[English] 日本語
Yorodumi
- PDB-7ab4: Crystal structure of the Escherichia coli toxin-antitoxin system ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ab4
TitleCrystal structure of the Escherichia coli toxin-antitoxin system HipBST (HipT S59A)
Components
  • (HipA_C domain-containing protein) x 2
  • Couple_hipA domain-containing protein
  • Predicted transcriptional regulator, XRE family
KeywordsTOXIN / antitoxin / kinase / HTH / HipA / HipT / HipB / HipS / HipBA / HipBST / bacteria / TrpS / phosphorylation / trans-autophosphorylation
Function / homology
Function and homology information


protein serine/threonine kinase activity / DNA binding / cytosol
Similarity search - Function
HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / Helix-turn-helix / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
HipA-like C-terminal domain-containing protein / HipA N-terminal subdomain 1 domain-containing protein / Predicted transcriptional regulator, XRE family
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.34 Å
AuthorsBaerentsen, R.L. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0030646 Denmark
Danish National Research FoundationDNRF120 Denmark
CitationJournal: Biorxiv / Year: 2022
Title: Structural basis for regulation of a tripartite toxin-antitoxin system by dual phosphorylation
Authors: Baerentsen, R.L. / Nielsen, S.V. / Lyngso, J. / Bisiak, F. / Pedersen, J.S. / Gerdes, K. / Sorensen, M.A. / Brodersen, D.E.
History
DepositionSep 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Predicted transcriptional regulator, XRE family
B: Couple_hipA domain-containing protein
C: HipA_C domain-containing protein
D: Predicted transcriptional regulator, XRE family
E: Couple_hipA domain-containing protein
F: HipA_C domain-containing protein


Theoretical massNumber of molelcules
Total (without water)125,0546
Polymers125,0546
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-55 kcal/mol
Surface area45870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.257, 107.146, 58.449
Angle α, β, γ (deg.)90.000, 90.710, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 36 through 37 and (name N...
21(chain D and (resid 36 through 77 or resid 79 through 81 or resid 83 through 107))
12(chain B and (resid 2 or resid 5 or resid...
22(chain E and (resid 2 or resid 5 or resid...
13(chain C and (resid 2 through 12 or resid 14...
23(chain F and (resid 2 through 12 or resid 14...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 36 through 37 and (name N...A36 - 37
121(chain A and ((resid 36 through 37 and (name N...A36 - 107
131(chain A and ((resid 36 through 37 and (name N...A36 - 107
141(chain A and ((resid 36 through 37 and (name N...A36 - 107
151(chain A and ((resid 36 through 37 and (name N...A36 - 107
211(chain D and (resid 36 through 77 or resid 79 through 81 or resid 83 through 107))D36 - 77
221(chain D and (resid 36 through 77 or resid 79 through 81 or resid 83 through 107))D79 - 81
231(chain D and (resid 36 through 77 or resid 79 through 81 or resid 83 through 107))D83 - 107
112(chain B and (resid 2 or resid 5 or resid...B2
122(chain B and (resid 2 or resid 5 or resid...B5
132(chain B and (resid 2 or resid 5 or resid...B7 - 11
142(chain B and (resid 2 or resid 5 or resid...B13 - 15
152(chain B and (resid 2 or resid 5 or resid...B17
162(chain B and (resid 2 or resid 5 or resid...B69
172(chain B and (resid 2 or resid 5 or resid...B2 - 101
182(chain B and (resid 2 or resid 5 or resid...B2 - 101
192(chain B and (resid 2 or resid 5 or resid...B2 - 101
212(chain E and (resid 2 or resid 5 or resid...E2
222(chain E and (resid 2 or resid 5 or resid...E5
232(chain E and (resid 2 or resid 5 or resid...E7 - 11
242(chain E and (resid 2 or resid 5 or resid...E1
252(chain E and (resid 2 or resid 5 or resid...E80 - 8
262(chain E and (resid 2 or resid 5 or resid...E3
272(chain E and (resid 2 or resid 5 or resid...E85 - 101
113(chain C and (resid 2 through 12 or resid 14...C2 - 12
123(chain C and (resid 2 through 12 or resid 14...C14 - 32
133(chain C and (resid 2 through 12 or resid 14...C34 - 46
143(chain C and (resid 2 through 12 or resid 14...C55 - 56
153(chain C and (resid 2 through 12 or resid 14...C58 - 69
163(chain C and (resid 2 through 12 or resid 14...C71 - 69
173(chain C and (resid 2 through 12 or resid 14...C170 - 221
183(chain C and (resid 2 through 12 or resid 14...C224 - 321
193(chain C and (resid 2 through 12 or resid 14...C323 - 338
213(chain F and (resid 2 through 12 or resid 14...F2 - 12
223(chain F and (resid 2 through 12 or resid 14...F14 - 32
233(chain F and (resid 2 through 12 or resid 14...F34 - 46
243(chain F and (resid 2 through 12 or resid 14...F48
253(chain F and (resid 2 through 12 or resid 14...F0
263(chain F and (resid 2 through 12 or resid 14...F55 - 56
273(chain F and (resid 2 through 12 or resid 14...F51 - 69
283(chain F and (resid 2 through 12 or resid 14...F71 - 125
293(chain F and (resid 2 through 12 or resid 14...F2 - 341
2103(chain F and (resid 2 through 12 or resid 14...F170 - 221
2113(chain F and (resid 2 through 12 or resid 14...F323 - 338

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Predicted transcriptional regulator, XRE family


Mass: 11720.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: E2348C_3787 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL98
#2: Protein Couple_hipA domain-containing protein


Mass: 11713.165 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: E2348C_3786 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL97
#3: Protein HipA_C domain-containing protein


Mass: 39053.102 Da / Num. of mol.: 1 / Mutation: S59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: E2348C_3785 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL96
#4: Protein HipA_C domain-containing protein


Mass: 39133.082 Da / Num. of mol.: 1 / Mutation: S59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: E2348C_3785 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL96
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.71 % / Description: Plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M BICINE, 6% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2020
RadiationMonochromator: At 26 m, Si (111), double crystal monochromator, horizontally deflecting, LN2 side-cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.24→50.59 Å / Num. obs: 45019 / % possible obs: 81.9 % / Redundancy: 4.108 % / Biso Wilson estimate: 96.02 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.332 / Rrim(I) all: 0.381 / Χ2: 0.83 / Net I/σ(I): 4.73 / Num. measured all: 184956 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.24-3.324.0973.3160.5512868400531410.1673.80778.4
3.32-3.424.1112.4210.7313791399933550.2042.7883.9
3.42-3.514.081.8940.9613097382632100.3092.17483.9
3.51-3.624.1521.611.313061379531460.4181.84482.9
3.62-3.744.0751.2861.6912063358829600.5061.47582.5
3.74-3.874.1131.1072.1812143354629520.5841.27283.2
3.87-4.024.1120.8232.8911412335927750.7120.94482.6
4.02-4.184.1040.7153.4111204332227300.8270.8282.2
4.18-4.374.0110.5144.210285311425640.8850.59182.3
4.37-4.584.1760.4145.6410139296224280.8990.47482
4.58-4.834.1990.3077.279965288523730.9450.35282.3
4.83-5.124.1540.2977.349085266421870.9430.3482.1
5.12-5.484.2270.2857.178708250420600.9460.32682.3
5.48-5.924.2370.2777.288178236119300.9490.31781.7
5.92-6.484.2030.2697.487478218917790.950.30781.3
6.48-7.253.7010.2017.855644196815250.960.23577.5
7.25-8.373.9240.11311.355391171613740.9870.1380.1
8.37-10.254.0790.0716.444773144711700.9940.07980.9
10.25-14.494.2840.05619.26387311359040.9950.06479.6
14.49-50.593.9430.04919.4817986074560.9960.05675.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.4 Å50.59 Å
Translation7.4 Å50.59 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
XSCALEVERSION Mar 15, 2019 BUILT=20190315data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD-code from depostion entry D_1292109701

Resolution: 3.34→50.59 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 1085 4.82 %RANDOM
Rwork0.202 21448 --
obs0.2041 22533 87.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 295.56 Å2 / Biso mean: 103.8043 Å2 / Biso min: 39.31 Å2
Refinement stepCycle: final / Resolution: 3.34→50.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8233 0 0 8 8241
Biso mean---54.87 -
Num. residues----1023
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A410X-RAY DIFFRACTION8.674TORSIONAL
12D410X-RAY DIFFRACTION8.674TORSIONAL
21B490X-RAY DIFFRACTION8.674TORSIONAL
22E490X-RAY DIFFRACTION8.674TORSIONAL
31C1904X-RAY DIFFRACTION8.674TORSIONAL
32F1904X-RAY DIFFRACTION8.674TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.34-3.490.32531210.28552590271185
3.49-3.670.30981390.27272741288090
3.67-3.910.32241500.25442731288190
3.91-4.210.26251240.21852717284189
4.21-4.630.24141340.19552664279888
4.63-5.30.2181480.16982703285188
5.3-6.670.23631330.20662656278987
6.68-50.590.19541360.16142646278284
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)
17.427-6.5631-4.77486.06074.43563.461-0.794-1.35290.73060.27230.7638-0.98060.76760.639-0.13170.88430.03560.20771.08370.13320.786394.98-27.03522.519
29.23726.22883.27974.39621.76444.34530.6913-1.1751-0.10021.9423-0.37470.03440.2738-0.52210.16550.66530.06630.07450.69670.00820.566690.2-15.42924.89
33.38431.64060.71046.3418-0.16775.637-0.011-0.03320.2361-0.6243-0.13070.6570.2124-0.28660.2330.5347-0.00920.16090.62260.03440.577486.743-12.73816.459
43.1947-1.49121.58397.56343.37063.24620.63212.0905-0.41710.08931.1251-0.60090.53011.0996-1.22491.03610.17610.18731.3727-0.41371.7561136.386-21.13918.158
55.3171.78612.2048.44673.11422.0494-1.00270.264-1.67830.57920.4383-0.19150.55621.1429-0.38991.3810.25290.22170.9603-0.28361.4297130.546-22.90319.898
64.6730.41660.48374.85872.58148.9271-0.4782-1.0107-1.7363-0.83470.3645-1.70612.16491.9120.19191.06230.32560.02650.90480.02631.6643130.226-26.28413.068
73.69811.03522.35345.87834.22885.99210.42590.2641-0.04751.192-0.73020.73390.6935-0.89730.44360.94240.16960.2591.1260.02331.4797120.235-20.9715.432
88.05182.95860.31062.00670.29752.09460.12060.9257-0.3376-0.6068-0.293-0.78471.97191.37170.32711.36980.24820.29341.2233-0.22421.696125.485-25.9738.826
97.25062.31234.16587.8957-1.42766.7186-0.79570.59090.1788-0.435-0.2828-1.60511.35330.22231.34180.76440.14810.01431.0785-0.27311.1936129.69-13.81610.586
106.04994.14263.48972.99682.12692.18150.6325-0.6752-0.7922-1.75350.68330.0126-0.5135-0.0701-1.64760.79440.17330.16441.6344-0.15651.8098137.7830.19519.175
116.03414.07433.10723.62391.18473.2312-0.85240.2006-0.05-1.70471.2412-1.39580.50681.82041.17171.8015-0.56690.72842.98320.05513.2228143.661-7.94413.239
127.95412.03914.07059.66992.67426.3862-0.22180.381-0.1795-1.19560.64540.6597-1.26560.25030.43311.29380.20340.29040.8955-0.00910.9013134.328-11.17621.723
134.99091.13731.20898.16514.80727.3687-0.5107-0.5173-1.58131.93930.1607-2.04291.54111.06760.40890.980.1271-0.17340.99930.3951.5957134.891-19.57722.825
146.1234-1.88471.67734.6469-1.65315.9638-0.1778-1.48960.53781.3105-0.0164-0.09460.1392-0.2234-0.11320.8178-0.07640.11141.0258-0.15210.6826113.16214.6540.574
155.9608-0.34082.30573.14070.87041.42980.0266-0.38030.4783-0.04910.05260.16110.15711.0746-0.19290.5649-0.1106-0.05920.8755-0.08390.517131.8579.00529.575
166.2653-0.73211.94235.7083-0.414.59510.2933-0.33370.117-0.1541-0.0188-0.63940.05440.3729-0.41270.60.08860.13450.907-0.04380.7287128.8774.39430.046
173.88360.90511.52972.1870.98592.42870.07430.0825-0.1144-0.0561-0.0751-0.20080.15020.2265-0.13190.67250.01120.20960.65290.04930.4556116.8461.36218.66
182.2464-0.12321.33111.82340.42393.20660.00370.42550.1451-0.3428-0.08630.0112-0.10910.09230.09580.85930.01770.26130.73780.01630.6383108.1926.9199.595
199.03850.51260.94844.71740.98513.63170.35610.1481.0433-0.6513-0.3514-0.0064-1.2046-0.52710.23560.8404-0.0010.21110.79540.13180.6676108.05218.66213.504
209.662-1.85497.88257.43291.28797.8087-0.15841.28311.0239-0.5537-0.9115-1.75310.74810.8433-0.61570.6835-0.10820.12710.9870.12990.72896.673-28.59910.337
218.38256.88342.88049.22364.78793.88960.35931.36110.0435-0.16450.12980.31370.13180.646-0.49850.7091-0.01920.03890.9811-0.05430.464886.509-32.2794.279
228.30462.37273.21627.60720.4491.30660.82090.60890.98130.7929-0.51971.5201-0.0984-0.2819-0.18390.7595-0.1090.18390.73310.03120.58372.712-35.6298.131
237.53924.22074.43234.47774.5284.56350.00010.20711.4743-0.6779-0.7491.5985-0.5667-0.06171.17451.1980.10840.03740.78990.0430.726978.317-24.5263.421
247.9864.1322.63645.14684.16364.8325-0.0321-0.68980.2674-0.52160.38050.9257-0.7929-0.723-0.40120.73640.03510.30310.5850.07960.515880.338-27.27613.858
257.58675.40964.14355.02614.31443.6087-0.90280.60950.19451.12721.2033-0.5977-0.14791.2849-0.39870.5501-0.0003-0.06530.5478-0.06570.538291.434-28.59516.902
260.39720.0298-1.82064.22-0.47628.16470.1816-2.3048-1.32760.8321-0.2398-0.90190.22831.8443-0.87981.08540.30880.05262.16710.42061.428107.726-62.0329.559
275.5558-3.332-0.8574.68680.84360.16890.3391-0.3531-0.75022.9529-0.8195-1.2015-1.43581.74461.35471.37910.4818-1.08842.3223-0.1731.2873104.507-60.13138.693
283.4885-0.7331-3.26883.4459-2.61896.7823-0.8633-0.81440.07810.32010.5346-1.85360.55672.28870.20630.7834-0.1738-0.18331.6538-0.38011.2247104.184-50.98530.8
293.3973-3.1626-3.1337.4621-2.53739.4855-0.2130.2977-0.48041.10170.17250.3947-0.43180.80790.29111.09240.1671-0.16011.5354-0.39411.204796.005-61.84933.192
304.76032.4223.03955.9641-3.9098.1837-0.68271.247-1.5507-2.5386-0.45032.71750.86550.1219-0.16741.80460.6998-0.1841.567-0.5711.438989.88-74.00523.681
313.8058-3.3133-2.7374.97930.65333.4149-1.369-0.3641-1.71330.1075-0.77320.73211.79820.13750.86832.01590.25520.1042.1902-0.06482.240494.652-79.01930.363
324.4022-2.86020.00045.013-0.27376.0953-0.0347-0.8468-0.13230.52660.53260.31430.50650.9032-1.0550.98110.1575-0.19931.33150.06611.2326103.077-67.95425.163
333.2987-0.9498-0.31014.8615-0.973.37390.37130.5887-0.2549-0.8999-0.288-0.57480.16390.83790.07361.03280.150.09580.7184-0.13990.70284.676-74.8142.156
344.6867-3.78671.18316.2831.82476.03930.18030.4302-0.1412-0.4185-0.0043-0.62430.75620.2685-0.17110.7169-0.04140.12120.6161-0.01010.557286.417-70.9738.476
351.824-1.7228-0.99084.41343.47585.1961-0.04850.1-0.0782-0.20970.06350.13120.41490.4364-0.26020.8720.1070.07770.8223-0.05860.77889.048-67.58614.631
361.992-1.56411.20742.73130.67784.4040.0078-0.19980.24930.2065-0.0853-0.24710.49190.02230.18960.5706-0.0630.08150.4910.01420.400978.963-54.40422.435
372.8761-0.7758-0.60673.84940.77085.0874-0.1095-0.0869-0.01150.51920.17160.42650.2656-0.2960.09030.5842-0.03940.11780.5263-0.03010.481169.856-56.09219.105
386.29770.8312-0.76874.713-1.27797.2559-0.7129-0.1547-0.30741.6631-0.14762.5820.7097-0.45160.60650.7782-0.07050.17120.7834-0.09581.141862.637-62.77612.272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 36:44 )A36 - 44
2X-RAY DIFFRACTION2( CHAIN A AND RESID 45:59 )A45 - 59
3X-RAY DIFFRACTION3( CHAIN A AND RESID 60:107 )A60 - 107
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:9 )B2 - 9
5X-RAY DIFFRACTION5( CHAIN B AND RESID 10:19 )B10 - 19
6X-RAY DIFFRACTION6( CHAIN B AND RESID 20:33 )B20 - 33
7X-RAY DIFFRACTION7( CHAIN B AND RESID 34:43 )B34 - 43
8X-RAY DIFFRACTION8( CHAIN B AND RESID 44:50 )B44 - 50
9X-RAY DIFFRACTION9( CHAIN B AND RESID 51:60 )B51 - 60
10X-RAY DIFFRACTION10( CHAIN B AND RESID 61:73 )B61 - 73
11X-RAY DIFFRACTION11( CHAIN B AND RESID 74:81 )B74 - 81
12X-RAY DIFFRACTION12( CHAIN B AND RESID 82:95 )B82 - 95
13X-RAY DIFFRACTION13( CHAIN B AND RESID 96:101 )B96 - 101
14X-RAY DIFFRACTION14( CHAIN C AND RESID 2:28 )C2 - 28
15X-RAY DIFFRACTION15( CHAIN C AND RESID 29:57 )C29 - 57
16X-RAY DIFFRACTION16( CHAIN C AND RESID 58:94 )C58 - 94
17X-RAY DIFFRACTION17( CHAIN C AND RESID 95:219 )C95 - 219
18X-RAY DIFFRACTION18( CHAIN C AND RESID 220:313 )C220 - 313
19X-RAY DIFFRACTION19( CHAIN C AND RESID 314:340 )C314 - 340
20X-RAY DIFFRACTION20( CHAIN D AND RESID 36:44 )D36 - 44
21X-RAY DIFFRACTION21( CHAIN D AND RESID 45:59 )D45 - 59
22X-RAY DIFFRACTION22( CHAIN D AND RESID 60:73 )D60 - 73
23X-RAY DIFFRACTION23( CHAIN D AND RESID 74:86 )D74 - 86
24X-RAY DIFFRACTION24( CHAIN D AND RESID 87:98 )D87 - 98
25X-RAY DIFFRACTION25( CHAIN D AND RESID 99:107 )D99 - 107
26X-RAY DIFFRACTION26( CHAIN E AND RESID 2:19 )E2 - 19
27X-RAY DIFFRACTION27( CHAIN E AND RESID 20:28 )E20 - 28
28X-RAY DIFFRACTION28( CHAIN E AND RESID 29:50 )E29 - 50
29X-RAY DIFFRACTION29( CHAIN E AND RESID 51:60 )E51 - 60
30X-RAY DIFFRACTION30( CHAIN E AND RESID 61:65 )E61 - 65
31X-RAY DIFFRACTION31( CHAIN E AND RESID 66:80 )E66 - 80
32X-RAY DIFFRACTION32( CHAIN E AND RESID 81:101 )E81 - 101
33X-RAY DIFFRACTION33( CHAIN F AND RESID 2:58 )F2 - 58
34X-RAY DIFFRACTION34( CHAIN F AND RESID 59:120 )F59 - 120
35X-RAY DIFFRACTION35( CHAIN F AND RESID 121:165 )F121 - 165
36X-RAY DIFFRACTION36( CHAIN F AND RESID 166:220 )F166 - 220
37X-RAY DIFFRACTION37( CHAIN F AND RESID 221:313 )F221 - 313
38X-RAY DIFFRACTION38( CHAIN F AND RESID 314:341 )F314 - 341

+
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