[English] 日本語
Yorodumi
- PDB-5luq: Crystal Structure of Human DNA-dependent Protein Kinase Catalytic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5luq
TitleCrystal Structure of Human DNA-dependent Protein Kinase Catalytic Subunit (DNA-PKcs)
Components
  • C-terminal fragment of KU80 (KU80ct194)
  • DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit
KeywordsTRANSFERASE / DNA-PKcs / Kinase / DNA repair / NHEJ / double strand break repair / HEAT repeat
Function / homology
Function and homology information


positive regulation of platelet formation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / T cell receptor V(D)J recombination / DNA-dependent protein kinase complex / double-strand break repair via alternative nonhomologous end joining / DNA-dependent protein kinase activity / pro-B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex ...positive regulation of platelet formation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / T cell receptor V(D)J recombination / DNA-dependent protein kinase complex / double-strand break repair via alternative nonhomologous end joining / DNA-dependent protein kinase activity / pro-B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / immunoglobulin V(D)J recombination / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / regulation of epithelial cell proliferation / telomere capping / ectopic germ cell programmed cell death / maturation of 5.8S rRNA / U3 snoRNA binding / regulation of hematopoietic stem cell differentiation / T cell lineage commitment / B cell lineage commitment / positive regulation of double-strand break repair via nonhomologous end joining / somitogenesis / small-subunit processome / mitotic G1 DNA damage checkpoint signaling / activation of innate immune response / protein modification process => GO:0036211 / telomere maintenance / negative regulation of protein phosphorylation / Nonhomologous End-Joining (NHEJ) / positive regulation of translation / positive regulation of erythrocyte differentiation / protein destabilization / protein-DNA complex / response to gamma radiation / regulation of circadian rhythm / double-strand break repair / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / rhythmic process / intrinsic apoptotic signaling pathway in response to DNA damage / E3 ubiquitin ligases ubiquitinate target proteins / brain development / T cell differentiation in thymus / peptidyl-threonine phosphorylation / double-stranded DNA binding / heart development / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / transcription regulator complex / non-specific serine/threonine protein kinase / peptidyl-serine phosphorylation / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / cellular response to DNA damage stimulus / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / innate immune response / protein phosphorylation / negative regulation of apoptotic process / protein serine/threonine/tyrosine kinase activity / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / membrane / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
DNA-dependent protein kinase catalytic subunit, CC3 / NUC194 / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-PKcs, CC5 / FAT domain / PIK-related kinase, FAT / FATC domain / FATC ...DNA-dependent protein kinase catalytic subunit, CC3 / NUC194 / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-PKcs, CC5 / FAT domain / PIK-related kinase, FAT / FATC domain / FATC / FAT domain profile. / FATC domain profile. / PIK-related kinase / FATC domain / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DNA-dependent protein kinase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.3 Å
AuthorsSibanda, B.L. / Chirgadze, D.Y. / Ascher, D.B. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust093167/Z/10/Z United Kingdom
CitationJournal: Science / Year: 2017
Title: DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair.
Authors: Sibanda, B.L. / Chirgadze, D.Y. / Ascher, D.B. / Blundell, T.L.
History
DepositionSep 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Mar 28, 2018Group: Source and taxonomy / Category: entity_src_gen / entity_src_nat
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _entity_src_nat.common_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit
K: C-terminal fragment of KU80 (KU80ct194)
B: DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit
S: C-terminal fragment of KU80 (KU80ct194)


Theoretical massNumber of molelcules
Total (without water)972,4814
Polymers972,4814
Non-polymers00
Water0
1
A: DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit
K: C-terminal fragment of KU80 (KU80ct194)


Theoretical massNumber of molelcules
Total (without water)486,2402
Polymers486,2402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-16 kcal/mol
Surface area177500 Å2
MethodPISA
2
B: DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit
S: C-terminal fragment of KU80 (KU80ct194)


Theoretical massNumber of molelcules
Total (without water)486,2402
Polymers486,2402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-17 kcal/mol
Surface area176280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.120, 132.640, 296.590
Angle α, β, γ (deg.)90.00, 105.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit / DNA-PKcs / DNPK1 / p460


Mass: 469618.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa
References: UniProt: P78527, non-specific serine/threonine protein kinase
#2: Protein C-terminal fragment of KU80 (KU80ct194)


Mass: 16621.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGAT3 / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)
13.2762
23.2762
Crystal grow
Temperature (K)Crystal-IDMethodDetailsPH range
2931vapor diffusion, hanging drop0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 18% PEG 80006.2-6.7
2932vapor diffusion, hanging drop0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 8% PEG 80006.2-6.7

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.9791
SYNCHROTRONESRF ID23-120.9791
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELMay 23, 2012
DECTRIS PILATUS 6M-F2PIXELJun 25, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.97911
ReflectionResolution: 4.3→49.92 Å / Num. obs: 84530 / % possible obs: 99.9 % / Redundancy: 35.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 15.4
Reflection shellResolution: 4.3→4.41 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 4.3→49.92 Å / SU ML: 1.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 55.75
RfactorNum. reflection% reflection
Rfree0.437 1978 2.34 %
Rwork0.3862 --
obs0.3874 84530 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.3→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59694 0 0 0 59694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00960886
X-RAY DIFFRACTIONf_angle_d1.54282328
X-RAY DIFFRACTIONf_dihedral_angle_d14.86837258
X-RAY DIFFRACTIONf_chiral_restr0.0689336
X-RAY DIFFRACTIONf_plane_restr0.01110524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3-4.40750.44111340.44665463X-RAY DIFFRACTION91
4.4075-4.52660.49631350.44325631X-RAY DIFFRACTION95
4.5266-4.65970.50771400.44775752X-RAY DIFFRACTION96
4.6597-4.810.51021400.4585782X-RAY DIFFRACTION97
4.81-4.98180.47831420.46175842X-RAY DIFFRACTION97
4.9818-5.1810.49991350.45355859X-RAY DIFFRACTION98
5.181-5.41660.50991450.45495943X-RAY DIFFRACTION99
5.4166-5.70180.51911400.46055941X-RAY DIFFRACTION99
5.7018-6.05840.45671340.46286007X-RAY DIFFRACTION99
6.0584-6.52530.53041470.45715986X-RAY DIFFRACTION100
6.5253-7.18020.46661420.44136008X-RAY DIFFRACTION100
7.1802-8.21520.45461440.38836061X-RAY DIFFRACTION100
8.2152-10.33520.36071480.28446087X-RAY DIFFRACTION100
10.3352-49.92340.37881520.33186190X-RAY DIFFRACTION100
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)
10.6182-0.20920.37960.2659-0.13760.3206-0.1841-0.8431-0.53971.14820.5762-0.03350.5243-0.08310.16652.02130.8059-0.40092.1286-0.66831.302939.0522-30.555788.0704
20.0973-0.0661-0.1110.04630.06360.1204-0.1299-0.15550.16830.12410.1290.14460.15780.34680.13611.89371.15630.55393.6237-1.38050.749655.5157-13.890899.6993
30.2189-0.10990.00420.16010.19180.2904-0.0857-0.97820.73120.579-0.0831-0.83951.3429-0.3460.00042.45160.698-0.17673.102-0.34511.67579.7448-13.780588.2267
40.078-0.07160.08420.0486-0.07260.0401-0.4432-0.8084-0.29670.3320.1017-1.09060.3227-0.4255-0.00052.44530.6522-0.67482.3025-0.13272.34882.2607-10.575864.6066
50.8740.042-0.06420.70740.64423.1195-1.02630.2321-0.02430.09230.04270.34621.1901-0.7267-1.8341.28520.38990.53140.69170.18261.080968.71-7.923347.8809
60.33070.03210.0850.2741-0.40580.4225-0.27790.7832-0.4249-0.71150.36140.62460.8064-0.75270.19141.7276-0.4314-0.27260.05670.38630.853370.227-7.73933.4802
70.1937-0.0649-0.1689-0.01020.06670.102-0.03620.50420.30420.4236-0.34280.3406-0.49220.18710.00021.46740.36070.27772.07070.76732.436664.979410.35934.0397
80.4658-0.0047-0.01940.31230.05390.34430.5151-0.06820.20890.62030.4340.2650.7814-0.78580.76080.48581.24411.01963.9521-0.39940.968144.26157.217130.1705
90.2092-0.087-0.25030.03980.14030.27271.7480.08260.3087-0.21940.55620.09240.3277-0.35760.01032.31980.3939-0.57984.1617-0.74593.141924.2336-19.6747.6635
100.2061-0.3008-0.30050.24560.14640.119-0.2156-1.802-0.30480.67890.9616-0.26930.44630.72040.12111.2705-0.55070.30532.64281.06951.437143.0167-20.12387.947
110.375-0.361-0.28070.5790.42320.33550.01920.0554-0.3618-0.12730.2035-0.7348-0.36640.06450.0689-1.2366-0.94932.12772.65921.25460.007166.99-7.4949-3.9255
120.19260.1326-0.20220.0267-0.09370.1838-0.90110.46940.58040.6682-0.0083-1.4966-0.74660.3030.00012.15950.4189-0.01922.19570.4362.509682.604616.0866-2.604
130.0209-0.09230.01590.0323-0.09930.0595-1.0659-0.3831-0.07330.2997-0.527-0.99620.75510.6952-0.00131.9592-0.2427-0.20332.02790.53423.270388.707417.233313.3704
140.08140.06420.16830.14650.05640.1409-0.3382-1.77270.60510.47491.00760.00460.54670.35210.00092.85330.0613-0.29831.5566-0.44172.56696.901617.206937.3366
150.7283-0.8530.51010.84610.38160.7682-0.2545-0.6649-0.3761.47511.12290.24150.9988-0.72870.9871-0.86071.4988-1.0285-0.07850.67430.2446103.4733-13.283751.2569
160.00280.0155-0.00860.1516-0.1220.13350.06460.14320.0961-0.1025-0.18020.43970.13140.01090.08121.91480.95670.2531.82490.62331.831587.4149-17.628242.3351
170.0845-0.2101-0.07640.28040.3052-0.050.48150.01140.35350.0986-0.1952-0.59290.63230.6395-0.73790.71160.1529-0.15060.1186-0.44221.052295.9667-44.89251.3078
180.3780.39350.00740.3421-0.40840.92560.6648-0.7144-0.06230.3271-0.012-0.13330.25420.25590.00041.78150.30630.12681.5813-0.28131.802265.7711-66.709454.8756
190.19440.26860.14930.1648-0.08410.3009-0.086-0.07570.8849-0.8573-0.610.5897-0.6689-1.1821-3.119-0.34580.29751.68282.1280.6765-0.391816.1063-44.075758.1714
200.0396-0.11570.07920.2729-0.02090.2205-0.17220.47130.0343-0.38940.09830.76210.1869-0.23350.01431.163-1.54040.08923.09971.51972.844217.1989-32.365925.5646
210.0568-0.02610.0710.0954-0.01480.05470.1264-0.68550.13940.05110.5194-0.80890.38810.22960.00222.9599-0.1703-1.34353.8952-0.97472.792741.2758-35.294329.0494
220.04290.06280.01010.07950.10910.02880.74230.2985-0.6022-0.36130.4649-0.65420.45540.59380.00141.1573-0.18590.58363.25540.79052.625535.9002-33.534813.2183
231.698-0.30450.54980.0268-0.13740.9973-1.0191-0.02541.5072-0.30080.3261-0.4281-0.8872-1.2784-0.30670.4684-0.32840.91743.84961.55812.74697.2579-8.524519.4489
240.0961-0.11210.02430.0673-0.02320.0973-0.4877-0.02090.2559-0.33-0.65841.16460.16870.1154-0.00013.18310.64930.04524.45071.17812.509-0.19519.383726.5569
250.0410.02350.04490.29410.15680.13890.2622-0.6535-0.18470.0951-0.6707-0.5372-0.35220.7837-0.82231.10910.06870.27652.70940.86671.18299.005611.486446.2455
260.0908-0.0541-0.05280.310.32080.1497-0.1691-1.10670.16710.6591-0.55230.34560.0016-0.0257-0.00522.63450.8869-0.75692.6606-0.63972.616928.857616.472743.177
270.036-0.0877-0.03630.13660.09660.07-1.7082-0.20360.6217-0.1408-0.3085-0.0655-0.74620.815-03.67191.2284-0.82152.4283-0.42572.696420.977840.489333.4782
280.39520.3719-0.35340.3401-0.25810.35930.32230.3550.95930.14170.3828-0.2874-0.8807-0.70850.39931.06090.89040.59031.9895-1.2711.260919.356153.488119.0601
290.0293-0.11210.04670.1218-0.05380.1623-0.1535-0.27170.76270.7027-0.1167-0.2141-1.32881.0975-0.00761.95030.465-0.28072.4128-0.47632.585641.807840.7979-1.4242
300.0751-0.1307-0.10360.1370.0163-0.00630.29171.37230.0344-0.70660.4489-0.02190.3433-0.4676-0.00022.3965-0.39820.25662.6588-0.10891.604441.076117.1044-31.9316
31-0.0017-0.06180.09570.863-0.1770.7613-0.1916-1.2873-0.23980.1504-0.2338-0.8428-0.30050.2501-0.8250.74360.32651.78871.48180.39490.452548.462611.7741-4.954
320.0366-0.08590.01690.31270.00680.08370.47770.97450.17951.1766-0.6247-0.19430.11450.8148-0.00632.30440.28-0.45312.28520.14561.245532.402619.9050.8266
330.93970.6839-0.13351.36320.96521.9941-0.55190.88010.1613-0.5707-0.63690.8658-0.6218-1.1597-1.08261.1324-1.43560.12043.80851.2280.993910.79581.6316-11.1168
340.06720.1316-0.14980.0304-0.19220.1229-0.6620.27460.49530.1019-0.8815-0.73450.52970.5912-0.00940.49730.31220.04852.43540.12051.973319.027912.9315-1.8924
350.22770.20740.25610.40750.35410.26530.2937-0.8052-0.0249-1.3277-0.2901-0.38110.96630.4202-0.00131.78160.5163-0.29012.8136-0.10312.352913.720225.2047-6.0894
361.31940.02980.24190.2977-0.10380.3697-0.4316-0.56710.6950.3268-0.21920.3469-0.751-0.4591-0.45822.0585-0.2729-0.07253.92080.21371.2528-43.175895.0508142.9455
370.1407-0.02220.07870.35450.10860.35350.18340.05840.11320.92310.02370.34010.12380.47320.36061.78650.79510.95752.3110.35580.7941-59.317372.874144.6662
380.06330.00810.25210.14610.07230.3082-0.7541-0.2096-1.0225-0.11120.08060.57770.26380.5889-0.00022.11870.57660.64772.98390.03852.006-67.244960.2319122.7989
390.1511-0.1815-0.00740.1099-0.0111-0.06480.9265-0.97941.131-0.3321-0.276-0.25720.0383-0.05840.00032.12360.4984-0.3472.53060.28361.8003-51.77948.8926109.2844
400.1195-0.37630.01071.0041-0.1294-0.0201-0.0137-0.21710.5696-0.2842-0.2166-1.3249-0.57070.2071-0.13750.96990.85671.03160.0983-0.33820.9875-29.498547.4147110.5107
410.9706-0.5846-0.26930.6607-0.00590.84880.33591.08810.2721-0.97750.0063-0.5692-0.12510.97271.43451.17551.88-0.50441.48590.32660.9942-19.520140.995102.4836
420.7899-0.15370.60650.339-0.32260.63950.5644-0.9588-1.13880.4723-0.10150.51580.217-1.28710.09482.80920.81840.43461.7893-0.47251.5548-17.540528.7422115.5422
430.0477-0.16690.0630.1618-0.20130.61860.3560.42260.2166-0.0493-0.4897-0.4595-1.53290.117-0.11771.52380.01960.08982.36160.3131-0.195-1.32538.7116126.4733
440.57290.1847-0.26530.6175-0.22490.14730.72670.08370.50630.2920.30720.32490.67380.64420.34251.96821.04790.32153.2165-1.31091.829929.368661.3869113.6436
450.0028-0.1432-0.03150.30520.09280.1241-1.2453-0.7184-1.5814-0.703-0.14940.47350.06851.4982-0.01362.52230.09580.04241.41590.28231.844517.594554.4377100.6163
460.23430.2931-0.09240.564-0.060.08530.34651.19781.2694-1.32040.27711.17621.06770.54830.11212.4731.2004-0.18171.9135-1.12671.502412.069929.431685.4433
470.6475-0.0316-0.39140.4931-0.07890.2967-0.70080.6201-1.02170.32450.2140.49770.3815-0.34210.10931.81911.9916-0.63730.2134-0.73372.85820.85863.872688.6073
480.26330.2565-0.20880.407-0.39260.42750.3078-0.05710.5801-1.01260.8229-0.3414-0.227-0.19280.90872.92710.0681-0.795-0.242-0.92912.6734-15.82575.842292.1669
490.1005-0.00250.00940.0880.0059-0.03070.34170.0011-0.38851.08380.0160.33870.4652-1.64880.00012.7335-0.1120.04911.5294-0.16792.7765-39.636810.8132100.413
500.3709-0.33790.41911.0493-0.47710.60090.0671-0.18020.44321.33230.82350.26170.5948-0.6608-0.1739-0.08271.1904-0.4775-0.8440.36760.9816-55.05738.425987.1932
510.1690.0307-0.00310.0237-0.0211-0.001-0.2057-0.11070.62080.47530.2944-0.1936-0.77980.1468-0.00332.51220.00310.82321.79970.48022.6096-37.002445.520891.3717
520.6409-0.21390.29430.05810.15311.8859-0.0189-0.356-0.19740.43790.7385-0.19751.10860.34291.4878-0.18710.45560.2164-0.3866-0.12250.3663-50.082968.043475.1221
530.2923-1.05720.54540.03241.12380.4956-0.5602-0.90940.11260.85480.228-0.72340.2791-0.3157-0.01662.19010.2743-0.40171.5587-0.23651.1921-33.9488100.567883.618
540.3721-0.011-0.33570.75330.02670.35-0.1069-1.04150.67630.1547-0.3289-0.2664-0.96470.2144-1.60252.59490.6487-0.65830.9082-0.69711.1503-5.308104.2741130.0672
550.7148-0.27680.15350.13890.11150.5876-0.6558-0.57070.2139-0.4904-0.65230.02610.33050.4167-0.20012.6140.59910.8770.31480.34362.676819.344481.8951119.0534
560.07910.01390.12680.0923-0.04650.13090.46311.32970.19460.2349-0.8640.5168-0.00130.36160.00042.71090.79510.58863.0215-0.78253.06143.160274.978102.1332
570.0251-0.0087-0.01030.0877-0.06490.0304-0.15230.3878-0.2474-0.0281-0.42720.71970.1949-0.0339-0.00053.29450.6583-0.27342.09880.29132.652918.013868.8924101.0362
580.0836-0.0382-0.23950.45670.25510.2495-0.41-0.6448-0.34220.5971.0381-0.92410.82071.03640.00032.75350.27320.0371.70910.04451.390629.995365.214136.4934
590.4379-0.21390.21860.1071-0.09490.1152-1.14310.25730.91980.3165-1.07280.054-0.46370.5892-0.0223.38770.2002-0.16052.8875-0.18731.513229.14249.1863161.6777
600.0872-0.06740.0380.1260.01620.3499-0.0979-0.03250.27980.0197-0.3540.4021-1.14470.13870.66292.79120.9477-0.78732.365-0.66960.89516.325257.3117160.8644
610.1169-0.0935-0.02910.2175-0.09380.0531.1465-0.3221.0634-0.1725-0.8134-0.02841.5307-0.639101.8985-0.5024-0.5481.96310.27252.2526-2.329841.7006148.2615
620.1036-0.0364-0.1414-0.1325-0.17230.21740.4127-0.20730.44261.88870.097-0.82120.0661-1.32240.00012.06150.0679-0.27031.90140.46642.762110.182522.8316162.2882
630.14130.20510.0390.46860.21580.176-0.1981-0.662-0.5940.77590.1878-0.22620.27770.43820.09981.54650.0002-0.43311.85451.0632.420723.77167.1961162.3982
640.3391-0.1296-0.12560.20070.03950.10660.41340.7308-0.14640.1738-1.28340.08550.0646-0.0753-0.00042.16470.05760.12552.6519-0.48673.15426.0272.8246130.2669
650.2741-0.0011-0.03860.17930.03540.0866-0.05391.7583-0.0854-0.81880.17160.25230.1438-0.57950.00022.905-0.09750.53823.1916-1.15492.940850.846714.8161102.3319
660.4139-0.52710.31720.674-0.49650.3505-0.52510.65260.21041.3441-0.1932-0.89080.53170.1054-0.15712.78560.68340.49362.53270.05871.214424.436421.7757108.3255
670.0787-0.05570.07-0.0720.00340.02470.04260.5409-1.17030.13450.32290.05170.90680.0995-0.00011.165-0.5928-0.49261.96470.25672.185929.628624.7898126.3898
680.16710.0733-0.0609-0.0046-0.06760.2842-0.1603-0.1844-0.10621.12810.0558-0.254-0.5226-0.20720.00011.76740.0803-0.4592.0613-0.34222.553352.052945.2224124.3387
69-0.0217-0.0760.00840.14930.09960.0021-0.72030.4482-0.5432-1.10310.026-0.15780.47531.3052-0.00111.26440.13140.76081.69630.06011.371139.526935.3043130.0278
700.41360.1918-0.22010.0782-0.28590.4535-1.29451.04771.2409-0.0380.1967-0.3011-0.39170.7273-0.00272.91940.4566-1.09542.81560.07492.670946.286926.3899138.2406
710.0278-0.0168-0.03840.02980.01280.00090.14560.462-0.22070.01510.15140.06950.31840.2749-0.00024.80230.3817-1.25513.89870.50633.419346.5468-56.897449.7977
720.02-0.0009-0.01530.0125-0.01330.0166-0.0682-0.28940.0020.09620.08830.0977-0.02660.0223-0.00012.05640.2020.56732.95760.24622.800789.2903-81.046844.2304
730.01730.0267-0.0010.0018-0.0010.0128-0.30550.19010.0105-0.7557-0.6386-0.3083-0.2040.13580.0022.26220.11681.30262.84720.31673.4317-19.268297.9106101.5621
740.02620.03380.00940.02920.00410.0142-0.0079-0.1336-0.2180.3585-0.2813-0.2734-0.2366-0.27690.00031.1203-0.0725-0.13351.5366-0.43531.6912-39.724899.401855.9924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 10 through 144)
2X-RAY DIFFRACTION2(chain 'A' and resid 145 through 236)
3X-RAY DIFFRACTION3(chain 'A' and resid 237 through 379)
4X-RAY DIFFRACTION4(chain 'A' and resid 380 through 471)
5X-RAY DIFFRACTION5(chain 'A' and resid 472 through 542)
6X-RAY DIFFRACTION6(chain 'A' and resid 543 through 630)
7X-RAY DIFFRACTION7(chain 'A' and resid 631 through 722)
8X-RAY DIFFRACTION8(chain 'A' and resid 723 through 878)
9X-RAY DIFFRACTION9(chain 'A' and resid 879 through 904)
10X-RAY DIFFRACTION10(chain 'A' and resid 905 through 1045)
11X-RAY DIFFRACTION11(chain 'A' and resid 1046 through 1180)
12X-RAY DIFFRACTION12(chain 'A' and resid 1213 through 1308)
13X-RAY DIFFRACTION13(chain 'A' and resid 1323 through 1420)
14X-RAY DIFFRACTION14(chain 'A' and resid 1421 through 1526)
15X-RAY DIFFRACTION15(chain 'A' and resid 1548 through 1763)
16X-RAY DIFFRACTION16(chain 'A' and resid 1787 through 1822)
17X-RAY DIFFRACTION17(chain 'A' and resid 1856 through 1975)
18X-RAY DIFFRACTION18(chain 'A' and resid 1976 through 2310)
19X-RAY DIFFRACTION19(chain 'A' and resid 2311 through 2514)
20X-RAY DIFFRACTION20(chain 'A' and resid 2515 through 2576)
21X-RAY DIFFRACTION21(chain 'A' and resid 2602 through 2665)
22X-RAY DIFFRACTION22(chain 'A' and resid 2774 through 2802)
23X-RAY DIFFRACTION23(chain 'A' and resid 2803 through 2943)
24X-RAY DIFFRACTION24(chain 'A' and resid 2944 through 3006)
25X-RAY DIFFRACTION25(chain 'A' and resid 3008 through 3095)
26X-RAY DIFFRACTION26(chain 'A' and resid 3096 through 3199)
27X-RAY DIFFRACTION27(chain 'A' and resid 3227 through 3314)
28X-RAY DIFFRACTION28(chain 'A' and resid 3315 through 3405)
29X-RAY DIFFRACTION29(chain 'A' and resid 3406 through 3576)
30X-RAY DIFFRACTION30(chain 'A' and resid 3577 through 3680)
31X-RAY DIFFRACTION31(chain 'A' and resid 3681 through 3755)
32X-RAY DIFFRACTION32(chain 'A' and resid 3756 through 3808)
33X-RAY DIFFRACTION33(chain 'A' and resid 3809 through 3894)
34X-RAY DIFFRACTION34(chain 'A' and resid 3895 through 3972)
35X-RAY DIFFRACTION35(chain 'A' and resid 3973 through 4128)
36X-RAY DIFFRACTION36(chain 'B' and resid 10 through 144)
37X-RAY DIFFRACTION37(chain 'B' and resid 145 through 236)
38X-RAY DIFFRACTION38(chain 'B' and resid 237 through 379)
39X-RAY DIFFRACTION39(chain 'B' and resid 380 through 471)
40X-RAY DIFFRACTION40(chain 'B' and resid 472 through 542)
41X-RAY DIFFRACTION41(chain 'B' and resid 543 through 630)
42X-RAY DIFFRACTION42(chain 'B' and resid 631 through 722)
43X-RAY DIFFRACTION43(chain 'B' and resid 723 through 878)
44X-RAY DIFFRACTION44(chain 'B' and resid 879 through 904)
45X-RAY DIFFRACTION45(chain 'B' and resid 905 through 1045)
46X-RAY DIFFRACTION46(chain 'B' and resid 1046 through 1180)
47X-RAY DIFFRACTION47(chain 'B' and resid 1213 through 1308)
48X-RAY DIFFRACTION48(chain 'B' and resid 1323 through 1420)
49X-RAY DIFFRACTION49(chain 'B' and resid 1421 through 1526)
50X-RAY DIFFRACTION50(chain 'B' and resid 1548 through 1763)
51X-RAY DIFFRACTION51(chain 'B' and resid 1787 through 1822)
52X-RAY DIFFRACTION52(chain 'B' and resid 1856 through 1975)
53X-RAY DIFFRACTION53(chain 'B' and resid 1976 through 2310)
54X-RAY DIFFRACTION54(chain 'B' and resid 2311 through 2514)
55X-RAY DIFFRACTION55(chain 'B' and resid 2515 through 2576)
56X-RAY DIFFRACTION56(chain 'B' and resid 2602 through 2665)
57X-RAY DIFFRACTION57(chain 'B' and resid 2774 through 2802)
58X-RAY DIFFRACTION58(chain 'B' and resid 2803 through 2943)
59X-RAY DIFFRACTION59(chain 'B' and resid 2944 through 3006)
60X-RAY DIFFRACTION60(chain 'B' and resid 3008 through 3095)
61X-RAY DIFFRACTION61(chain 'B' and resid 3096 through 3199)
62X-RAY DIFFRACTION62(chain 'B' and resid 3227 through 3314)
63X-RAY DIFFRACTION63(chain 'B' and resid 3315 through 3405)
64X-RAY DIFFRACTION64(chain 'B' and resid 3406 through 3576)
65X-RAY DIFFRACTION65(chain 'B' and resid 3577 through 3680)
66X-RAY DIFFRACTION66(chain 'B' and resid 3681 through 3755)
67X-RAY DIFFRACTION67(chain 'B' and resid 3756 through 3808)
68X-RAY DIFFRACTION68(chain 'B' and resid 3809 through 3894)
69X-RAY DIFFRACTION69(chain 'B' and resid 3895 through 3972)
70X-RAY DIFFRACTION70(chain 'B' and resid 3973 through 4128)
71X-RAY DIFFRACTION71(chain 'K' and resid 101 through 133)
72X-RAY DIFFRACTION72(chain 'K' and resid 201 through 221)
73X-RAY DIFFRACTION73(chain 'S' and resid 101 through 133)
74X-RAY DIFFRACTION74(chain 'S' and resid 201 through 221)

+
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