[English] 日本語
Yorodumi
- PDB-5tvp: SUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tvp
TitleSUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex
Components
  • DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
  • Small ubiquitin-related modifier 2
  • Tyrosyl-DNA phosphodiesterase 2
Keywordshydrolase/dna / hydrolase / dna repair / endonuclease/exonuclease/phosphatase (EEP) domain / hydrolase-dna complex
Function / homology
Function and homology information


SUMO is proteolytically processed / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / SUMOylation of RNA binding proteins / tyrosyl-RNA phosphodiesterase activity / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins ...SUMO is proteolytically processed / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / SUMOylation of RNA binding proteins / tyrosyl-RNA phosphodiesterase activity / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / 5'-tyrosyl-DNA phosphodiesterase activity / SUMOylation of intracellular receptors / Nonhomologous End-Joining (NHEJ) / Formation of Incision Complex in GG-NER / Processing of DNA double-strand break ends / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / SUMO transferase activity / aggresome / protein sumoylation / neuron development / postsynaptic cytosol / presynaptic cytosol / hippocampal mossy fiber to CA3 synapse / PML body / GABA-ergic synapse / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / presynapse / single-stranded DNA binding / manganese ion binding / endonuclease activity / postsynapse / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / cytoplasm
Similarity search - Function
: / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Ubiquitin homologues ...: / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / Small ubiquitin-related modifier 2 / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsSchellenberg, M.J. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Science / Year: 2017
Title: ZATT (ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links.
Authors: Schellenberg, M.J. / Lieberman, J.A. / Herrero-Ruiz, A. / Butler, L.R. / Williams, J.G. / Munoz-Cabello, A.M. / Mueller, G.A. / London, R.E. / Cortes-Ledesma, F. / Williams, R.S.
History
DepositionNov 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: Tyrosyl-DNA phosphodiesterase 2
J: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
O: Tyrosyl-DNA phosphodiesterase 2
P: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
Q: Small ubiquitin-related modifier 2
E: Tyrosyl-DNA phosphodiesterase 2
F: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
G: Tyrosyl-DNA phosphodiesterase 2
H: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
A: Tyrosyl-DNA phosphodiesterase 2
D: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
K: Tyrosyl-DNA phosphodiesterase 2
L: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
M: Tyrosyl-DNA phosphodiesterase 2
N: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,10242
Polymers262,33417
Non-polymers1,76825
Water12,430690
1
I: Tyrosyl-DNA phosphodiesterase 2
J: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
E: Tyrosyl-DNA phosphodiesterase 2
F: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,68710
Polymers63,2424
Non-polymers4456
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: Tyrosyl-DNA phosphodiesterase 2
P: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
G: Tyrosyl-DNA phosphodiesterase 2
H: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,86613
Polymers63,2424
Non-polymers6249
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
Q: Small ubiquitin-related modifier 2
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
A: Tyrosyl-DNA phosphodiesterase 2
D: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,95710
Polymers72,6085
Non-polymers3505
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: Tyrosyl-DNA phosphodiesterase 2
L: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
M: Tyrosyl-DNA phosphodiesterase 2
N: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5929
Polymers63,2424
Non-polymers3505
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.547, 113.772, 125.434
Angle α, β, γ (deg.)90.000, 91.520, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 9 molecules IOEGBAKMQ

#1: Protein
Tyrosyl-DNA phosphodiesterase 2 / Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ...Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / TRAF and TNF receptor-associated protein


Mass: 28905.230 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdp2, Ttrap / Cell line (production host): Rosetta 2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JJX7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#3: Protein Small ubiquitin-related modifier 2 / SUMO-2 / SMT3 homolog 2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 9365.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sumo2, Smt3b, Smt3h2 / Cell line (production host): Rosetta2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61957

-
DNA chain , 1 types, 8 molecules JPFHCDLN

#2: DNA chain
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')


Mass: 2715.799 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: synthetic DNA sequence / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 715 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM citrate-phosphate, 200mM NaCl, 12% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 116619 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 39.79 Å2 / Rmerge(I) obs: 0.147 / Net I/av σ(I): 5.896 / Net I/σ(I): 4.2
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.4-2.493.4198.9
2.49-2.593.5199.3
2.59-2.73.7199.7
2.7-2.853.7199.6
2.85-3.023.8199.80.716
3.02-3.263.7199.80.391
3.26-3.583.711000.213
3.58-4.13.7199.90.122
4.1-5.173.7199.80.081
5.17-503.7199.70.07

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GZ1

4gz1


Resolution: 2.399→49.273 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.58
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 5881 5.07 %RANDOM
Rwork0.1908 ---
obs0.193 115887 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.92 Å2 / Biso mean: 55.168 Å2 / Biso min: 7.92 Å2
Refinement stepCycle: final / Resolution: 2.399→49.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16473 1472 100 690 18735
Biso mean--53.52 41.73 -
Num. residues----2147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618561
X-RAY DIFFRACTIONf_angle_d0.73725398
X-RAY DIFFRACTIONf_chiral_restr0.0482812
X-RAY DIFFRACTIONf_plane_restr0.0053016
X-RAY DIFFRACTIONf_dihedral_angle_d13.6910830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3986-2.42580.40151630.36943299346289
2.4258-2.45440.36371860.3433527371395
2.4544-2.48430.36851900.33153523371396
2.4843-2.51580.36222020.32553582378497
2.5158-2.54890.31141950.31223627382298
2.5489-2.58380.33621750.30913606378199
2.5838-2.62070.36011880.301637253913100
2.6207-2.65980.3542140.29993653386799
2.6598-2.70140.33462010.291636403841100
2.7014-2.74560.32161980.274736973895100
2.7456-2.7930.31521970.265236973894100
2.793-2.84380.33192070.258836693876100
2.8438-2.89850.29611950.248936633858100
2.8985-2.95760.32891880.241637263914100
2.9576-3.02190.26312040.23236813885100
3.0219-3.09220.26042010.216836873888100
3.0922-3.16950.29792140.222936503864100
3.1695-3.25520.25892010.197937323933100
3.2552-3.3510.23061780.186236843862100
3.351-3.45910.22341760.175837503926100
3.4591-3.58270.22211820.175137053887100
3.5827-3.72610.21932010.163336913892100
3.7261-3.89560.22631910.153337243915100
3.8956-4.10090.17552020.142337333935100
4.1009-4.35770.16012010.127336933894100
4.3577-4.69390.15742140.115736883902100
4.6939-5.16580.13861870.115537403927100
5.1658-5.91230.20692010.141337323933100
5.9123-7.44470.18742200.174637473967100
7.4447-49.28330.19532090.16533735394498
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)
10.0297-0.0291-0.05360.14470.21340.3089-0.0761-0.00510.1744-0.39660.1177-0.4653-0.1278-0.03180.00110.422-0.01250.06940.43780.01530.521862.3647-14.318717.1278
20.0775-0.0415-0.00480.06030.08020.1336-0.0970.3097-0.1679-0.02730.07440.02870.49020.2435-00.5277-0.03380.07680.5131-0.0070.546167.683-19.362811.3388
30.3073-0.0427-0.02150.01840.00450.2219-0.08540.32540.1849-0.26860.1350.0309-0.2076-0.041-00.4978-0.0120.06790.4370.05130.472563.5089-8.124110.1031
40.4766-0.2944-0.26140.38950.11610.15360.29660.21260.4351-0.4864-0.1158-0.0139-0.1971-0.32360.02730.54940.0138-0.06960.47740.07810.417152.037-5.45079.6963
50.89040.17970.12031.18720.05170.93270.1866-0.12210.32630.4295-0.02450.2479-0.2635-0.014500.49410.00040.1320.37460.00330.498957.5591-7.381327.8921
60.0879-0.0420.05210.06650.04970.13060.11240.11120.40040.05670.10870.12290.0339-0.099300.4368-0.02480.05160.41060.05740.495147.7334-15.032924.8566
70.06720.03770.00520.0772-0.13030.3048-0.33170.0431-0.13130.11570.2133-0.16380.0771-0.044800.3756-0.0330.03240.3188-0.02070.334663.8399-20.292319.7874
80.3365-0.0659-0.42290.02360.10230.50210.22940.4831-0.30040.72920.0371-0.4642-0.1944-0.14110.06710.6446-0.0312-0.22060.4662-0.05980.595581.2796-1.200233.7731
90.3453-0.14460.07410.22120.07590.1511-0.3402-0.0682-0.36760.04160.31260.01010.001-0.3472-0.0010.5485-0.0950.10990.49180.05670.46932.203764.49850.1126
100.13990.07930.01260.15680.0470.0795-0.3209-0.2369-0.2892-0.17360.07170.15070.2158-0.3357-0.00010.5769-0.12960.12060.54240.06780.624728.048358.566349.8613
110.8192-0.47460.37770.69030.26810.8198-0.3019-0.0897-0.2758-0.20850.13130.12970.7752-0.4465-0.31960.7287-0.3915-0.00290.5470.06140.670827.798452.322742.8106
120.7657-0.1484-0.98640.1593-0.09831.9047-0.55510.0062-0.53280.123-0.00620.07770.80090.359-0.02541.0712-0.22770.25910.42350.05240.709637.849746.579943.8999
131.17950.5378-0.7480.2715-0.34130.49-0.5321-0.0051-0.675-0.6458-0.1012-0.68330.7510.2707-0.87860.952-0.0430.3360.2811-0.01370.800844.277649.655641.489
141.2181-0.19780.56861.4815-0.69950.8955-0.37320.0592-0.2882-0.53710.1385-0.45630.38950.0558-0.24420.5658-0.08380.18350.3517-0.00220.501844.743862.484842.4231
151.66010.4396-0.79461.04590.74611.39370.04130.4831-0.69670.851-0.2914-0.05240.2090.2764-0.87090.73150.2326-0.26140.58410.14831.252451.804150.499966.7144
160.0628-0.0292-0.00220.01290.00640.0206-0.26050.28710.0587-0.21780.2762-0.38540.3021-0.2508-00.66020.09240.10930.75110.04270.558348.868417.519619.584
170.05580.01740.03880.00790.0070.0343-0.1190.0596-0.03690.0055-0.2906-0.04540.0119-0.04680.00021.11870.5010.17711.60350.05990.926943.237116.795640.1998
180.2545-0.0368-0.09870.3334-0.11450.1393-0.4695-0.56920.39860.25870.19830.01390.0173-0.0002-00.65350.1135-0.12380.8061-0.13050.797150.433423.624630.0059
190.0119-0.0060.00520.0046-0.00580.0052-0.0989-0.0174-0.0044-0.0766-0.08030.1467-0.23670.174200.4510.0891-0.15480.68320.09410.863958.130619.286222.1288
200.0168-0.0062-0.00320.01720.00910.00620.0025-0.058-0.0267-0.35750.18350.2310.1010.1919-0.00010.9801-0.00980.01980.74220.00850.828751.622612.488821.9115
210.00940.01860.00920.02490.01470.0235-0.4417-0.48640.0793-0.10480.0273-0.24310.0815-0.0384-00.91030.316-0.08180.9721-0.04270.52650.390517.029335.2939
220.25990.1371-0.20340.0925-0.09570.1451-0.0691-0.1980.033-0.0758-0.10390.08960.09050.14850.00010.42120.04480.00210.4557-0.01580.2493101.17518.165147.9703
230.2610.0369-0.12060.1407-0.01920.3421-0.06440.12160.0962-0.12090.260.0997-0.07730.3837-00.3963-0.02030.02090.4702-0.03550.3416106.441218.178743.3037
240.0633-0.0480.04020.0372-0.01170.14120.1351-0.1081-0.07230.1273-0.2357-0.16910.09080.110800.31620.05590.01950.4803-0.0080.446108.53968.873546.9071
250.64570.92330.54091.60241.2261.4023-0.0409-0.1129-0.2725-0.0570.4203-0.03260.08140.4760.38640.22940.1494-0.07430.55410.0210.4156111.519910.893357.0357
261.27230.4321-0.29850.8575-0.18810.7911-0.0493-0.158-0.20930.1595-0.00790.20950.3235-0.0138-0.00090.43230.06260.0080.3920.01570.325694.3359.080659.2702
270.2672-0.0170.02390.37490.13390.05820.081-0.1143-0.14460.12170.0852-0.02090.2186-0.13290.21020.1122-0.0048-0.14770.398-0.04690.154285.497519.029843.7106
280.312-0.0414-0.09860.083-0.0370.08310.0671-0.1095-0.19930.05620.0015-0.0529-0.15760.3163-00.35330.0522-0.04910.4492-0.0040.311697.610920.036763.905
290.4053-0.01650.09040.68630.14090.09530.1086-0.20950.0339-0.22240.14130.123-0.36320.06160.02080.277-0.03160.00710.4069-0.02310.2798.149223.671447.9891
300.03790.1451-0.17680.5063-0.63720.7856-0.17260.0007-0.145-0.2661-0.31580.11490.12820.0035-0.31280.3428-0.0353-0.07820.501-0.12940.591981.75012.417134.2886
310.12880.3371-0.13691.2531-0.43580.1726-0.10940.12860.08580.28020.170.1888-0.07810.26210.36940.22680.0819-0.04570.488-0.03710.274869.627630.103581.431
320.07430.06680.09590.10260.0680.14630.4116-0.6235-0.22580.10440.14210.19070.6552-0.28060.00970.62710.04390.07840.46490.03430.525963.975624.880186.5606
330.2617-0.03920.01110.06960.14650.37320.1701-0.25470.20570.05310.13860.1978-0.34730.058400.35540.04890.040.4235-0.07750.400769.71635.089589.2108
341.23020.5406-1.00921.4834-0.92911.03690.0346-0.35680.36610.23660.4725-0.1353-0.35460.4940.32740.36920.0137-0.08090.541-0.14850.335181.432936.149389.3252
350.84720.5386-1.07461.0901-0.66151.63610.28210.07810.450.0320.26740.2121-0.53550.09111.42320.3318-0.1003-0.02080.4094-0.23540.456576.06344.935580.7463
360.93950.4062-0.61280.7184-0.49940.70250.4992-0.027-0.0581-0.02480.268-0.00220.1340.20922.43110.15080.0082-0.16190.5866-0.16480.335379.557138.004179.3163
371.3841-0.3020.04151.86970.64720.29920.15830.27130.5729-0.87180.2339-0.4564-0.61470.41341.01530.4733-0.16220.14310.5407-0.08450.344879.581240.56869.1242
381.02830.30510.40281.9202-0.10190.869-0.04710.0616-0.2093-0.50060.07460.05490.0496-0.04810.44980.1377-0.0039-0.13340.45310.01240.2464.070729.000667.1542
390.41840.41870.361.28990.61250.3878-0.05950.0021-0.1369-0.35150.3216-0.5826-0.10970.33670.46080.2039-0.0165-0.07240.5656-0.2220.403783.659528.654272.8163
400.07230.0370.04450.20690.30030.3727-0.25110.1524-0.00130.11430.15110.0060.31060.127100.30570.03740.00860.4077-0.01930.381567.233224.956577.8244
410.4486-0.1381-0.10380.03710.00020.34760.0794-0.0313-0.0711-0.54830.13790.6193-0.0589-0.06540.60860.91290.0186-0.40540.51580.33420.884951.51147.468566.7762
420.5825-0.34010.23360.38990.00910.6549-0.1102-0.2920.041-0.07560.1512-0.03540.0497-0.054100.44070.00440.04330.4089-0.02560.381417.136530.968823.4887
430.16940.08280.12950.04550.09370.22510.1318-0.36020.3312-0.01460.0997-0.2114-0.1409-0.056800.3903-0.0436-0.03640.3985-0.10020.452728.670636.983126.5661
440.9687-0.4504-0.16661.1142-0.08680.76730.24360.12250.3327-0.369-0.1099-0.28-0.12060.07560.00310.3980.03220.070.33140.04090.387224.007133.35969.6266
450.48020.17630.08780.17220.11450.11710.06490.2838-0.01460.3993-0.22610.4067-0.43080.2207-0.0220.91520.1535-0.08890.46570.09260.5396-0.155344.54071.8241
460.2444-0.1429-0.61692.85740.00221.786-0.16810.23710.0880.5171-0.13380.18930.1691-0.1425-1.01570.177-0.056-0.07320.3808-0.01680.1973-17.415561.0016-16.8334
470.2260.06070.04530.02180.01290.0107-0.1796-0.1310.53750.2474-0.71410.10630.2945-0.4668-0.0240.5947-0.0440.0810.5052-0.06970.514-23.424665.6604-11.611
480.09050.0891-0.05480.12970.03680.16570.0274-0.1922-0.0305-0.0837-0.24540.20370.3009-0.4542-00.4496-0.06930.050.4881-0.06960.4405-24.303557.2166-15.5243
490.1286-0.19-0.19930.5220.68311.8228-0.06820.0638-0.22380.3851-0.31640.22490.6385-0.2247-0.37250.373-0.0985-0.00040.3412-0.04730.3675-19.225850.3856-23.3808
500.4655-0.018-0.1629-0.0003-0.00490.1656-0.12840.163-0.66710.13690.0609-0.41850.33980.2868-0.03740.65890.08680.00270.39760.02130.5747-3.109546.4352-22.5059
510.5524-0.3579-0.18280.59510.07970.3993-0.05430.1552-0.03550.1209-0.0098-0.09960.24510.0864-00.4267-0.0348-0.02050.392-0.01190.3749-4.978160.5218-23.015
520.6371-0.0731-0.0932.32090.16870.0261-0.11980.05340.14760.75410.08560.17820.07870.133-0.36510.1523-0.0037-0.1360.4220.07630.2099-14.922767.0124-15.1254
530.7503-0.2707-0.58140.11220.21470.456-0.29-0.0002-0.44840.4872-0.004-0.15480.13090.3216-0.33990.75060.1938-0.20540.50420.07510.565-0.493447.84021.9791
540.09810.1391-0.03591.329-0.5630.2774-0.0892-0.28450.090.47090.29720.3342-0.02210.1780.10240.40410.00630.03410.3756-0.05660.305997.036941.987550.3779
550.09160.0626-0.00880.09110.07840.1190.3144-0.39940.19530.1597-0.11340.1816-0.31140.0119-00.5445-0.01380.14110.5036-0.11190.460798.59648.216353.7913
560.3790.2242-0.14450.24680.0960.32640.3864-0.22470.5540.1511-0.11180.08-0.41540.29340.00910.6253-0.07110.06320.5198-0.09460.4578105.485154.215151.5099
570.52680.2753-0.25520.606-0.43270.89460.20360.04290.4587-0.13990.04510.016-0.3510.099400.5492-0.02270.11670.3783-0.0130.4409103.855153.897634.7056
580.17250.1693-0.05570.42760.08770.1113-0.33940.02870.021-0.32320.38260.02240.214-0.14150.00280.40340.0261-0.04520.41140.04310.399791.047238.682134.9243
590.17720.03280.22220.55210.26880.4236-0.0181-0.06880.17620.01180.20810.06140.12210.1578-00.35260.0088-0.00360.4346-0.04910.3015103.480140.038441.1075
600.66790.4172-0.47340.37850.11061.92520.4550.36190.2928-0.1047-0.11490.7642-0.50110.16990.49510.69430.062-0.22060.48650.22440.890275.536655.614135.4948
611.115-0.11580.46580.0530.11891.0606-0.40730.3787-0.36170.3858-0.1563-0.06730.15130.2313-0.10840.6332-0.12010.11240.3617-0.0620.410459.931374.033217.3609
620.2990.0661-0.21890.0328-0.07380.1893-0.2462-0.12950.0330.1689-0.0112-0.12030.3294-0.3333-00.665-0.06780.1490.5247-0.00140.51853.455474.513120.4339
630.09080.0532-0.02430.0397-0.04010.0921-0.09980.2392-0.1922-0.1959-0.16680.01680.8132-0.088-0.00230.8333-0.21710.20960.5388-0.07410.464451.812764.925216.7815
640.1319-0.1848-0.10640.27930.07520.312-0.29690.2018-0.42960.2373-0.03570.31310.5667-0.6191-0.02080.5651-0.27030.10760.6485-0.11080.503751.970466.49756.3241
650.94420.1434-0.41940.3715-0.59921.2475-0.40010.3663-0.6273-0.301-0.0526-0.34981.3083-0.1166-0.53980.8276-0.05740.29810.3953-0.10580.637767.376661.68399.6292
661.3748-1.41181.35971.4998-1.23062.1489-0.39990.4593-0.53260.0295-0.1643-0.2710.18370.3002-1.43650.6449-0.06730.35830.5747-0.13160.614474.529569.88712.4173
670.29560.08-0.03890.2526-0.19760.2279-0.27540.1425-0.2157-0.18670.1177-0.27090.28760.2163-0.00670.5821-0.0440.08330.45270.0250.488271.559675.664614.5393
680.43960.28050.14690.4556-0.0450.1158-0.19940.10580.11070.3120.12650.14080.2668-0.10840.00450.55280.0020.13710.41560.03520.436663.164479.310617.9823
69-0.0019-0.0025-0.00190.13370.11170.088-0.06430.1239-0.10610.4453-0.1955-0.17120.24440.17360.00010.82620.18810.07330.62460.18870.968276.051458.337436.32
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'I' and (resid 121 through 138 )I121 - 138
2X-RAY DIFFRACTION2chain 'I' and (resid 139 through 153 )I139 - 153
3X-RAY DIFFRACTION3chain 'I' and (resid 154 through 190 )I154 - 190
4X-RAY DIFFRACTION4chain 'I' and (resid 191 through 208 )I191 - 208
5X-RAY DIFFRACTION5chain 'I' and (resid 209 through 325 )I209 - 325
6X-RAY DIFFRACTION6chain 'I' and (resid 326 through 345 )I326 - 345
7X-RAY DIFFRACTION7chain 'I' and (resid 346 through 369 )I346 - 369
8X-RAY DIFFRACTION8chain 'J' and (resid 2 through 10 )J2 - 10
9X-RAY DIFFRACTION9chain 'O' and (resid 121 through 153 )O121 - 153
10X-RAY DIFFRACTION10chain 'O' and (resid 154 through 174 )O154 - 174
11X-RAY DIFFRACTION11chain 'O' and (resid 175 through 208 )O175 - 208
12X-RAY DIFFRACTION12chain 'O' and (resid 209 through 225 )O209 - 225
13X-RAY DIFFRACTION13chain 'O' and (resid 226 through 259 )O226 - 259
14X-RAY DIFFRACTION14chain 'O' and (resid 260 through 369 )O260 - 369
15X-RAY DIFFRACTION15chain 'P' and (resid 2 through 10 )P2 - 10
16X-RAY DIFFRACTION16chain 'Q' and (resid 13 through 23 )Q13 - 23
17X-RAY DIFFRACTION17chain 'Q' and (resid 24 through 28 )Q24 - 28
18X-RAY DIFFRACTION18chain 'Q' and (resid 29 through 71 )Q29 - 71
19X-RAY DIFFRACTION19chain 'Q' and (resid 72 through 76 )Q72 - 76
20X-RAY DIFFRACTION20chain 'Q' and (resid 77 through 81 )Q77 - 81
21X-RAY DIFFRACTION21chain 'Q' and (resid 82 through 88 )Q82 - 88
22X-RAY DIFFRACTION22chain 'E' and (resid 121 through 138 )E121 - 138
23X-RAY DIFFRACTION23chain 'E' and (resid 139 through 174 )E139 - 174
24X-RAY DIFFRACTION24chain 'E' and (resid 175 through 190 )E175 - 190
25X-RAY DIFFRACTION25chain 'E' and (resid 191 through 208 )E191 - 208
26X-RAY DIFFRACTION26chain 'E' and (resid 209 through 303 )E209 - 303
27X-RAY DIFFRACTION27chain 'E' and (resid 304 through 325 )E304 - 325
28X-RAY DIFFRACTION28chain 'E' and (resid 326 through 345 )E326 - 345
29X-RAY DIFFRACTION29chain 'E' and (resid 346 through 370 )E346 - 370
30X-RAY DIFFRACTION30chain 'F' and (resid 2 through 10 )F2 - 10
31X-RAY DIFFRACTION31chain 'G' and (resid 121 through 138 )G121 - 138
32X-RAY DIFFRACTION32chain 'G' and (resid 139 through 153 )G139 - 153
33X-RAY DIFFRACTION33chain 'G' and (resid 154 through 190 )G154 - 190
34X-RAY DIFFRACTION34chain 'G' and (resid 191 through 208 )G191 - 208
35X-RAY DIFFRACTION35chain 'G' and (resid 209 through 225 )G209 - 225
36X-RAY DIFFRACTION36chain 'G' and (resid 226 through 240 )G226 - 240
37X-RAY DIFFRACTION37chain 'G' and (resid 241 through 296 )G241 - 296
38X-RAY DIFFRACTION38chain 'G' and (resid 297 through 325 )G297 - 325
39X-RAY DIFFRACTION39chain 'G' and (resid 326 through 345 )G326 - 345
40X-RAY DIFFRACTION40chain 'G' and (resid 346 through 369 )G346 - 369
41X-RAY DIFFRACTION41chain 'H' and (resid 2 through 10 )H2 - 10
42X-RAY DIFFRACTION42chain 'B' and (resid 117 through 190 )B117 - 190
43X-RAY DIFFRACTION43chain 'B' and (resid 191 through 208 )B191 - 208
44X-RAY DIFFRACTION44chain 'B' and (resid 209 through 370 )B209 - 370
45X-RAY DIFFRACTION45chain 'C' and (resid 2 through 10 )C2 - 10
46X-RAY DIFFRACTION46chain 'A' and (resid 121 through 138 )A121 - 138
47X-RAY DIFFRACTION47chain 'A' and (resid 139 through 153 )A139 - 153
48X-RAY DIFFRACTION48chain 'A' and (resid 154 through 174 )A154 - 174
49X-RAY DIFFRACTION49chain 'A' and (resid 175 through 240 )A175 - 240
50X-RAY DIFFRACTION50chain 'A' and (resid 241 through 260 )A241 - 260
51X-RAY DIFFRACTION51chain 'A' and (resid 261 through 345 )A261 - 345
52X-RAY DIFFRACTION52chain 'A' and (resid 346 through 369 )A346 - 369
53X-RAY DIFFRACTION53chain 'D' and (resid 2 through 10 )D2 - 10
54X-RAY DIFFRACTION54chain 'K' and (resid 121 through 153 )K121 - 153
55X-RAY DIFFRACTION55chain 'K' and (resid 154 through 174 )K154 - 174
56X-RAY DIFFRACTION56chain 'K' and (resid 175 through 208 )K175 - 208
57X-RAY DIFFRACTION57chain 'K' and (resid 209 through 296 )K209 - 296
58X-RAY DIFFRACTION58chain 'K' and (resid 297 through 325 )K297 - 325
59X-RAY DIFFRACTION59chain 'K' and (resid 326 through 369 )K326 - 369
60X-RAY DIFFRACTION60chain 'L' and (resid 2 through 10 )L2 - 10
61X-RAY DIFFRACTION61chain 'M' and (resid 121 through 138 )M121 - 138
62X-RAY DIFFRACTION62chain 'M' and (resid 139 through 174 )M139 - 174
63X-RAY DIFFRACTION63chain 'M' and (resid 175 through 190 )M175 - 190
64X-RAY DIFFRACTION64chain 'M' and (resid 191 through 208 )M191 - 208
65X-RAY DIFFRACTION65chain 'M' and (resid 209 through 282 )M209 - 282
66X-RAY DIFFRACTION66chain 'M' and (resid 283 through 296 )M283 - 296
67X-RAY DIFFRACTION67chain 'M' and (resid 297 through 345 )M297 - 345
68X-RAY DIFFRACTION68chain 'M' and (resid 346 through 370 )M346 - 370
69X-RAY DIFFRACTION69chain 'N' and (resid 2 through 10 )N2 - 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