[English] 日本語
Yorodumi
- PDB-6s5e: Non-square conformation of KtrA A80P mutant ring with bound ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s5e
TitleNon-square conformation of KtrA A80P mutant ring with bound ATP
ComponentsKtr system potassium uptake protein A
KeywordsTRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / non-square conformation octameric ring / atp
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits ...Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.893 Å
AuthorsTeixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/29863/2017 Portugal
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-007274 Portugal
CitationJournal: Elife / Year: 2019
Title: Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.
Authors: Teixeira-Duarte, C.M. / Fonseca, F. / Morais Cabral, J.H.
History
DepositionJul 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,60016
Polymers199,5428
Non-polymers4,0578
Water0
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
hetero molecules

C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
hetero molecules

E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,60016
Polymers199,5428
Non-polymers4,0578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)85.695, 133.873, 205.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 24942.797 Da / Num. of mol.: 8 / Mutation: A80P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 100mM HEPES-NaOH pH 7.5, 1% PEG 6000, 2% 2-Methyl-2,4-pentanediol (MPD)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.89→49.63 Å / Num. obs: 22230 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Net I/σ(I): 10.3
Reflection shellResolution: 3.89→4.2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.339 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4413 / CC1/2: 0.83 / Rpim(I) all: 0.561 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4j90
Resolution: 3.893→47.877 Å / SU ML: 0.82 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 42.02
RfactorNum. reflection% reflection
Rfree0.3172 4197 10.16 %
Rwork0.2602 --
obs0.2661 22230 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.893→47.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13664 0 248 0 13912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314144
X-RAY DIFFRACTIONf_angle_d0.88319168
X-RAY DIFFRACTIONf_dihedral_angle_d16.4165304
X-RAY DIFFRACTIONf_chiral_restr0.032208
X-RAY DIFFRACTIONf_plane_restr0.0032408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.893-3.93720.60331280.53051033X-RAY DIFFRACTION84
3.9372-3.98350.53951380.48451225X-RAY DIFFRACTION99
3.9835-4.03210.5631430.47741261X-RAY DIFFRACTION100
4.0321-4.08310.45841550.43351241X-RAY DIFFRACTION99
4.0831-4.13680.48681290.42391204X-RAY DIFFRACTION100
4.1368-4.19340.40951290.39861312X-RAY DIFFRACTION100
4.1934-4.25330.39371460.3581239X-RAY DIFFRACTION99
4.2533-4.31680.37581590.33571216X-RAY DIFFRACTION100
4.3168-4.38420.2987980.33971268X-RAY DIFFRACTION100
4.3842-4.4560.43891480.32641260X-RAY DIFFRACTION100
4.456-4.53280.4381300.32641283X-RAY DIFFRACTION100
4.5328-4.61510.37381420.32321180X-RAY DIFFRACTION99
4.6151-4.70380.49571550.31491231X-RAY DIFFRACTION99
4.7038-4.79970.37651210.32241291X-RAY DIFFRACTION100
4.7997-4.9040.35721430.34611220X-RAY DIFFRACTION99
4.904-5.0180.36681470.31241238X-RAY DIFFRACTION100
5.018-5.14330.44341400.30311233X-RAY DIFFRACTION100
5.1433-5.28220.31491160.2931271X-RAY DIFFRACTION99
5.2822-5.43740.30271560.29571233X-RAY DIFFRACTION99
5.4374-5.61270.39211500.29461230X-RAY DIFFRACTION100
5.6127-5.8130.3711290.28761277X-RAY DIFFRACTION100
5.813-6.04530.35321400.30431240X-RAY DIFFRACTION100
6.0453-6.31980.36521520.30241231X-RAY DIFFRACTION100
6.3198-6.65220.4081200.31351288X-RAY DIFFRACTION100
6.6522-7.06770.37321210.28161265X-RAY DIFFRACTION100
7.0677-7.61150.3391800.2641209X-RAY DIFFRACTION100
7.6115-8.37380.30621620.22011232X-RAY DIFFRACTION100
8.3738-9.5770.22851420.17241244X-RAY DIFFRACTION100
9.577-12.03430.21251320.14461240X-RAY DIFFRACTION99
12.0343-47.88050.22481460.21161226X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.8553-0.1607-0.65846.76190.70437.8237-0.7706-1.28110.04260.5444-0.15681.27712.0276-2.69690.84441.8121-1.04360.78932.1992-0.18731.55767.5806-22.08022.6099
25.38130.81390.26744.10410.87833.0599-0.5274-2.0049-1.46123.4642-1.18152.0437-0.0565-1.63140.55482.3211-0.6650.97563.33350.15340.68139.7632-19.632911.1387
39.5578-0.75142.00256.67345.64086.01120.7193-2.37040.5924-0.52380.9525-1.0483-0.17922.7016-1.40281.3642-0.74660.17123.1802-0.6911.29420.3146-10.13427.5204
43.8092-3.1086-3.35086.58070.33373.7101-0.18551.148-0.9975-0.28090.21311.1667-2.74621.056-0.34251.17320.2082-0.21363.2505-0.44141.32521.0234-11.2609-19.7424
51.4469-2.70391.62984.97-2.99481.8051-0.5814-0.5547-0.2075-0.98150.28450.023-0.5575-0.6584-0.03583.45881.78430.23243.07180.0213-0.276923.6816-19.1014-40.7215
62.0102-0.72862.59626.4154-0.32099.77661.79451.2909-0.5364-2.7342-1.139-0.2432-0.16561.4789-0.72251.54170.3147-0.21992.3993-0.22181.049525.2065-19.9531-32.4097
77.7986-0.7543-2.76329.20435.3913.94881.6921-0.59841.6052-0.0325-1.6735-1.2-1.10860.5454-0.19381.0555-0.27790.27691.59650.01251.005815.19431.3229-17.4074
87.9398-2.6099-2.43719.54641.96746.2811.1117-0.4711.0923-0.8652-0.6521-1.0811-0.9102-2.8207-0.63550.94760.167-0.00342.0508-0.12610.88418.03387.6941-16.9815
95.9304-2.54583.62838.0156-1.36162.91370.9870.2980.11240.80430.7182-0.1716-1.1839-0.3656-0.76451.21110.0344-0.25690.9056-0.2490.904-3.87040.313-17.6467
107.8756-1.96124.83753.95540.21566.522-1.2657-0.4703-1.7134-0.78340.0267-0.67120.2033-1.42490.24690.42340.0072-0.5862.5458-1.34642.14830.4298-8.0978-18.1182
115.4799-2.53890.16234.50941.10220.3694-0.05520.0933-0.2312-0.50180.2053-0.675-0.62370.4540.02121.5934-1.584-0.27232.21710.18671.882514.397-18.559-6.6246
127.1552-1.22193.16453.0359-2.73183.1233-1.1291-0.8313-1.13821.86130.90921.34670.3591-1.3701-0.03610.8792-0.11510.40911.8480.26851.563822.3058-26.2893-13.5271
133.5568-2.85110.72233.8692-2.9266.23760.4230.9437-0.9773-0.48480.4568-0.01320.09280.5637-0.88111.9156-0.1376-0.27181.54680.54021.304736.957-29.3625-13.672
146.4061.0105-0.25975.67870.41187.3474-1.08110.8432-0.22560.51920.3436-0.08990.08060.71120.38961.41150.0564-0.19281.94310.45931.08432.2339-30.5044-12.7838
153.8822-1.3447-1.35264.2974-2.20615.655-0.14061.20490.1674-0.396-0.4327-0.11690.86582.00280.56381.52240.7131-0.32781.75790.07351.588130.1913-13.292-75.5871
162.03031.6322-0.12582.1333-4.90392.01850.2307-0.15650.5036-1.0326-1.4421-0.59011.05772.6530.62811.65830.3592-0.23882.3989-0.27131.096425.1019-6.0378-83.8473
174.96321.0386-5.20843.29780.92936.89961.90860.58570.3111-0.6521-0.5950.38780.1353-2.9645-0.9781.10180.3919-0.16012.31740.5641.703615.7178-0.656-75.0996
182.73341.2798-2.53174.39961.1333.08610.14090.291.2274-0.5450.07592.34850.08210.5082-0.2781.1407-0.1124-0.45742.24821.09311.9403-0.4463-8.4905-50.876
198.0199-7.7708-6.42449.30324.39127.12141.985-0.0828-2.03391.1428-1.9132-0.76830.1644-1.419-0.29691.583-0.4487-1.03262.16731.13052.9568-1.8204-16.3941-49.9242
204.01163.20310.7464.85413.19963.44740.5331-0.4276-0.1001-0.8836-0.59872.6328-0.6539-2.5080.36251.83150.72530.38472.61511.08543.3432-2.7001-10.5275-48.7996
219.29781.66668.93716.5508-0.67489.45641.2838-0.23392.2744-0.6345-0.04570.4521-1.3807-0.2738-0.96790.94160.08490.22550.75010.25082.054912.61489.0596-58.5709
228.24921.9223-0.86742.1357-4.6982.0999-1.56091.04440.951-0.0148-0.53440.1998-0.0743-0.22511.36271.1477-0.28330.03331.4791-0.40892.109916.864515.9195-60.5749
238.78423.38345.38162.45131.53459.6655-0.3887-1.8671.1215-2.642-0.4291.7676-1.40732.49170.46381.2133-0.00950.42310.9248-0.65643.327121.248218.2286-55.0522
245.47951.81693.86412.09662.04237.2823-0.41280.13881.89390.39-3.0315-0.2734-0.89750.98140.52170.91240.93561.12910.3472-3.1512-1.176720.09269.5762-50.8957
259.0627-4.3349-0.60142.01376.24096.14140.7285-1.77122.22591.3341.4703-0.2215-1.34611.9763-1.75161.41050.21890.11810.8974-0.27290.661629.39827.1378-49.565
265.9449-1.47640.1216.2188-0.34652.7515-0.2155-1.3257-0.87510.17611.00160.79460.12360.6625-0.70210.7714-0.0610.01923.1120.22721.517424.8908-1.064-51.1479
275.52961.0705-1.71444.654-4.01973.47950.37670.20840.3915-1.05840.61581.16531.2809-0.8835-0.42211.76-0.6975-0.2417-2.63560.84931.623417.3794-10.9344-67.9563
284.29842.6144-2.18226.04080.54731.7501-2.2163-0.8427-0.31950.04542.0199-0.31090.0455-0.16710.23741.39830.3066-0.31721.1637-0.2081.9292.3757-20.4846-69.6681
294.30873.1599-2.94696.0708-0.93815.47940.07490.46260.575-0.18950.75390.80170.1287-1.1948-0.45692.37940.01780.06750.690.1062.9669-5.2493-19.2377-67.5913
300.605-0.09731.99910.0401-0.26046.558-0.2320.0045-0.6415-0.2384-0.42050.50980.9817-1.03220.65321.5883-0.8066-0.89152.20730.02393.2449-9.5826-19.0629-72.8739
318.0072-6.73340.81097.5327-1.42763.13060.31281.02760.0744-0.73931.26390.02941.83390.5619-0.96421.96220.0361-0.33282.1571-1.04552.62794.7668-24.5203-68.0493
324.47790.7198-1.15613.2178-1.28724.2896-1.2342-1.8863-0.10510.6760.0211-0.6604-1.05280.55780.72421.4042-0.5745-0.46172.2469-0.72950.940532.6066-52.0098-30.7258
334.3704-0.53161.35893.32370.59677.4420.8874-0.5569-0.1925-1.3769-0.62930.44361.6062-0.0658-0.29821.3824-0.1303-0.111.6256-0.07670.698819.4542-55.9681-61.5363
346.7578-2.555-1.46987.9946-0.00662.69450.2888-0.4035-2.02470.36930.30091.09520.75370.0012-0.39571.12970.0635-0.30011.3826-0.30570.852831.5855-77.5492-53.2249
358.0372-0.5356-1.03219.26410.08825.63890.96370.8583-0.08010.0034-0.4269-0.15470.53590.0746-0.39541.09180.31270.11252.0901-0.2350.713141.2514-70.5759-57.2406
362.0241-3.1077-3.66862.0466-4.31174.8884-0.53512.03850.9645-0.6134-0.2605-0.3469-1.059-0.13970.61280.8829-0.2861-0.10392.28730.31221.076443.7935-59.8114-55.0384
377.1999-4.20132.15064.3851-0.51291.45190.03721.45562.58660.065-0.77210.44130.3366-1.83790.75141.2214-0.0138-0.59711.3637-0.3491.906723.8774-47.7603-48.9721
383.54311.90142.48583.14432.90752.97890.7018-0.59340.89990.2861.6138-0.26770.9433-0.9506-1.00211.47210.6029-0.59972.695-1.09862.09954.4192-37.4685-47.9147
396.0437-0.10832.22399.293.625.3488-0.51622.00070.8306-0.3986-0.92340.86961.2878-1.7148-0.19981.09111.2336-1.17720.81020.55691.80398.1585-43.9942-54.735
400.2746-0.71680.96681.5464-2.27323.5034-0.0247-0.43081.20562.232-0.28040.1112-1.2619-1.63660.38750.0540.8003-2.05093.3598-1.94172.73872.1944-44.3232-51.3381
419.04325.95560.26251.9022-2.11357.4577-0.839-0.04480.7635-0.2621-0.1340.8348-1.27171.37770.74721.20950.0089-0.15711.9832-0.37471.007316.9772-37.8221-51.1258
428.1763-0.48684.98219.5991-1.82398.5349-0.99710.32581.8159-0.01120.6737-1.1935-0.75070.9359-0.12661.0648-0.22320.04061.4033-0.06091.435669.144315.1755.7781
432.36350.4083-2.33923.7827-1.05676.0689-0.7675-0.06212.5327-0.161-2.2284-1.2987-0.0419-0.15580.64812.0662-0.504-0.43381.9991-1.25560.147171.393713.858514.5344
448.7772-0.74784.64392.5258-1.26229.81150.1492-1.1159-0.91130.76670.37050.84040.4954-1.2542-0.52880.7278-0.5396-0.55814.3395-0.49211.011261.40253.536517.3291
452.61852.8133-0.17872.01217.11527.1391-0.49360.9255-0.84480.51560.6538-1.011.5675-1.6768-0.59450.1099-0.1678-0.71042.9615-1.53812.551354.4317-2.1929-3.8554
469.1994.6827-0.24615.7168-3.39043.25361.5194-0.5046-0.18111.61980.00420.81970.6863-0.0509-1.45161.45250.00520.13843.28290.10641.080544.13193.2341-8.6914
471.3798-0.9111.46975.56723.01285.48980.47080.63510.5503-0.7187-0.22780.831-0.7109-1.8707-0.25091.27720.0341-0.07192.41530.09441.571740.021311.806-21.6632
482.00873.3871.96298.2958-3.1772.0522-1.61940.2327-0.59830.31820.36440.82461.79550.19091.50561.6041-0.65140.16492.78340.11671.172738.39961.8206-14.568
496.3684-2.6847-3.27885.8644-2.2414.05140.72940.0193-1.9888-0.3560.2067-0.44870.4562-0.3355-0.46661.04340.3241-0.91512.70090.11541.920755.0046-10.9158-5.6055
502.9528-2.60030.36973.3846-1.31032.00470.4047-2.29480.11920.3919-0.7403-0.92782.1435-0.23040.12560.8912-0.0487-0.32642.3055-0.31042.320161.5889-19.1826-5.4554
518.54160.4677-0.53014.6835-2.28126.12250.61661.7313-3.3793-0.0527-0.15320.5605-0.14290.2-0.29741.1615-0.4905-1.03162.1279-2.8828-3.49566.3665-9.8045-13.7025
529.4526-3.3875-2.93796.04732.80265.2718-0.00070.9451.6581.03350.9208-1.1373-0.1453-0.0549-0.89931.2256-0.3081-0.03471.87860.54931.362558.86879.4445-5.2124
535.2269-1.09527.11560.1799-1.4839.5925-0.1058-0.18770.41720.1802-0.24911.4451-0.4767-1.110.15351.65981.1412-0.16762.6101-0.33312.61934.004923.19947.3841
542.7118-2.20810.4943.92721.95672.59930.2507-0.72560.0413-0.76760.84130.0336-0.8767-1.4056-0.69121.65150.6149-0.58311.9237-0.23873.069535.520716.9459-0.4432
550.3552-0.97831.8232.387-4.6229.0841-0.07560.04360.89590.62260.64860.2219-0.4115-0.8304-0.15361.62481.08380.06682.6829-0.02492.209331.072416.29454.7071
564.17613.76081.83323.44151.70310.73360.0962-2.031.67710.3367-0.67111.9605-0.65770.87820.56751.86370.4178-0.30273.2624-1.57482.648944.823923.43890.2825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 171 )
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 222 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 27 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 81 )
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 94 )
10X-RAY DIFFRACTION10chain 'B' and (resid 95 through 123 )
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 157 )
13X-RAY DIFFRACTION13chain 'B' and (resid 158 through 191 )
14X-RAY DIFFRACTION14chain 'B' and (resid 192 through 222 )
15X-RAY DIFFRACTION15chain 'C' and (resid 6 through 66 )
16X-RAY DIFFRACTION16chain 'C' and (resid 67 through 94 )
17X-RAY DIFFRACTION17chain 'C' and (resid 95 through 137 )
18X-RAY DIFFRACTION18chain 'C' and (resid 138 through 171 )
19X-RAY DIFFRACTION19chain 'C' and (resid 172 through 191 )
20X-RAY DIFFRACTION20chain 'C' and (resid 192 through 222 )
21X-RAY DIFFRACTION21chain 'D' and (resid 6 through 27 )
22X-RAY DIFFRACTION22chain 'D' and (resid 28 through 44 )
23X-RAY DIFFRACTION23chain 'D' and (resid 45 through 66 )
24X-RAY DIFFRACTION24chain 'D' and (resid 67 through 81 )
25X-RAY DIFFRACTION25chain 'D' and (resid 82 through 94 )
26X-RAY DIFFRACTION26chain 'D' and (resid 95 through 123 )
27X-RAY DIFFRACTION27chain 'D' and (resid 124 through 137 )
28X-RAY DIFFRACTION28chain 'D' and (resid 138 through 171 )
29X-RAY DIFFRACTION29chain 'D' and (resid 172 through 191 )
30X-RAY DIFFRACTION30chain 'D' and (resid 192 through 203 )
31X-RAY DIFFRACTION31chain 'D' and (resid 204 through 222 )
32X-RAY DIFFRACTION32chain 'E' and (resid 6 through 106 )
33X-RAY DIFFRACTION33chain 'E' and (resid 107 through 222 )
34X-RAY DIFFRACTION34chain 'F' and (resid 6 through 66 )
35X-RAY DIFFRACTION35chain 'F' and (resid 67 through 106 )
36X-RAY DIFFRACTION36chain 'F' and (resid 107 through 123 )
37X-RAY DIFFRACTION37chain 'F' and (resid 124 through 157 )
38X-RAY DIFFRACTION38chain 'F' and (resid 158 through 171 )
39X-RAY DIFFRACTION39chain 'F' and (resid 172 through 191 )
40X-RAY DIFFRACTION40chain 'F' and (resid 192 through 203 )
41X-RAY DIFFRACTION41chain 'F' and (resid 204 through 222 )
42X-RAY DIFFRACTION42chain 'G' and (resid 6 through 44 )
43X-RAY DIFFRACTION43chain 'G' and (resid 45 through 81 )
44X-RAY DIFFRACTION44chain 'G' and (resid 82 through 123 )
45X-RAY DIFFRACTION45chain 'G' and (resid 124 through 137 )
46X-RAY DIFFRACTION46chain 'G' and (resid 138 through 157 )
47X-RAY DIFFRACTION47chain 'G' and (resid 158 through 203 )
48X-RAY DIFFRACTION48chain 'G' and (resid 204 through 222 )
49X-RAY DIFFRACTION49chain 'H' and (resid 6 through 27 )
50X-RAY DIFFRACTION50chain 'H' and (resid 28 through 66 )
51X-RAY DIFFRACTION51chain 'H' and (resid 67 through 106 )
52X-RAY DIFFRACTION52chain 'H' and (resid 107 through 157 )
53X-RAY DIFFRACTION53chain 'H' and (resid 158 through 171 )
54X-RAY DIFFRACTION54chain 'H' and (resid 172 through 191 )
55X-RAY DIFFRACTION55chain 'H' and (resid 192 through 203 )
56X-RAY DIFFRACTION56chain 'H' and (resid 204 through 222 )

+
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