[English] 日本語
Yorodumi
- PDB-5nkm: SMG8-SMG9 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nkm
TitleSMG8-SMG9 complex
Components
  • (Protein smg-8) x 2
  • (Protein smg-9) x 2
KeywordsRNA BINDING PROTEIN / SMG8-SMG9 complex NMD effector proteins
Function / homology
Function and homology information


Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / striated muscle dense body / molecular sequestering activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cytoplasm
Similarity search - Function
Nonsense-mediated mRNA decay factor SMG8 / Nonsense-mediated mRNA decay factor SMG8/SMG9 / Smg8_Smg9 / Nonsense-mediated mRNA decay factor SMG9 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Nonsense-mediated mRNA decay factor SMG8 / Nonsense-mediated mRNA decay factor SMG9
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.493 Å
AuthorsLi, L. / Basquin, J. / Conti, E.
CitationJournal: RNA / Year: 2017
Title: Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins.
Authors: Li, L. / Lingaraju, M. / Basquin, C. / Basquin, J. / Conti, E.
History
DepositionMar 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein smg-8
B: Protein smg-9
C: Protein smg-8
D: Protein smg-9
E: Protein smg-8
F: Protein smg-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,87621
Polymers258,7376
Non-polymers1,13915
Water3,063170
1
A: Protein smg-8
B: Protein smg-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7494
Polymers87,6252
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-10 kcal/mol
Surface area26960 Å2
MethodPISA
2
C: Protein smg-8
D: Protein smg-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8219
Polymers86,2392
Non-polymers5837
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint6 kcal/mol
Surface area27210 Å2
MethodPISA
3
E: Protein smg-8
F: Protein smg-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3058
Polymers84,8732
Non-polymers4326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-6 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.085, 111.085, 374.474
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 59 through 82 or (resid 83...
21(chain D and (resid 59 through 80 or (resid 81...
31(chain F and (resid 59 through 80 or (resid 81...
12(chain A and (resid 1 through 127 or (resid 128...
22(chain C and (resid 1 through 7 or (resid 8...
32(chain E and (resid 1 through 4 or (resid 5...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111MSEMSESERSER(chain B and (resid 59 through 82 or (resid 83...BB59 - 821 - 24
121SERSERSERSER(chain B and (resid 59 through 82 or (resid 83...BB8325
131MSEMSEASPASP(chain B and (resid 59 through 82 or (resid 83...BB59 - 3641 - 306
141MSEMSEASPASP(chain B and (resid 59 through 82 or (resid 83...BB59 - 3641 - 306
151MSEMSEASPASP(chain B and (resid 59 through 82 or (resid 83...BB59 - 3641 - 306
161MSEMSEASPASP(chain B and (resid 59 through 82 or (resid 83...BB59 - 3641 - 306
211MSEMSELEULEU(chain D and (resid 59 through 80 or (resid 81...DD59 - 801 - 22
221THRTHRTHRTHR(chain D and (resid 59 through 80 or (resid 81...DD8123
231MSEMSETHRTHR(chain D and (resid 59 through 80 or (resid 81...DD59 - 3631 - 305
241MSEMSETHRTHR(chain D and (resid 59 through 80 or (resid 81...DD59 - 3631 - 305
251MSEMSETHRTHR(chain D and (resid 59 through 80 or (resid 81...DD59 - 3631 - 305
261MSEMSETHRTHR(chain D and (resid 59 through 80 or (resid 81...DD59 - 3631 - 305
311MSEMSELEULEU(chain F and (resid 59 through 80 or (resid 81...FF59 - 801 - 22
321THRTHRTHRTHR(chain F and (resid 59 through 80 or (resid 81...FF8123
331MSEMSETHRTHR(chain F and (resid 59 through 80 or (resid 81...FF59 - 3631 - 305
341MSEMSETHRTHR(chain F and (resid 59 through 80 or (resid 81...FF59 - 3631 - 305
351MSEMSETHRTHR(chain F and (resid 59 through 80 or (resid 81...FF59 - 3631 - 305
361MSEMSETHRTHR(chain F and (resid 59 through 80 or (resid 81...FF59 - 3631 - 305
112MSEMSEGLUGLU(chain A and (resid 1 through 127 or (resid 128...AA1 - 1271 - 127
122GLNGLNGLNGLN(chain A and (resid 1 through 127 or (resid 128...AA128128
132MSEMSESERSER(chain A and (resid 1 through 127 or (resid 128...AA1 - 4201 - 420
142MSEMSESERSER(chain A and (resid 1 through 127 or (resid 128...AA1 - 4201 - 420
152MSEMSESERSER(chain A and (resid 1 through 127 or (resid 128...AA1 - 4201 - 420
162MSEMSESERSER(chain A and (resid 1 through 127 or (resid 128...AA1 - 4201 - 420
212MSEMSEVALVAL(chain C and (resid 1 through 7 or (resid 8...CC1 - 71 - 7
222GLUGLUGLUGLU(chain C and (resid 1 through 7 or (resid 8...CC88
232MSEMSESERSER(chain C and (resid 1 through 7 or (resid 8...CC1 - 4201 - 420
242MSEMSESERSER(chain C and (resid 1 through 7 or (resid 8...CC1 - 4201 - 420
252MSEMSESERSER(chain C and (resid 1 through 7 or (resid 8...CC1 - 4201 - 420
262MSEMSESERSER(chain C and (resid 1 through 7 or (resid 8...CC1 - 4201 - 420
312MSEMSEALAALA(chain E and (resid 1 through 4 or (resid 5...EE1 - 41 - 4
322LYSLYSLYSLYS(chain E and (resid 1 through 4 or (resid 5...EE55
332MSEMSEGLNGLN(chain E and (resid 1 through 4 or (resid 5...EE1 - 4191 - 419
342MSEMSEGLNGLN(chain E and (resid 1 through 4 or (resid 5...EE1 - 4191 - 419
352MSEMSEGLNGLN(chain E and (resid 1 through 4 or (resid 5...EE1 - 4191 - 419
362MSEMSEGLNGLN(chain E and (resid 1 through 4 or (resid 5...EE1 - 4191 - 419

NCS ensembles :
ID
1
2

-
Components

-
Protein , 4 types, 6 molecules ACBDFE

#1: Protein Protein smg-8 / Suppressor with morphogenetic effect on genitalia protein 8


Mass: 50393.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smg-8, K04B12.3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O62301
#2: Protein Protein smg-9 / Suppressor with morphogenetic effect on genitalia protein 9


Mass: 37231.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smg-9, Y54E2A.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9XWJ1
#3: Protein Protein smg-9 / Suppressor with morphogenetic effect on genitalia protein 9


Mass: 35845.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smg-9, Y54E2A.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9XWJ1
#4: Protein Protein smg-8 / Suppressor with morphogenetic effect on genitalia protein 8


Mass: 49027.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smg-8, K04B12.3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O62301

-
Non-polymers , 4 types, 185 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 10% PEG3350, 0.1M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.493→52.36 Å / Num. obs: 188934 / % possible obs: 98 % / Redundancy: 39 % / Rmerge(I) obs: 0.1374 / Net I/σ(I): 27.25
Reflection shellResolution: 2.493→2.583 Å / Rmerge(I) obs: 2.587

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.493→62.412 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.41
RfactorNum. reflection% reflection
Rfree0.2602 8972 4.99 %
Rwork0.2247 --
obs0.2264 179816 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 264.81 Å2 / Biso mean: 96.4963 Å2 / Biso min: 49.12 Å2
Refinement stepCycle: final / Resolution: 2.493→62.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14115 0 184 170 14469
Biso mean--115.86 75.87 -
Num. residues----1824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314373
X-RAY DIFFRACTIONf_angle_d0.56819433
X-RAY DIFFRACTIONf_chiral_restr0.042308
X-RAY DIFFRACTIONf_plane_restr0.0042500
X-RAY DIFFRACTIONf_dihedral_angle_d13.2558762
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B4224X-RAY DIFFRACTION9.595TORSIONAL
12D4224X-RAY DIFFRACTION9.595TORSIONAL
13F4224X-RAY DIFFRACTION9.595TORSIONAL
21A5583X-RAY DIFFRACTION9.595TORSIONAL
22C5583X-RAY DIFFRACTION9.595TORSIONAL
23E5583X-RAY DIFFRACTION9.595TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4934-2.52180.4923170.43515383570094
2.5218-2.55140.3963060.386856335939100
2.5514-2.58260.33863160.360257816097100
2.5826-2.61530.41542720.356356355907100
2.6153-2.64970.34352620.342158066068100
2.6497-2.6860.35672940.334356215915100
2.686-2.72430.32133060.323957166022100
2.7243-2.7650.35143410.329456846025100
2.765-2.80820.33483320.312456375969100
2.8082-2.85420.32683140.306157626076100
2.8542-2.90350.37212340.291357916025100
2.9035-2.95630.33632570.295456695926100
2.9563-3.01310.31273020.278957846086100
3.0131-3.07460.2843040.271256685972100
3.0746-3.14150.30343000.270856945994100
3.1415-3.21450.26542980.262456695967100
3.2145-3.29490.2773040.251356976001100
3.2949-3.3840.28242960.254457816077100
3.384-3.48360.29032740.246557386012100
3.4836-3.5960.26123140.230456735987100
3.596-3.72450.25883000.217757126012100
3.7245-3.87360.2373180.198656445962100
3.8736-4.04990.23113520.195156315983100
4.0499-4.26340.21913300.187157386068100
4.2634-4.53040.22342680.166757095977100
4.5304-4.88010.20263340.168556866020100
4.8801-5.37090.21563060.189157106016100
5.3709-6.14750.25892510.218757646015100
6.1475-7.74290.25473010.216257066007100
7.7429-62.43190.23732690.191157225991100
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)
18.06460.8942-2.18043.33114.83738.56630.9057-1.68221.99470.79330.5667-2.5854-0.44961.8837-1.27380.7685-0.1358-0.20110.692-0.19921.6622100.6302196.5642421.3497
25.6357-3.0033-0.43725.8507-0.09391.9494-0.01780.0440.8172-0.0785-0.0346-1.251-0.44290.30640.01550.6707-0.08310.01540.62380.08620.94399.8085193.6927412.6272
33.1541-2.9468-4.0022.78983.61078.0077-0.3030.13910.72990.52250.1436-0.82560.27580.4560.31390.60150.0285-0.07760.70830.00410.8833102.4455171.6276420.7473
46.82860.63530.85628.3176-1.60222.397-0.02730.20680.7051-0.2234-0.1012-0.47380.25560.62270.09210.61320.07080.10740.63280.08990.6589.9864185.8831411.4945
51.8252-1.2901-0.2844.4640.26796.593-0.0903-0.1688-0.12590.47850.05810.9302-0.21320.05190.00050.5251-0.03320.09410.6330.01570.829981.811187.8307420.3169
69.2445-0.52133.64497.9157-2.6512.19380.49080.31420.6032-1.2648-0.34750.50240.7366-1.31040.05871.0082-0.0516-0.00321.2461-0.1040.99883.3114183.3283393.4271
72.4884-0.93971.29811.89140.263.175-0.0460.11770.359-0.0067-0.04460.1324-0.37030.00860.13360.6102-0.00370.10660.62410.0580.803184.7553190.8435412.1427
84.5113-3.70293.31775.727-5.48855.2216-0.0294-0.9875-0.24440.63030.58621.15220.2779-0.045-0.4850.86530.06690.02240.84460.18830.599597.4957152.8172428.5623
98.79824.05672.7695.43370.57448.17281.2195-0.7468-0.89711.1584-0.3447-1.08930.99380.068-0.83690.90540.0521-0.15190.86150.18590.816105.5002149.9783427.204
100.73981.405-1.51794.3926-2.32733.2892-0.6426-0.40560.11890.87670.60850.0821-0.3613-0.4194-0.22051.91-0.5189-0.52132.13230.72630.8241103.6895142.8782440.6336
114.60395.3318-4.72876.1786-5.45194.8862-0.31971.0561-0.4676-1.0265-0.0021-0.50842.1714-0.8160.54660.8139-0.02670.06730.8548-0.15490.836293.7466147.5236390.1926
121.9880.3332-0.35862.4628-0.66681.27520.11720.49220.089-0.24460.1637-0.38160.53510.1069-0.14130.68060.03310.0060.697-0.25321.154793.9126140.8491396.7455
131.5649-2.2562.5434.8054-2.33837.211-0.18160.8418-0.0007-0.49030.008-0.7770.05160.48160.17120.5408-0.03280.17690.87320.05010.7232101.9956157.1964389.5318
149.3282-0.5308-0.41035.47040.87325.9867-0.14410.4048-0.5685-0.40730.12080.2235-0.18190.8053-0.0730.6257-0.07010.02140.8344-0.0370.813295.9897153.385393.2517
153.92013.4914-1.85358.4224-2.54364.03690.07840.1991-0.07450.0066-0.1292-0.27850.1651-0.04720.05010.39620.0469-0.01920.66990.00120.5001100.8534158.4546406.5789
168.695.0347-0.79125.8707-3.64938.5634-0.08560.6129-0.06080.24930.6892-0.6797-0.33750.3795-0.5590.62660.0468-0.00510.7720.08870.9488113.7033175.22402.2659
174.6958-0.73040.77543.2854-1.63516.71950.1770.1343-0.0526-0.1293-0.2462-1.1408-0.05781.00590.19160.53770.09240.09060.70730.05820.9667111.0812164.9524403.7883
183.5838-2.9966-3.99073.5164.13375.86070.38242.1298-0.1449-2.3376-1.0653-1.18330.02170.76570.22170.93680.19940.2141.4332-0.08790.8482112.501159.6323389.1354
193.3967-0.4618-1.25886.75021.3454.9867-0.02270.1671-0.7227-0.3843-0.0362-0.33790.4130.37090.03460.52380.0356-0.03790.5796-0.01390.9139100.731144.6257408.0397
206.8832-1.46874.65312.3273-1.76813.55150.6271-0.31672.0655-0.3815-0.1905-1.3661-0.9751-1.1223-0.30480.9723-0.00050.15311.16820.15121.900985.3529162.3669419.1383
218.43391.9131.16143.9010.49781.92960.20010.0157-1.2672-0.01730.0992-0.33290.25910.1539-0.36570.61670.1126-0.01070.4617-0.12390.792469.6149123.6651405.5877
224.1982-4.2437-1.48444.3372.01265.9316-0.4052-0.0884-2.75840.57720.13351.55860.8124-0.25120.10630.68660.0790.08930.64130.10331.162744.9713127.0148413.9481
238.4334-1.2738-2.36136.2024-1.9721.8306-0.2405-0.0975-0.13520.16920.24370.49590.2-0.48110.0390.56960.0853-0.05560.522-0.13960.461162.2922138.4461408.1219
243.51570.75820.50211.4576-0.60796.8238-0.0267-0.61930.14820.46130.1428-0.522-0.08710.2228-0.11620.67170.1337-0.07480.6563-0.14050.820275.6249141.0865416.2759
253.1429-0.8553-0.17190.7861-1.92327.0810.32551.4356-0.16490.00580.1735-1.2346-0.9718-0.7957-0.70650.7557-0.02630.01760.8590.10850.780365.3475145.3505389.6864
264.7384-0.53460.55164.0845-0.86633.0672-0.1460.02170.11720.03230.216-0.4308-0.090.0056-0.09970.58160.0297-0.010.5403-0.15590.59172.4221138.3324406.1325
271.20630.5677-0.91183.69572.30342.86080.0474-1.50180.34011.01540.9075-0.2554-0.7702-0.3647-0.22971.11850.44640.69081.33130.35120.626933.2019143.2907424.5675
283.31112.97681.72983.01192.56483.899-0.0739-0.60770.31540.7094-0.82311.2135-0.1567-2.37070.35631.11770.44911.08361.71820.48981.887117.2145140.6057424.2406
297.2713-3.4192.56883.66572.60947.9630.1628-2.1984-0.98551.83781.09862.53360.4362-1.1335-0.96020.98760.01380.37651.05970.36711.404329.2768137.1656419.2416
304.73942.99835.00354.59426.51939.4495-0.9106-1.7792-1.35910.896-1.636-0.71412.1809-0.90952.02151.84450.40860.51051.65210.50571.138823.5429138.0675433.6554
318.00170.5179-0.23257.09863.07888.530.16410.538-0.4488-1.3097-0.44541.1246-0.2331-0.51480.19990.71760.1347-0.19140.723-0.00610.891628.3029156.4268392.195
323.7457-1.5375-4.93595.42430.12559.0226-0.33881.5985-0.392-1.2224-00.84860.4947-0.69590.30950.75250.0066-0.16950.7882-0.21670.794932.5914141.915388.7292
332.00226.83792.42996.37584.30694.59820.0412.8525-1.0223-3.76992.40890.89571.98960.5066-2.08082.41720.3859-0.60941.3569-0.24051.284237.9219145.0691374.5828
342.93030.21640.34742.89531.07313.42880.07920.5072-0.1451-1.3384-0.21860.5849-0.2074-0.2530.00880.87310.0628-0.13510.6321-0.08230.760334.4209149.8621390.6865
356.15330.05020.67374.3642-4.33674.701-0.87590.0767-0.5171-0.5471-0.4512-0.506-2.82640.86161.40891.30970.0523-0.23940.94410.06790.88550.0481151.1718404.2112
362.9448-2.17841.549.0799-0.5474.72880.0784-0.141-0.60870.1346-0.06080.42840.06810.07950.04660.4798-0.06340.00820.4792-0.00350.578938.2286141.2741403.3231
374.6143-2.6424-1.82065.68551.98154.59410.07710.2515-1.437-0.3298-0.12391.45490.0334-0.13120.16650.5794-0.0704-0.13460.5925-0.10431.139935.919130.4872398.7074
385.18662.86012.0053.1358-0.65552.93751.34990.6479-1.2263-1.1931-0.91210.52451.4552-1.1359-0.10491.45820.1491-0.40081.1385-0.16191.197331.4028131.4157382.6019
394.70572.2484-1.00196.88044.66784.5427-0.06540.4813-1.3358-0.0142-0.55171.95790.1579-0.89920.54990.62520.042-0.07450.792-0.02531.494821.3381145.762402.352
403.72851.91793.79439.33133.88744.31350.33650.0565-0.90490.21180.9283-2.30960.23590.1854-1.2770.81820.1467-0.08320.8343-0.02741.044541.7328149.9251414.3332
416.35230.79510.86028.88330.14041.7932-0.00190.03990.48420.2283-0.07760.9097-0.1042-0.45460.06210.43560.12450.00220.610.04460.676220.8155183.5236407.9236
428.49767.88652.76419.69783.94893.4930.01470.05850.18360.20.21940.3691-0.1927-0.2905-0.19490.59490.08890.0470.66170.12310.748527.2514189.8737410.4214
435.30224.53062.49754.23562.96422.8524-0.0183-0.33480.3362-0.028-0.24070.4826-0.2982-0.17830.29930.56340.111-0.02320.5870.03460.558335.5375187.9881414.7307
442.69270.6568-1.17774.2674-0.51772.87180.0205-0.3229-0.42170.3125-0-0.38730.0601-0.0535-0.00950.56780.0326-0.08940.64470.10310.700936.8557173.0657414.6664
455.70360.58321.9925.3466-0.35042.8226-0.64562.21661.6101-0.98161.09810.01010.06720.0267-0.40161.7542-0.0108-0.12471.10040.09871.1238.0014185.4276384.6868
466.82770.53843.24125.64770.07766.0341-0.02070.7122-0.0409-0.81450.0733-0.5255-0.08180.38280.00420.56440.06490.12910.54960.01230.552239.0152174.9828397.751
477.47033.96093.50174.4884.02088.96630.1019-0.4575-0.03930.59410.04761.10950.3229-0.3742-0.12890.59090.0675-0.01260.66170.14910.659225.124174.0292419.2546
487.2764.17683.3712.98942.59142.2660.4414-0.4878-0.2580.9292-0.30560.55430.0444-0.2919-0.37991.08990.032-0.17630.81190.03850.656855.5511202.4723432.5111
497.3374-1.3468-0.19016.4089-2.92356.06340.6535-1.59680.42531.5173-0.135-0.4802-1.2466-0.2583-0.57991.3553-0.0923-0.0491.0909-0.16170.667254.8325211.5207432.138
509.36853.2741.24414.9102-3.06953.42230.09711.3427-2.139-3.2542-1.5622-0.06434.4532.10991.22182.02480.4969-0.19171.4816-0.43271.076957.4833212.1849446.3383
517.7405-2.27582.87554.3594-5.53016.9127-0.44650.84430.4987-0.1643-0.0946-0.4539-0.48740.43160.80660.69810.04710.07770.77540.19870.914769.9606204.0047399.7936
522.7623-2.3692-1.10783.07593.53646.9768-0.37010.90411.60180.1143-0.3472-0.2932-1.20860.81060.57340.802-0.1748-0.0820.71160.28861.555372.505214.7492402.4142
535.6861.68691.20761.71362.81837.9853-0.25020.79110.4524-0.404-0.11850.0227-0.81170.1540.54340.66740.0258-0.11470.68610.22250.783959.1452208.3655395.1402
541.56970.0395-0.33315.6475-4.9117.68830.45120.1959-2.93430.7913-0.8103-0.12232.0193-0.16070.45741.41530.1662-0.21530.8671-0.13171.280855.7492193.3775404.9792
554.58761.86431.77993.22860.70515.1336-0.31890.01520.460.10670.0448-0.0528-0.39630.04410.41040.66220.0747-0.07760.48150.02060.722950.1127206.1778408.8433
562.70133.084-0.07496.47473.24023.9375-0.2406-0.0131.73020.1390.02060.4571-0.4596-0.43560.32650.74180.0897-0.11170.5681-0.0691.047941.5545211.6088411.7377
578.50663.7525-1.89457.01-3.01731.3291-0.75151.42011.0559-0.83810.79790.57030.3016-0.039-0.051.0732-0.0918-0.15380.85160.34540.870246.2809215.083394.208
588.8089-2.8421-2.48477.10441.61443.3471-0.3947-0.41662.12370.04720.5999-0.4279-1.13750.1483-0.19631.03710.0269-0.11090.73510.06531.515263.782220.8802410.9632
599.7709-0.4854-0.81197.7037-5.2433.80920.24670.1861-0.19270.6418-0.2729-0.34620.35151.8280.23750.90430.1189-0.1920.7553-0.11061.180167.4776206.4809416.5038
603.3314.8351-3.82547.2513-5.83494.72871.41890.3242-1.167-1.6833-0.76293.611.50470.8697-0.83060.91940.1363-0.32680.7895-0.07761.506856.4472192.0732420.1106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:6)A1 - 6
2X-RAY DIFFRACTION2(chain A and resid 7:92)A7 - 92
3X-RAY DIFFRACTION3(chain A and resid 93:109)A93 - 109
4X-RAY DIFFRACTION4(chain A and resid 110:133)A110 - 133
5X-RAY DIFFRACTION5(chain A and resid 134:191)A134 - 191
6X-RAY DIFFRACTION6(chain A and resid 192:221)A192 - 221
7X-RAY DIFFRACTION7(chain A and resid 222:329)A222 - 329
8X-RAY DIFFRACTION8(chain A and resid 330:388)A330 - 388
9X-RAY DIFFRACTION9(chain A and resid 389:413)A389 - 413
10X-RAY DIFFRACTION10(chain A and resid 414:420)A414 - 420
11X-RAY DIFFRACTION11(chain B and resid 59:66)B59 - 66
12X-RAY DIFFRACTION12(chain B and resid 67:84)B67 - 84
13X-RAY DIFFRACTION13(chain B and resid 85:117)B85 - 117
14X-RAY DIFFRACTION14(chain B and resid 118:155)B118 - 155
15X-RAY DIFFRACTION15(chain B and resid 172:247)B172 - 247
16X-RAY DIFFRACTION16(chain B and resid 248:257)B248 - 257
17X-RAY DIFFRACTION17(chain B and resid 258:307)B258 - 307
18X-RAY DIFFRACTION18(chain B and resid 308:320)B308 - 320
19X-RAY DIFFRACTION19(chain B and resid 321:358)B321 - 358
20X-RAY DIFFRACTION20(chain B and resid 359:364)B359 - 364
21X-RAY DIFFRACTION21(chain C and resid 1:86)C1 - 86
22X-RAY DIFFRACTION22(chain C and resid 87:105)C87 - 105
23X-RAY DIFFRACTION23(chain C and resid 106:148)C106 - 148
24X-RAY DIFFRACTION24(chain C and resid 149:191)C149 - 191
25X-RAY DIFFRACTION25(chain C and resid 192:222)C192 - 222
26X-RAY DIFFRACTION26(chain C and resid 223:329)C223 - 329
27X-RAY DIFFRACTION27(chain C and resid 330:384)C330 - 384
28X-RAY DIFFRACTION28(chain C and resid 385:393)C385 - 393
29X-RAY DIFFRACTION29(chain C and resid 394:406)C394 - 406
30X-RAY DIFFRACTION30(chain C and resid 407:420)C407 - 420
31X-RAY DIFFRACTION31(chain D and resid 59:81)D59 - 81
32X-RAY DIFFRACTION32(chain D and resid 82:109)D82 - 109
33X-RAY DIFFRACTION33(chain D and resid 110:118)D110 - 118
34X-RAY DIFFRACTION34(chain D and resid 119:154)D119 - 154
35X-RAY DIFFRACTION35(chain D and resid 155:174)D155 - 174
36X-RAY DIFFRACTION36(chain D and resid 175:219)D175 - 219
37X-RAY DIFFRACTION37(chain D and resid 220:284)D220 - 284
38X-RAY DIFFRACTION38(chain D and resid 305:320)D305 - 320
39X-RAY DIFFRACTION39(chain D and resid 321:351)D321 - 351
40X-RAY DIFFRACTION40(chain D and resid 352:363)D352 - 363
41X-RAY DIFFRACTION41(chain E and resid 1:67)E1 - 67
42X-RAY DIFFRACTION42(chain E and resid 68:92)E68 - 92
43X-RAY DIFFRACTION43(chain E and resid 93:129)E93 - 129
44X-RAY DIFFRACTION44(chain E and resid 130:191)E130 - 191
45X-RAY DIFFRACTION45(chain E and resid 192:207)E192 - 207
46X-RAY DIFFRACTION46(chain E and resid 208:302)E208 - 302
47X-RAY DIFFRACTION47(chain E and resid 303:328)E303 - 328
48X-RAY DIFFRACTION48(chain E and resid 329:386)E329 - 386
49X-RAY DIFFRACTION49(chain E and resid 387:413)E387 - 413
50X-RAY DIFFRACTION50(chain E and resid 414:419)E414 - 419
51X-RAY DIFFRACTION51(chain F and resid 59:71)F59 - 71
52X-RAY DIFFRACTION52(chain F and resid 72:84)F72 - 84
53X-RAY DIFFRACTION53(chain F and resid 85:151)F85 - 151
54X-RAY DIFFRACTION54(chain F and resid 152:173)F152 - 173
55X-RAY DIFFRACTION55(chain F and resid 174:256)F174 - 256
56X-RAY DIFFRACTION56(chain F and resid 257:277)F257 - 277
57X-RAY DIFFRACTION57(chain F and resid 278:322)F278 - 322
58X-RAY DIFFRACTION58(chain F and resid 323:339)F323 - 339
59X-RAY DIFFRACTION59(chain F and resid 340:353)F340 - 353
60X-RAY DIFFRACTION60(chain F and resid 354:363)F354 - 363

+
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