[English] 日本語
Yorodumi
- PDB-6x61: Crystal structure of the N-terminal thioredoxin domain of SasA in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x61
TitleCrystal structure of the N-terminal thioredoxin domain of SasA in complex with the N-terminal CI domain of KaiC from Thermosynchococcus elongatus
Components
  • Adaptive-response sensory-kinase SasA
  • Circadian clock protein kinase KaiC
KeywordsTRANSCRIPTION/TRANSFERASE / Transcription regulator / complex / circadian clock / TRANSCRIPTION / TRANSCRIPTION-TRANSFERASE complex
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / protein serine/threonine/tyrosine kinase activity / regulation of circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / kinase activity / protein autophosphorylation / 3-phosphoinositide-dependent protein kinase activity ...histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / protein serine/threonine/tyrosine kinase activity / regulation of circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / kinase activity / protein autophosphorylation / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / protein serine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
Adaptive-response sensory-kinase SasA / KaiB domain / KaiB domain / KaiB / Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain ...Adaptive-response sensory-kinase SasA / KaiB domain / KaiB domain / KaiB / Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Thioredoxin-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Circadian clock oscillator protein KaiC / Adaptive-response sensory kinase SasA
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSwan, J.A. / Tripathi, S.M. / Partch, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121507 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107521 United States
CitationJournal: Science / Year: 2021
Title: Reconstitution of an intact clock reveals mechanisms of circadian timekeeping.
Authors: Chavan, A.G. / Swan, J.A. / Heisler, J. / Sancar, C. / Ernst, D.C. / Fang, M. / Palacios, J.G. / Spangler, R.K. / Bagshaw, C.R. / Tripathi, S. / Crosby, P. / Golden, S.S. / Partch, C.L. / LiWang, A.
History
DepositionMay 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Circadian clock protein kinase KaiC
B: Adaptive-response sensory-kinase SasA
C: Circadian clock protein kinase KaiC
D: Adaptive-response sensory-kinase SasA
E: Circadian clock protein kinase KaiC
F: Adaptive-response sensory-kinase SasA
G: Circadian clock protein kinase KaiC
H: Adaptive-response sensory-kinase SasA
I: Circadian clock protein kinase KaiC
J: Adaptive-response sensory-kinase SasA
K: Circadian clock protein kinase KaiC
L: Adaptive-response sensory-kinase SasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,77418
Polymers242,20412
Non-polymers5706
Water00
1
A: Circadian clock protein kinase KaiC
B: Adaptive-response sensory-kinase SasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4623
Polymers40,3672
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-12 kcal/mol
Surface area15070 Å2
MethodPISA
2
C: Circadian clock protein kinase KaiC
D: Adaptive-response sensory-kinase SasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4623
Polymers40,3672
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-12 kcal/mol
Surface area14610 Å2
MethodPISA
3
E: Circadian clock protein kinase KaiC
F: Adaptive-response sensory-kinase SasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4623
Polymers40,3672
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-11 kcal/mol
Surface area15180 Å2
MethodPISA
4
G: Circadian clock protein kinase KaiC
H: Adaptive-response sensory-kinase SasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4623
Polymers40,3672
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-12 kcal/mol
Surface area15440 Å2
MethodPISA
5
I: Circadian clock protein kinase KaiC
J: Adaptive-response sensory-kinase SasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4623
Polymers40,3672
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-11 kcal/mol
Surface area14900 Å2
MethodPISA
6
K: Circadian clock protein kinase KaiC
L: Adaptive-response sensory-kinase SasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4623
Polymers40,3672
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-12 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.600, 121.580, 133.590
Angle α, β, γ (deg.)90.00, 108.78, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Circadian clock protein kinase KaiC


Mass: 27738.166 Da / Num. of mol.: 6 / Fragment: N-terminal CI domain / Mutation: R41A, K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: kaiC, tlr0483 / Production host: Escherichia coli (E. coli)
References: UniProt: Q79V60, non-specific serine/threonine protein kinase
#2: Protein
Adaptive-response sensory-kinase SasA


Mass: 12629.217 Da / Num. of mol.: 6 / Fragment: N-terminal thioredoxin domain / Mutation: P16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: sasA, tlr0029 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DMT2, histidine kinase
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.41 % / Description: flat plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.26 M NaH2PO4, 0.54 M K2HPO4 (pH unadjusted), 0.1 M Glycine pH 10.5, 0.2 M Li2SO4, 22 degrees C

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 3.2→49.05 Å / Num. obs: 53267 / % possible obs: 98.8 % / Redundancy: 2.9 % / CC1/2: 0.95 / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.5
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4635 / CC1/2: 0.58

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JWO

5jwo


Resolution: 3.2→49.049 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 2634 4.95 %
Rwork0.2217 --
obs0.2239 53220 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→49.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15469 0 30 0 15499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315818
X-RAY DIFFRACTIONf_angle_d0.77821460
X-RAY DIFFRACTIONf_dihedral_angle_d5.0599460
X-RAY DIFFRACTIONf_chiral_restr0.0472422
X-RAY DIFFRACTIONf_plane_restr0.0042774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.25820.35391350.30092692X-RAY DIFFRACTION99
3.2582-3.32090.31451410.28912637X-RAY DIFFRACTION99
3.3209-3.38860.29891360.28742679X-RAY DIFFRACTION99
3.3886-3.46230.3471430.2782671X-RAY DIFFRACTION99
3.4623-3.54280.31671220.272657X-RAY DIFFRACTION99
3.5428-3.63140.3421410.25442638X-RAY DIFFRACTION99
3.6314-3.72950.3011370.23892671X-RAY DIFFRACTION99
3.7295-3.83930.25981330.23572701X-RAY DIFFRACTION100
3.8393-3.96310.28331610.2282625X-RAY DIFFRACTION99
3.9631-4.10470.28621410.22152638X-RAY DIFFRACTION99
4.1047-4.2690.24741480.20272680X-RAY DIFFRACTION99
4.269-4.46310.26031520.18812659X-RAY DIFFRACTION99
4.4631-4.69820.20421410.18152655X-RAY DIFFRACTION99
4.6982-4.99230.24681420.17852637X-RAY DIFFRACTION99
4.9923-5.37740.23681600.19412644X-RAY DIFFRACTION98
5.3774-5.91770.24921220.21452656X-RAY DIFFRACTION98
5.9177-6.77210.23511180.22012702X-RAY DIFFRACTION98
6.7721-8.52480.24511360.21112660X-RAY DIFFRACTION97
8.5248-490.21471250.20412684X-RAY DIFFRACTION96
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)
16.2888-0.24020.22250.9934-0.48230.2559-0.1614-0.28060.63780.12240.1745-0.29120.31190.35350.11171.14370.0255-0.29730.5603-0.01230.382872.28590.348126.004
22.72580.10330.88940.00710.06110.7674-0.1232-0.15160.4190.32370.0693-0.3554-0.12340.16070.06081.01840.2464-0.79970.7423-0.19350.179776.45784.501128.817
35.8874-2.41224.99893.7108-3.41948.9160.08520.4423-0.25820.32660.4194-0.1768-0.24080.7828-0.44930.6550.1263-0.05740.4052-0.02530.240267.11682.076111.503
43.18240.29892.80350.0995-0.30428.2424-0.29590.15630.1481.14110.284-0.0305-0.59650.09530.16680.8654-0.0224-0.03040.3726-0.0140.118358.66184.495116.379
52.1673-2.5891.12043.5598-1.70171.03470.26540.0535-0.0430.4262-0.50650.4343-0.2697-0.39590.11871.06350.1712-0.1480.5746-0.05160.366954.18994.761122.503
63.5668-0.1476-1.8270.6811-0.18625.9718-0.146-0.1530.0256-0.4576-0.66210.72160.1108-0.77850.71810.74030.1114-0.02270.412-0.12560.204952.2596.102127.542
78.0102-3.7456-3.76073.6209-1.33166.9937-0.1693-0.3685-0.37360.7547-0.5009-0.0557-0.2442-0.06190.69830.7970.0801-0.09220.40570.00480.289851.88896.985135.415
81.5438-0.4620.46191.6988-2.11663.1611-0.0453-0.291-0.03260.16540.05640.1364-0.0838-0.2078-0.10961.89310.0958-0.4140.23930.28260.170759.11898.626140.796
97.82334.8295-0.12115.6563-1.99191.48570.1103-0.319-0.94750.3153-0.3328-0.5962-0.1401-0.24670.24540.32590.0252-0.09950.1893-0.0540.258970.23576.70699.523
103.83642.6665-0.52623.5876-3.34775.2025-0.17250.7896-0.54440.32530.1494-0.3599-0.31-1.1818-0.14990.28890.0413-0.12470.4783-0.04510.31965.17273.9893.412
114.44790.0126-1.4292.13373.48916.172-0.4355-0.2164-0.22630.4894-0.2744-0.5694-0.17260.61320.46710.34720.0094-0.16550.33120.17420.372175.39776.49398.902
124.7831-0.6319-3.23695.5138-2.30783.54320.26350.08060.04740.41140.0628-0.458-0.0239-0.0797-0.27590.4028-0.0331-0.08650.2145-0.01570.280971.29786.30696.611
136.09690.419-3.31993.4155-1.50056.2904-0.30830.2725-0.24710.23580.2126-0.68250.5627-0.09720.25670.55190.0536-0.25130.3396-0.13260.539442.36548.46471.801
142.8218-0.5991-1.2552.7602-2.13682.92130.08570.0099-0.07670.0330.03460.24790.0122-0.1068-0.08950.2964-0.0912-0.1560.3584-0.03710.451632.79159.45778.167
157.88856.1645.60217.84236.69768.17820.5872-0.45440.13750.3407-0.7380.42290.1646-0.69740.10910.30510.005-0.00660.2964-0.02110.211432.4764.7789.216
168.18055.1636-1.10255.1435-1.06824.76620.4238-0.23240.02470.5712-0.08050.2006-0.08730.0172-0.2820.41040.0237-0.10730.1969-0.0160.30543.60261.76689.547
177.2114.6422-0.01355.38753.125.1613-0.08250.54040.3547-0.4399-0.012-0.396-0.7140.42340.21920.3276-0.0579-0.02530.3951-0.05280.410446.89165.41572.991
186.4676-4.32724.82724.0545-4.96498.5584-0.44270.17090.133-0.88240.1867-0.25130.0787-0.29310.07210.5275-0.1395-0.02730.3826-0.14680.484245.25158.97563.761
196.983-0.50923.57496.464-0.01533.6151-0.28740.4243-0.04040.0603-0.21860.1672-0.8122-0.18670.50220.95080.0189-0.15880.3959-0.08030.420436.56556.54861.6
203.9901-2.3482.37033.753-2.72842.1689-1.0416-1.54630.42730.25731.0377-0.33430.50590.3459-0.04340.7871-0.0485-0.00570.5201-0.18650.455643.04568.541106.967
214.18631.0922.12988.78752.90092.63630.2079-0.93170.18240.6724-0.5450.67770.4932-1.15360.40780.6318-0.07790.02710.6224-0.08450.428839.08174.628107.682
225.09234.0363-2.00213.547-1.64841.33430.277-0.17150.24940.9859-0.37271.4877-0.2724-1.02550.17940.7050.27890.39181.37340.06430.724328.8785.652112.571
231.0764-1.58950.95143.3169-0.46441.9962-0.35690.19260.4015-0.37720.19821.397-0.1913-0.25690.1560.4094-0.0687-0.32140.52430.00440.69523.23488.49162.726
244.9546-0.36590.11274.93371.38843.0929-0.19370.1358-0.1759-0.59550.2505-0.14530.3291-0.1206-0.08450.5885-0.1445-0.23930.66770.10310.309836.34988.9955.133
255.16820.91652.0792.2413-2.25454.1326-0.03231.0912-0.3803-0.3789-0.3942-0.73270.35711.21620.460.37030.00360.09570.64060.02390.532350.5787.61874.883
264.51620.6693-1.15933.0791-0.27374.0178-0.1237-0.01540.1563-0.54070.01650.48960.09340.03380.05190.29720.0157-0.17870.2830.00270.341135.75891.22371.896
277.7865-1.96345.65230.8825-1.73224.353-0.0185-0.8268-0.59220.88070.14290.2997-0.4941-0.7353-0.05480.4921-0.0564-0.04080.87280.0280.299229.59586.20479.315
284.5459-2.3151-0.62574.3349-3.31354.3013-0.1057-0.20160.0137-0.9698-0.17961.15320.4767-0.21320.33730.2767-0.1384-0.17520.31490.00470.626621.36773.23866.874
296.6182-3.6375-3.32192.74053.42375.35370.36860.111-0.0052-0.4138-0.36250.5009-0.1869-0.560.13210.7217-0.0598-0.22880.28460.07950.658615.5381.34163.854
308.2382-6.5218-5.49535.19684.33436.82070.76370.52121.1328-0.4288-0.2611-0.4043-0.1989-0.5267-0.53560.3295-0.01780.03670.44320.08050.163657.46699.70374.594
315.6099-5.2271-2.87364.99472.92467.6809-0.0524-0.3715-0.43470.7926-0.28270.0147-0.63170.13950.22610.3807-0.1324-0.03640.29640.07030.240859.383102.36782.244
321.9580.29630.98415.9522-1.5825.66350.4531-0.1147-0.8806-1.1388-0.4177-0.3845-0.18230.1959-0.08420.52660.16330.00960.50640.13470.310672.20597.00776.134
337.112-2.85122.29088.2429-1.28884.16250.14860.30370.0694-0.4819-0.1341-0.1814-0.02280.21470.00180.2935-0.0136-0.02320.2448-0.01410.157159.76792.56273.044
343.93381.9275-0.36513.70870.29082.9020.16160.8198-0.6351-0.9817-0.32520.0927-0.1633-0.3060.26270.5810.2068-0.09920.4627-0.1740.409573.84158.40271.767
356.723-0.5956-2.02067.54270.86058.49070.29760.1853-1.2459-0.3496-0.6560.36740.6021-0.29850.43520.25620.0442-0.03650.3081-0.080.480182.23549.94779.034
366.1532-0.669-0.71075.72991.97741.9463-0.23440.5128-1.1862-0.4110.4253-0.38870.25110.794-0.00110.46040.24490.17360.6319-0.10850.413788.95350.99977.75
378.00453.5243-6.0068.76631.20496.5781-0.732-0.9731-0.61671.0663-0.1351-1.56311.0730.61240.57790.38010.0674-0.1560.65660.0040.358378.04554.549101.324
388.7302-2.1279-5.79273.53061.77757.81260.1027-0.3736-0.2113-0.049-0.1164-0.5562-0.0620.42540.11010.163-0.0014-0.01930.310.08360.246178.51962.46289.357
391.2337-0.38592.35893.1361.48066.20810.75470.3092-0.45870.02120.04190.29021.0056-1.0904-0.19950.41570.1421-0.13120.3027-0.1490.499966.32558.23785.986
403.18973.5872-0.48775.38981.5393.37240.29960.253-0.7435-1.094-0.23790.3197-0.0109-0.0779-0.01120.5740.2056-0.38090.3706-0.16420.656462.11455.13576.169
418.1487-1.8118-0.63741.443-1.74083.4742-0.02381.16360.18670.4743-0.3274-0.3645-0.7341-0.8430.42740.77610.2422-0.33360.7862-0.21870.593162.43761.54468.523
426.99866.5634-0.88036.8501-3.38049.4169-0.2670.943-0.2316-1.90370.2927-0.64130.64820.8576-0.14590.69550.1033-0.07830.4707-0.2290.499768.48749.68564.1
436.2644-3.86191.79167.639-0.68492.4949-0.1487-0.5636-0.14270.2738-0.0918-0.0298-0.2152-0.36730.21680.58980.0293-0.23720.65450.24170.285887.64763.368105.277
442.165-0.8449-1.04335.2511-4.24324.9047-0.3806-1.14950.61160.78220.3115-0.927-0.9041-0.17030.05050.8164-0.138-0.25750.58750.06750.450386.0966.778112.986
455.6674-1.9510.24755.072-3.64913.56240.0275-0.58360.27890.3718-0.5692-1.12470.39462.14760.55470.6739-0.0715-0.17690.62310.18390.575393.25158.705111.958
463.54871.17460.51422.2624-0.97415.004-0.2672-0.1476-0.68750.6235-0.2953-0.95660.62290.72440.40910.54240.1857-0.06320.40950.11140.407585.67452.905108.289
473.87340.5661-0.90310.4677-0.86771.80480.4015-0.2808-0.12731.1952-0.4677-1.4099-0.89010.62440.1190.626-0.4064-0.37970.57230.27911.187482.529122.42780.736
484.32446.3215.07719.28167.41765.9632-0.55911.24251.3813-0.98880.17950.7102-0.19790.06520.41560.34290.09190.01580.65290.19740.57160.52121.56567.145
496.33921.947-2.88963.7082-0.26784.38160.37440.62910.11370.1073-0.4092-0.8955-0.2049-0.03560.00220.26890.0201-0.01840.32480.16840.365670.574113.85673.649
503.00391.0115-0.00882.51790.58480.8076-0.2953-0.00240.51190.5457-0.181-0.0678-0.82010.08280.27520.9814-0.1416-0.24630.3710.17950.409668.435120.03889.893
511.30571.10740.85281.52280.9161.96190.1427-0.5448-0.070.4707-0.1443-0.4961-0.38110.39380.24761.3872-0.5674-1.26260.81760.27060.374379.802120.63397.532
525.7665-2.11373.19859.2578-5.39253.9080.0977-0.0033-0.4685-1.2483-0.047-0.04730.70080.4608-0.11110.53020.19010.12260.43110.07740.240258.623111.43954.511
534.08431.30350.67731.90651.86231.9432-0.12740.7606-0.1307-0.7306-0.0257-0.3215-0.54250.71110.18590.33060.19070.26830.7610.3220.437865.411118.06454.055
544.7465-0.3388-0.36584.7799-0.18542.76640.2797-0.470.443-0.3387-0.7881-1.1709-0.2127-0.0880.43280.2310.0351-0.02630.66020.11790.378260.013123.60356.966
552.4543-2.6193.03418.0651-3.25729.20320.36340.84630.5193-0.2046-0.31610.2995-1.19170.0331-0.08970.39160.14650.01560.56140.22910.526552.149127.71351.984
566.5445-1.95180.83819.4001-6.19524.4126-0.53-0.1930.4114-0.17790.7391-0.4296-0.6927-0.1254-0.24071.0029-0.047-0.160.3667-0.12250.440763.768127.787113.187
571.5322-0.2667-0.6170.98871.23171.8274-0.0486-0.23780.11040.0202-0.1819-0.329-0.4261-0.05080.12151.0770.1168-0.24850.3749-0.04180.290852.856116.797117.366
584.9175-1.3178-1.62453.30174.13896.8679-0.1312-0.297-0.10170.4252-0.52910.3201-0.1468-0.77640.67630.77150.1073-0.16230.2693-0.00170.27743.644111.537111.234
596.0290.124-0.69440.89111.88884.3579-0.11410.0458-0.00220.82760.034-0.1057-0.1931-0.15430.1010.7489-0.0338-0.15690.2196-0.01030.270850.02114.575102.022
605.35044.5616-0.41364.44871.36435.58360.5327-0.7223-1.6335-0.0968-0.3649-0.46390.81290.219-0.42621.1349-0.057-0.25850.461-0.04290.380463.747110.997109.424
616.88183.5195-1.96145.63351.7135.8895-0.74980.07760.26920.14940.266-0.2085-0.55670.44030.57490.7936-0.0411-0.14540.36430.00950.28666.663110.857108.543
625.8722.7463-3.24048.0655-1.13447.4298-0.0904-0.4283-0.2123-0.4648-0.169-0.57510.24430.67180.32030.7342-0.1044-0.2720.391-0.07730.577571.809117.357115.605
630.05340.4549-0.17665.85641.20287.12980.5775-0.2577-0.24130.4304-0.4242-0.227-0.46450.69080.00811.2197-0.0214-0.4050.50970.00770.624468.593119.776124.022
646.1617-4.0024-2.48875.6719-0.28688.43590.558-0.24161.24880.21420.62730.2104-0.0171-0.252-1.02340.657-0.1309-0.20310.5281-0.19260.511335.408107.70592.363
654.975.72411.11827.26861.35937.47310.1799-0.04311.52440.6249-0.20560.65870.31660.00530.1920.58190.1286-0.00810.3432-0.13510.654434.138103.81384.727
666.4832-0.0652.66762.17773.87258.9509-0.4866-0.67240.0352-0.1862-0.35660.7431-0.282-1.50030.76710.73440.0424-0.08290.5774-0.12910.549731.753103.85597.988
677.51792.6019-1.88486.7386-4.09512.50790.1959-1.6098-0.2950.0286-0.16680.62671.6053-0.86980.08170.601-0.32870.02660.70490.07240.358132.81391.49394.759
683.23681.85933.10864.58971.4994.0517-0.1066-0.87340.11810.8527-0.47690.0149-0.1988-1.06030.33061.53590.03560.05560.8230.06020.221756.06784.524138.179
690.85780.1233-0.53020.79660.4262.0759-0.2173-0.2484-0.13330.5023-0.15080.00620.08270.3802-0.18111.27390.0653-0.2620.4372-0.06740.024763.70489.943131.419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN K AND RESID 51:73 )K51 - 73
2X-RAY DIFFRACTION2( CHAIN K AND RESID 74:90 )K74 - 90
3X-RAY DIFFRACTION3( CHAIN K AND RESID 91:120 )K91 - 120
4X-RAY DIFFRACTION4( CHAIN K AND RESID 121:157 )K121 - 157
5X-RAY DIFFRACTION5( CHAIN K AND RESID 158:180 )K158 - 180
6X-RAY DIFFRACTION6( CHAIN K AND RESID 181:195 )K181 - 195
7X-RAY DIFFRACTION7( CHAIN K AND RESID 196:216 )K196 - 216
8X-RAY DIFFRACTION8( CHAIN K AND RESID 217:231 )K217 - 231
9X-RAY DIFFRACTION9( CHAIN L AND RESID 15:21 )L15 - 21
10X-RAY DIFFRACTION10( CHAIN L AND RESID 22:34 )L22 - 34
11X-RAY DIFFRACTION11( CHAIN L AND RESID 35:58 )L35 - 58
12X-RAY DIFFRACTION12( CHAIN L AND RESID 59:94 )L59 - 94
13X-RAY DIFFRACTION13( CHAIN A AND RESID 19:23 )A19 - 23
14X-RAY DIFFRACTION14( CHAIN A AND RESID 24:73 )A24 - 73
15X-RAY DIFFRACTION15( CHAIN A AND RESID 74:106 )A74 - 106
16X-RAY DIFFRACTION16( CHAIN A AND RESID 107:157 )A107 - 157
17X-RAY DIFFRACTION17( CHAIN A AND RESID 158:195 )A158 - 195
18X-RAY DIFFRACTION18( CHAIN A AND RESID 196:216 )A196 - 216
19X-RAY DIFFRACTION19( CHAIN A AND RESID 217:231 )A217 - 231
20X-RAY DIFFRACTION20( CHAIN B AND RESID 15:21 )B15 - 21
21X-RAY DIFFRACTION21( CHAIN B AND RESID 22:93 )B22 - 93
22X-RAY DIFFRACTION22( CHAIN B AND RESID 94:98 )B94 - 98
23X-RAY DIFFRACTION23( CHAIN C AND RESID 19:48 )C19 - 48
24X-RAY DIFFRACTION24( CHAIN C AND RESID 49:90 )C49 - 90
25X-RAY DIFFRACTION25( CHAIN C AND RESID 91:106 )C91 - 106
26X-RAY DIFFRACTION26( CHAIN C AND RESID 107:175 )C107 - 175
27X-RAY DIFFRACTION27( CHAIN C AND RESID 176:186 )C176 - 186
28X-RAY DIFFRACTION28( CHAIN C AND RESID 187:207 )C187 - 207
29X-RAY DIFFRACTION29( CHAIN C AND RESID 208:232 )C208 - 232
30X-RAY DIFFRACTION30( CHAIN D AND RESID 15:21 )D15 - 21
31X-RAY DIFFRACTION31( CHAIN D AND RESID 22:34 )D22 - 34
32X-RAY DIFFRACTION32( CHAIN D AND RESID 35:44 )D35 - 44
33X-RAY DIFFRACTION33( CHAIN D AND RESID 45:99 )D45 - 99
34X-RAY DIFFRACTION34( CHAIN E AND RESID 19:48 )E19 - 48
35X-RAY DIFFRACTION35( CHAIN E AND RESID 49:73 )E49 - 73
36X-RAY DIFFRACTION36( CHAIN E AND RESID 74:90 )E74 - 90
37X-RAY DIFFRACTION37( CHAIN E AND RESID 91:106 )E91 - 106
38X-RAY DIFFRACTION38( CHAIN E AND RESID 107:156 )E107 - 156
39X-RAY DIFFRACTION39( CHAIN E AND RESID 157:176 )E157 - 176
40X-RAY DIFFRACTION40( CHAIN E AND RESID 177:208 )E177 - 208
41X-RAY DIFFRACTION41( CHAIN E AND RESID 209:220 )E209 - 220
42X-RAY DIFFRACTION42( CHAIN E AND RESID 221:231 )E221 - 231
43X-RAY DIFFRACTION43( CHAIN F AND RESID 16:21 )F16 - 21
44X-RAY DIFFRACTION44( CHAIN F AND RESID 22:34 )F22 - 34
45X-RAY DIFFRACTION45( CHAIN F AND RESID 35:52 )F35 - 52
46X-RAY DIFFRACTION46( CHAIN F AND RESID 53:98 )F53 - 98
47X-RAY DIFFRACTION47( CHAIN G AND RESID 19:90 )G19 - 90
48X-RAY DIFFRACTION48( CHAIN G AND RESID 91:106 )G91 - 106
49X-RAY DIFFRACTION49( CHAIN G AND RESID 107:156 )G107 - 156
50X-RAY DIFFRACTION50( CHAIN G AND RESID 157:199 )G157 - 199
51X-RAY DIFFRACTION51( CHAIN G AND RESID 200:231 )G200 - 231
52X-RAY DIFFRACTION52( CHAIN H AND RESID 16:35 )H16 - 35
53X-RAY DIFFRACTION53( CHAIN H AND RESID 36:65 )H36 - 65
54X-RAY DIFFRACTION54( CHAIN H AND RESID 66:82 )H66 - 82
55X-RAY DIFFRACTION55( CHAIN H AND RESID 83:102 )H83 - 102
56X-RAY DIFFRACTION56( CHAIN I AND RESID 20:23 )I20 - 23
57X-RAY DIFFRACTION57( CHAIN I AND RESID 24:73 )I24 - 73
58X-RAY DIFFRACTION58( CHAIN I AND RESID 74:106 )I74 - 106
59X-RAY DIFFRACTION59( CHAIN I AND RESID 107:157 )I107 - 157
60X-RAY DIFFRACTION60( CHAIN I AND RESID 158:175 )I158 - 175
61X-RAY DIFFRACTION61( CHAIN I AND RESID 176:195 )I176 - 195
62X-RAY DIFFRACTION62( CHAIN I AND RESID 196:216 )I196 - 216
63X-RAY DIFFRACTION63( CHAIN I AND RESID 217:231 )I217 - 231
64X-RAY DIFFRACTION64( CHAIN J AND RESID 15:21 )J15 - 21
65X-RAY DIFFRACTION65( CHAIN J AND RESID 22:34 )J22 - 34
66X-RAY DIFFRACTION66( CHAIN J AND RESID 35:82 )J35 - 82
67X-RAY DIFFRACTION67( CHAIN J AND RESID 83:95 )J83 - 95
68X-RAY DIFFRACTION68( CHAIN K AND RESID 19:23 )K19 - 23
69X-RAY DIFFRACTION69( CHAIN K AND RESID 24:50 )K24 - 50

+
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