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- PDB-7vpg: Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 compl... -

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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 / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / 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 / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / 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 / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / nuclear localization sequence binding / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / mitotic spindle pole / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / host cell Golgi membrane / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / serine-type peptidase activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / nuclear periphery / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / ubiquitin binding / HCMV Late Events / promoter-specific chromatin binding / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / ISG15 antiviral mechanism / fibrillar center / protein import into nucleus / HCMV Early Events / SARS-CoV-1 activates/modulates innate immune responses / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / microtubule binding / transcription coactivator activity / nuclear body / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / cell division / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / nucleus / membrane / 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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. ...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 peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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About Yorodumi

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News

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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

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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

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