.969039687004-0.3154438640850.502239928163-1.102881065170.5734515429860.5501240655950.818304944363-0.0817819271513-0.02274882411840.4516961371010.01566639704490.301333330115-38.140492290750.36207186644.57443681991
93.945123228842.288133897590.6896626700879.30698931666-1.378095833064.66163692370.08993134230520.4525118995920.109249106564-0.797307827843-0.03080344997540.597581655632-0.130747150682-0.455951011815-0.03688726556980.4300194691510.08650296416990.01062438132170.363983527062-0.000828462656580.292868081456-43.773863171633.3192159431-3.26909131365
109.599314437240.5480695641152.683491207832.02980122445-0.7946676541894.493611403560.3824075066810.644364248909-0.557386962379-1.44901844037-0.2211300170050.179398886427-0.050721346586-0.0205074447108-0.1076589701590.5046201108960.0224740832845-0.02075967293180.316054650844-0.03314546648640.377686183401-38.208260236321.8700517776-8.55213555481
112.35743277309-0.214079983402-0.5698518353070.877606061751-0.1061986552421.65922363931-0.07987737900110.343498703806-0.17818285833-0.0957845361966-0.0001967269901270.6038470079120.421875222212-0.6944106591190.07772373287630.374803208439-0.162876361081-0.04053682632760.532268914026-0.06902556540080.637022328699-0.99385219597846.574373910923.044485251
122.133784895080.853767881236-0.1886886239012.126994812030.7138179522732.22874706584-0.1042741428990.327982519503-0.142837338994-0.3849869488360.1201020619210.1646588196380.093010810133-0.250237845038-0.007262481144470.339217208523-0.0837863274123-0.02551524262520.316181892619-0.03184955275220.35201256965515.952515946654.529654724519.0968327769
133.05326827641-0.06666803211050.4137508307485.59864517848-1.916267842543.715806956570.210073352947-0.2779049591840.316126763666-0.432857270759-0.149286581719-0.294116061921-0.0117036937960.228294949629-0.0601317300330.262714149577-0.002390754367840.01598051379230.249585100696-0.03843837109690.34233981797423.14790189961.860793050529.8762410814
143.71569383437-0.1549458071020.7125815195234.30866198888-0.27109951282.568322979570.0272478089559-0.3153345806910.01285839668260.03157476790170.04041748951450.5521626960540.167870344041-0.152717710826-0.05107150705920.366370909354-0.09931153075260.04048470198560.314863493301-0.02151474858510.31239941779515.016582508457.8228229738.6719610362
152.763170866910.4532536012650.3266430029924.074064642580.3720747548471.102229050090.16159586343-0.336122431323-0.1778923607750.640258178715-0.2370917992330.401292275290.316247406645-0.1969748672590.04392142216430.441269447338-0.1140073822060.1170936665540.385509356243-0.02988387929460.36237895979211.208800917352.460994199545.2535912327
163.141407235871.482067726660.3363888383612.856390519220.3332913964343.007677862530.125528946843-0.247766229240.008208534742290.475626797203-0.2538984916840.8295136010330.524837031096-0.8003213295520.1236110527240.412904261693-0.1431633270890.1105228920660.401437684351-0.05217991482590.5480338087710.82048210653548.748760296140.5388331892
173.841598380160.322619299738-1.073164647582.3077265513-0.136932836642.489626931410.03135630208260.170750899909-0.1763479815820.35258258598-0.2761928379430.7478363989970.607879767244-0.7004249644530.2103210810730.418236172099-0.2058991857540.03184326476650.496146857728-0.08018835142890.6024743152171.402970658740.521672633436.1066471435
186.69020976361.30370612483-0.1288829825141.830606259432.244101412735.471047039250.601696622333-0.553817333650.03076136932650.620687346596-0.241551465788-0.5583826315060.314539787314-0.235710621718-0.3972769405110.677792809893-0.06809742145270.02872875971040.3639539858690.06963804428150.48113338772719.291338065633.694826244946.5763473209
192.617277867820.000647963122752-0.6289393238027.13838773096-2.92086313346.618930139360.207866922872-0.12266692824-0.5651483080320.58485311755-0.29345458529-0.05271273041260.4336405078660.2831769159660.08639899797640.410092768612-0.0350701571396-0.01610737402350.249246740142-0.01634907087210.43234355178422.341758986135.568872511138.1299748586
204.78385378795-3.10638962943-0.3015688629563.08705057283-2.154439743195.093743971560.06986776741660.391063824779-1.16433581909-0.306912843148-0.1152062070820.09504364480031.27949778316-0.30538158080.1541398113070.590655798721-0.08848803148920.1106463340250.283583132475-0.09839599701060.63815622065316.64183554732.484170927426.1733702973
215.48164797508-0.7875265616193.487587641351.458490056161.721449645135.835905302020.06379789991480.03439800646050.582373275769-0.170235588211-0.149681867730.0944771769836-1.08676840039-0.8829784701120.06387530049170.5072257058830.2178848101210.03506615897330.5074900412340.03455514868510.6452732953130.21780085187810.19539239732.9921843866
223.37030048271.345570285510.2841971787823.689502030260.5426129442793.05226416942-0.002786563132-0.4055484832770.169090420885-0.0219752118768-0.06075277248780.429772356766-0.173570940652-0.6352933932910.09332413202450.340960937990.02607811564350.05797659162010.418695375408-0.03898992881410.4181092727733.01173573706-1.056364013743.0781300949
233.485168694311.140465611360.08762013855693.544616486610.3237856840372.982117339020.104673104198-0.189785087260.1372191602150.264901620726-0.2583245762060.563616542491-0.0905017959545-0.5533140869440.09670059056530.3434168571440.03479957134510.103200087760.385217016929-0.05000226439330.4320824492884.47932873268-1.9058673836746.5761693524
242.34211076166-0.347671893547-0.5376633174593.267244322831.139601509413.52504376846-0.11885244469-0.372977788724-0.1698068214370.5589878576030.02219839431080.07856247886470.1821986438850.01104533070040.06543642408560.370548793250.03466157717330.0136688575110.2566302866920.01952329738260.25571278056618.8881220238-10.233196174745.6904214669
252.24302556032-0.6341515295120.2244860169693.89325501239-0.358695946434.522079847210.07937134087630.108082369762-0.188857629211-0.317763135575-0.0896655266918-0.107074489070.305304901745-0.1846625352620.01307128081160.279927150482-0.001904805626390.05352667281250.262253687407-0.01072768725170.27509563881919.1445691458-14.956810147926.5863585005
263.53875950780.406282107956-0.6457341864125.450638895940.1670577998883.31046997307-0.02111799063960.2343031781640.188949828609-0.8871612705510.08066979350640.209923707486-0.383700408109-0.315757158848-0.05517970643710.3398377476460.0204368826235-0.05720501744130.3092310322890.0002866508678210.24365618646911.5345345226-1.0355191459122.0314319083
271.81994376551-0.466372141980.6702499896413.265082511550.7538635017843.19048617789-0.0277999016201-0.01491380788780.214641486512-0.324079275469-0.07999679882260.573922912873-0.405328886883-0.5943207004230.131970841060.3226314754790.07475451476730.02480820558820.3869073327570.01650684406990.3218889468946.25385023232.4319915062327.4047777187
281.396654961110.470952068397-0.0629094950252.176724656962.253817394579.020200547030.244616101857-0.0359376163248-0.00635059886821-0.39747854991-0.032504679037-0.223085461313-0.927223394422-0.181371054732-0.2711741226320.440715793223-0.03436349426430.1434691333640.3674918003310.0647447959390.43809689132326.506735096510.805744923622.2596624586
292.534091911420.147202365519-0.3113068662352.07434916489-1.071584182518.11341876232-0.05133417042120.596989085492-0.107395567853-0.2006275068690.403185941350.158226326331-0.204670943237-0.334895554242-0.4285444060820.442508244113-0.05719497646410.1009322720110.4184722694870.03822457813020.44356583430321.98868500715.5321563340814.2798885644
302.01098084691-1.94598623735-0.7137014084494.13674210845-3.257086997397.76690469593-0.597817710418-0.1766988607760.0310020516938-1.026976034090.0158729136857-1.08660587253-0.4476204041510.9114627939660.7884600927240.481966049007-0.1278114457490.07643162354140.433554727140.01830883737480.58142408780831.06568284297.2860168604630.2553557875
318.641668164721.73124676983-0.09791829621851.00778790267-1.424819583822.025742571360.452105717082-0.158168372990.800887902449-0.398442960379-0.01191149969480.0212913708588-0.8932885381240.326251052412-0.3885714229620.4807559103740.007775047208540.01232321674250.322754626573-0.03930431302320.51627661024223.080598529611.593312913840.4518047016
321.51063401745-1.06925235754-0.3369002421521.604441276440.4375620914780.119425615749-0.248009039266-0.790012372197-0.393696407281.30678440180.352531470681-0.4012257417890.5080826117790.889333119552-0.05317431117520.8067382697440.175017867122-0.2638703411270.8527409662360.1256440661520.571939101223-18.012534091412.478489319770.3212080967
331.43982265394-0.6520455422730.08188972042171.597257378450.3115220446812.40252675347-0.0891572368801-0.04594638698210.1330409050670.3479117803750.00384435182489-0.394601561913-0.2545685589930.3142226256440.07661149218040.420868360931-0.0959129528943-0.1311300864650.5071525750730.05902416988980.350080368294-23.958976892828.790690159761.8437048229
344.817061594720.862896061844-1.93702641812.408822285071.841967868634.17623182186-0.256163846760.2705982385840.33472417385-0.3018094422040.1673594235320.107457457832-0.4266725078470.1794301155810.07901901372590.465813742463-0.0344565603269-0.1315553718130.329918439670.03578957801410.236326744159-36.129985407130.163506323452.623521018
353.004925143670.5247419800590.09515893459781.913832938851.772489041182.28930434335-0.00540305795311-0.1347917637180.164167270431-0.000613333682413-0.199837924688-0.019441854074-0.63429346681-0.06607679021030.1946555614250.444731020439-0.0022947289089-0.08979396603280.3580064443790.02715621537730.28365673938-41.257766656828.04689161653.0198380838
366.006533926591.54902333844-0.4999041139647.1815812146-3.943229382047.415091956560.2216957034110.2096125368060.09151511011770.4855568098650.005170528833650.139008871382-0.864814705135-0.49755093757-0.240481921980.3283055441920.0125314957964-0.02174078811950.2700471800030.001923891820240.202698654086-44.611390884522.37175325245.4053081001
374.25620683207-0.2367504505580.5912781345133.60294258987-0.8132794877945.430485104740.161275568546-0.277659134365-0.411769548172-0.019451387439-0.2694613649370.07144227782480.0132019734810.3054656231060.1702996474630.308056024081-0.0021030437938-0.06042337545550.2149359263680.01511722227440.233396092875-37.75401161312.043775300548.4575071258
383.6248854524-0.3580830203191.04550170793.478417958370.02848339534966.57871496580.0301611832209-0.243746205886-0.587398028639-0.0426189811098-0.161533672949-0.1086843727050.607196269167-0.01704130968140.09423062177390.3588509965520.00808986391712-0.03601658762020.272418274830.03804406108770.37839218121-39.93077570714.6823977491646.0999207466
394.337184301611.13570007495-2.210701797281.63932284339-0.5863461159085.45931292093-0.147447307127-0.405564889573-0.7631102089080.369230462424-0.410117332094-0.444403155930.4886848117130.261678700270.4978435241470.4854049340260.0305391811453-0.03846981839240.3951321427640.1209656178750.470389047217-31.46716297353.9797993511558.0838745093
401.944596265430.2545573842730.20313899332.168397455921.181718793171.86509482277-0.0754444110267-0.233164045234-0.2976576889870.58126575275-0.0596337075796-0.3253711691350.2145513387810.7029398829570.1063370111650.4840253454520.0498406515261-0.09471541413190.5436911138430.1477900203080.453743116097-24.75894932367.0110293916357.9194299317
413.88375626299-0.788063070625-0.7521628164692.895291746040.04459882773781.965114647610.230508578911-0.552981044362-0.5583336968270.472037329868-0.149553445686-0.3018606159520.02555058960980.447754896466-0.134976721540.424230388216-0.0489293397584-0.1546014547910.6224113215090.2054136217020.516159868362-25.74941895869.7427710814966.6373249424
422.035444029921.325184078892.105941304134.705524684612.313473902312.44371529023-0.0749633140805-0.266946138998-0.402847188143-0.235722522870.119791803505-0.1775136035230.0259250283167-0.390445074462-0.06125720820820.61912879766-0.07826937031820.07875623560760.6567971994490.2261272027110.481552617972-45.8879343973.5555735111772.2904647414
435.34968957902-0.305037071872-0.8605259836534.802287288650.3752239238883.253816975260.469193133311-0.0626202602909-1.05889252574-0.15906411405-0.758192181562-0.2199529123150.043592730886-0.4110765682690.2694395443741.10118498594-0.219443699646-0.1165675697620.6135048037670.08952419263440.766380223386-42.6547709019-8.3146338627162.6199822386
443.681154237530.1920338329-0.8341885629375.28751032142-0.7857326354444.05478726522-0.0378905905065-0.680242695692-0.3178132113510.725339088221-0.01539031862620.03916333600780.0487036297725-0.4067499917150.1236149797410.551937958007-0.0522033233202-0.005114548348190.506123600060.1056479473990.293036689504-43.524927690415.274033952372.8360384535
452.003991126411.77644081474-3.466076670356.08885556464-1.543092843849.512130183540.896607625935-0.06408483672870.7646510018140.574558586357-0.376304532662-0.259975548751-0.7533979799430.342363485744-0.5141235697390.6620159282830.0297912090115-0.09813063372120.318227975460.0121646299380.550058204899-23.707700105244.550323240315.8454676818
463.65935741838-2.938488653281.077284082536.535730554560.2793852797399.236463096820.526938230959-0.663115360881-0.179136541996-0.244969776747-0.1116588318890.2572932826131.08372911127-0.023403878048-0.3668508116880.792489350934-0.2090976693390.1946015141130.43064692146-0.05677544237880.4327585244436.9783741349152.368933274354.0428634416
476.461270835593.034707198570.8406712964116.2861608675-0.249935850315.731364254820.4457626055351.381155488290.147546171058-0.43367027773-0.269284123494-0.135004766369-0.0565371671898-0.53570821384-0.172300980250.5430865860540.1053785002130.07185453873410.592107695695-0.008390596220840.3748861134210.7718044797-6.2775985399711.7608336521
482.003716823571.60391298278-0.6061975405176.123669229520.09978257091324.40580909039-0.242530711492-0.0482316742517-0.78556117280.3847268138740.261985287450.1660894908060.1861374636590.0770216012347-0.03485818941980.6058249990060.03316093539020.0315325639790.4687314892090.1046380794510.565469729922-31.5300563842-4.893234702551.0407543381
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 41 )AA25 - 411 - 17
22chain 'A' and (resid 42 through 148 )AA42 - 14818 - 124
33chain 'A' and (resid 149 through 258 )AA149 - 258125 - 234
44chain 'A' and (resid 259 through 281 )AA259 - 281235 - 256
55chain 'A' and (resid 282 through 334 )AA282 - 334257 - 309
66chain 'A' and (resid 335 through 366 )AA335 - 366310 - 341
77chain 'B' and (resid 158 through 173 )BB158 - 1731 - 16
88chain 'B' and (resid 174 through 186 )BB174 - 18617 - 25
99chain 'B' and (resid 187 through 199 )BB187 - 19926 - 38
1010chain 'B' and (resid 200 through 213 )BB200 - 21339 - 52
1111chain 'C' and (resid 25 through 105 )CC25 - 1051 - 81
1212chain 'C' and (resid 106 through 187 )CC106 - 18782 - 163
1313chain 'C' and (resid 188 through 206 )CC188 - 206164 - 182
1414chain 'C' and (resid 207 through 235 )CC207 - 235183 - 211
1515chain 'C' and (resid 236 through 292 )CC236 - 292212 - 264
1616chain 'C' and (resid 293 through 334 )CC293 - 334265 - 306
1717chain 'C' and (resid 335 through 366 )CC335 - 366307 - 338
1818chain 'D' and (resid 158 through 186 )DD158 - 1861 - 21
1919chain 'D' and (resid 187 through 199 )DD187 - 19922 - 34
2020chain 'D' and (resid 200 through 213 )DD200 - 21335 - 48
2121chain 'E' and (resid 24 through 41 )EE24 - 411 - 18
2222chain 'E' and (resid 42 through 71 )EE42 - 7119 - 48
2323chain 'E' and (resid 72 through 105 )EE72 - 10549 - 82
2424chain 'E' and (resid 106 through 196 )EE106 - 19683 - 173
2525chain 'E' and (resid 197 through 258 )EE197 - 258174 - 235
2626chain 'E' and (resid 259 through 292 )EE259 - 292236 - 265
2727chain 'E' and (resid 293 through 365 )EE293 - 365266 - 338
2828chain 'F' and (resid 158 through 173 )FF158 - 1731 - 16
2929chain 'F' and (resid 174 through 191 )FF174 - 19117 - 32
3030chain 'F' and (resid 192 through 199 )FF192 - 19933 - 40
3131chain 'F' and (resid 200 through 213 )FF200 - 21341 - 54
3232chain 'G' and (resid 24 through 41 )GG24 - 411 - 18
3333chain 'G' and (resid 42 through 125 )GG42 - 12519 - 102
3434chain 'G' and (resid 126 through 148 )GG126 - 148103 - 125
3535chain 'G' and (resid 149 through 187 )GG149 - 187126 - 164
3636chain 'G' and (resid 188 through 206 )GG188 - 206165 - 183
3737chain 'G' and (resid 207 through 235 )GG207 - 235184 - 212
3838chain 'G' and (resid 236 through 258 )GG236 - 258213 - 235
3939chain 'G' and (resid 259 through 292 )GG259 - 292236 - 265
4040chain 'G' and (resid 293 through 334 )GG293 - 334266 - 307
4141chain 'G' and (resid 335 through 366 )GG335 - 366308 - 339
4242chain 'H' and (resid 158 through 172 )HH158 - 1721 - 15
4343chain 'H' and (resid 173 through 186 )HH173 - 18616 - 24
4444chain 'H' and (resid 187 through 213 )HH187 - 21325 - 51
4545chain 'X' and (resid 50 through 62 )XI50 - 621 - 13
4646chain 'I' and (resid 53 through 62 )IJ53 - 621 - 10
4747chain 'J' and (resid 53 through 62 )JK53 - 621 - 10
4848chain 'K' and (resid 53 through 62 )KL53 - 621 - 10

+
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