[English] 日本語
Yorodumi
- PDB-4zux: SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zux
TitleSAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome
Components
  • (DNA (145-MER)) x 2
  • (SAGA-associated factor ...) x 2
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Polyubiquitin-B
  • Transcription and mRNA export factor SUS1
  • Ubiquitin carboxyl-terminal hydrolase 8
KeywordsHydrolase/DNA / DUB / deubiquitinase / USP / chromatin / eraser / nucleosome / modified histone / macromolecular complex / Hydrolase-DNA complex
Function / homology
Function and homology information


RITS complex assembly / DUBm complex / nuclear retention of pre-mRNA at the site of transcription / regulation of nucleocytoplasmic transport / SLIK (SAGA-like) complex / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / transcription export complex 2 / SAGA complex / histone H3-K79 methylation / regulation of protein localization to chromatin ...RITS complex assembly / DUBm complex / nuclear retention of pre-mRNA at the site of transcription / regulation of nucleocytoplasmic transport / SLIK (SAGA-like) complex / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / transcription export complex 2 / SAGA complex / histone H3-K79 methylation / regulation of protein localization to chromatin / histone deubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / mitochondrion transport along microtubule / female meiosis I / fat pad development / poly(A)+ mRNA export from nucleus / positive regulation of protein monoubiquitination / histone H3-K4 methylation / male meiosis I / cellular protein-containing complex assembly / female gonad development / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / seminiferous tubule development / regulation of neuron death / energy homeostasis / nuclear pore / histone acetylation / molecular adaptor activity / transcription elongation from RNA polymerase II promoter / mRNA export from nucleus / regulation of proteasomal protein catabolic process / MyD88-independent toll-like receptor signaling pathway / RNA splicing / positive regulation of protein ubiquitination / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling / neuron projection morphogenesis / regulation of mitochondrial membrane potential / nucleotide-excision repair, DNA damage recognition / TRIF-dependent toll-like receptor signaling pathway / nucleotide-excision repair, DNA duplex unwinding / enzyme activator activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA-templated transcription, initiation / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / P-body / intracellular transport of virus / MyD88-dependent toll-like receptor signaling pathway / endosomal transport / nucleotide-excision repair, DNA incision, 5'-to lesion / regulation of protein localization / host cell / protein targeting to peroxisome / modification-dependent protein catabolic process / nucleotide-excision repair, DNA incision / error-free translesion synthesis / DNA damage response, detection of DNA damage / JNK cascade / nucleosome / stress-activated MAPK cascade / protein tag / endocytic vesicle membrane / interstrand cross-link repair / error-prone translesion synthesis / interleukin-1-mediated signaling pathway / regulation of transcription from RNA polymerase II promoter in response to hypoxia / I-kappaB kinase/NF-kappaB signaling / viral life cycle / transcription-coupled nucleotide-excision repair / translesion synthesis / negative regulation of transforming growth factor beta receptor signaling pathway / ubiquitinyl hydrolase 1 / cysteine-type peptidase activity / anaphase-promoting complex-dependent catabolic process / virion assembly / transforming growth factor beta receptor signaling pathway / thiol-dependent deubiquitinase / regulation of mRNA stability / transmembrane transport / chromatin organization / membrane organization / protein polyubiquitination / Wnt signaling pathway / ubiquitin-dependent protein catabolic process / mitochondrial outer membrane / transcription coactivator activity / vesicle / activation of MAPK activity / endosome membrane / positive regulation of NF-kappaB transcription factor activity / protein ubiquitination / protein deubiquitination / protein heterodimerization activity / neuron projection / positive regulation of apoptotic process / cytokine-mediated signaling pathway / neuronal cell body / endoplasmic reticulum membrane / cellular protein metabolic process
Ubiquitin specific protease, conserved site / Ubiquitin domain / Transcription factor EnY2 superfamily / SAGA-associated factor 73 / Ubiquitin carboxyl-terminal hydrolase 8 / CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Ubiquitin-like domain superfamily / Ubiquitin specific protease domain ...Ubiquitin specific protease, conserved site / Ubiquitin domain / Transcription factor EnY2 superfamily / SAGA-associated factor 73 / Ubiquitin carboxyl-terminal hydrolase 8 / CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Ubiquitin-like domain superfamily / Ubiquitin specific protease domain / Ubiquitin conserved site / Yeast SAGA-associated factor 11, N-terminal domain / Histone H4 / Histone H4, conserved site / Transcription factor, enhancer of yellow 2 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / SAGA complex, Sgf11 subunit / SCA7 domain / Papain-like cysteine peptidase superfamily / SAGA-associated factor 73, zinc finger domain / Histone-fold / SAGA-associated factor 11 N-terminal domain / Histone H3/CENP-A / Histone H2B / Ubiquitin-like domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Zinc finger domain / Core histone H2A/H2B/H3/H4 / Ubiquitin family / Sgf11 (transcriptional regulation protein) / Transcription factor e(y)2 / Zn-finger in ubiquitin-hydrolases and other protein / Ubiquitin carboxyl-terminal hydrolase / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / Zinc finger, UBP-type / Zinc finger, RING/FYVE/PHD-type / ENY2/SUS1 / Serum Albumin; Chain A, Domain 1 / Histone, subunit A / Histone, subunit A / Cysteine proteinases / Zinc/RING finger domain, C3HC4 (zinc finger) / Cathepsin B; Chain A / Herpes Virus-1 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Transcription and mRNA export factor SUS1 / SAGA-associated factor 11 / Histone H3.2 / Histone H4 / SAGA-associated factor 73 / Polyubiquitin-B / Histone H2A type 1 / Histone H2B 1.1 / SAGA-associated factor 11 / Ubiquitin carboxyl-terminal hydrolase 8
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Saccharomyces cerevisiae (baker's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.82 Å
AuthorsMorgan, M. / Wolberger, C.
CitationJournal: Science / Year: 2016
Title: Structural basis for histone H2B deubiquitination by the SAGA DUB module.
Authors: Morgan, M.T. / Haj-Yahya, M. / Ringel, A.E. / Bandi, P. / Brik, A. / Wolberger, C.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Derived calculations
Revision 1.2Mar 9, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (145-MER)
J: DNA (145-MER)
K: Histone H3.2
L: Histone H4
M: Histone H2A type 1
N: Histone H2B 1.1
O: Histone H3.2
P: Histone H4
Q: Histone H2A type 1
R: Histone H2B 1.1
S: DNA (145-MER)
T: DNA (145-MER)
U: Ubiquitin carboxyl-terminal hydrolase 8
V: Transcription and mRNA export factor SUS1
W: SAGA-associated factor 11
X: Polyubiquitin-B
Y: SAGA-associated factor 73
Z: Ubiquitin carboxyl-terminal hydrolase 8
a: Transcription and mRNA export factor SUS1
b: SAGA-associated factor 11
c: Polyubiquitin-B
d: SAGA-associated factor 73
e: Ubiquitin carboxyl-terminal hydrolase 8
f: Transcription and mRNA export factor SUS1
g: SAGA-associated factor 11
h: Polyubiquitin-B
i: SAGA-associated factor 73
j: Ubiquitin carboxyl-terminal hydrolase 8
k: Transcription and mRNA export factor SUS1
l: SAGA-associated factor 11
m: Polyubiquitin-B
n: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)784,45072
Polymers782,35740
Non-polymers2,09332
Water0
1
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (145-MER)
J: DNA (145-MER)
U: Ubiquitin carboxyl-terminal hydrolase 8
V: Transcription and mRNA export factor SUS1
W: SAGA-associated factor 11
X: Polyubiquitin-B
Y: SAGA-associated factor 73
Z: Ubiquitin carboxyl-terminal hydrolase 8
a: Transcription and mRNA export factor SUS1
b: SAGA-associated factor 11
c: Polyubiquitin-B
d: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,22536
Polymers391,17920
Non-polymers1,04716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Histone H3.2
L: Histone H4
M: Histone H2A type 1
N: Histone H2B 1.1
O: Histone H3.2
P: Histone H4
Q: Histone H2A type 1
R: Histone H2B 1.1
S: DNA (145-MER)
T: DNA (145-MER)
e: Ubiquitin carboxyl-terminal hydrolase 8
f: Transcription and mRNA export factor SUS1
g: SAGA-associated factor 11
h: Polyubiquitin-B
i: SAGA-associated factor 73
j: Ubiquitin carboxyl-terminal hydrolase 8
k: Transcription and mRNA export factor SUS1
l: SAGA-associated factor 11
m: Polyubiquitin-B
n: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,22536
Polymers391,17920
Non-polymers1,04716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)178.804, 179.174, 353.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 7 types, 28 molecules AEKOBFLPCGMQDHNRUZejVafkXchm

#1: Protein
Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein
Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein
Histone H2A type 1


Mass: 14109.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein
Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein
Ubiquitin carboxyl-terminal hydrolase 8 / Deubiquitinating enzyme 8 / Ubiquitin thioesterase 8 / Ubiquitin-specific-processing protease 8


Mass: 53731.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UBP8, YMR223W, YM9959.05 / Production host: Escherichia coli (E. coli) / References: UniProt: P50102, ubiquitinyl hydrolase 1
#8: Protein
Transcription and mRNA export factor SUS1


Mass: 11094.497 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SUS1, YBR111W-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WNK7
#10: Protein
Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

-
DNA chain , 2 types, 4 molecules ISJT

#5: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
SAGA-associated factor ... , 2 types, 8 molecules WbglYdin

#9: Protein
SAGA-associated factor 11


Mass: 11297.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: SGF11, SCY_5678 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZWK1, UniProt: Q03067*PLUS
#11: Protein
SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


Mass: 11538.081 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SGF73, YGL066W / Production host: Escherichia coli (E. coli) / References: UniProt: P53165

-
Non-polymers , 1 types, 32 molecules

#12: Chemical...
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.693→49.5 Å / Num. obs: 121413 / % possible obs: 99.28 % / Redundancy: 7.12 % / Rmerge(I) obs: 0.1053 / Net I/σ(I): 7.12

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementResolution: 3.82→49.498 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 49.29 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2559 3456 1.64 %
Rwork0.2338 --
Obs0.2369 210557 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.82→49.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37169 11878 32 0 49079
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551211
X-RAY DIFFRACTIONf_angle_d1.02371446
X-RAY DIFFRACTIONf_dihedral_angle_d24.33420103
X-RAY DIFFRACTIONf_chiral_restr0.0458075
X-RAY DIFFRACTIONf_plane_restr0.0057104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
3.8672-3.93220.41361930.40659800X-RAY DIFFRACTION97
3.9322-4.00170.37961930.37389735X-RAY DIFFRACTION98
4.0017-4.07640.34681930.35359819X-RAY DIFFRACTION98
4.0764-4.15710.39281910.34939738X-RAY DIFFRACTION97
4.1571-4.24450.35651900.33879620X-RAY DIFFRACTION97
4.2445-4.33980.3162700.33099855X-RAY DIFFRACTION98
4.3398-4.44420.34341230.32179885X-RAY DIFFRACTION98
4.4442-4.55950.29971920.32219711X-RAY DIFFRACTION98
4.5595-4.68780.27651990.31769836X-RAY DIFFRACTION98
4.6878-4.83190.30411980.3149808X-RAY DIFFRACTION98
4.8319-4.99550.33051940.3119678X-RAY DIFFRACTION97
4.9955-5.18370.29032000.29959733X-RAY DIFFRACTION97
5.1837-5.404000.29839867X-RAY DIFFRACTION99
5.404-5.66720.29931850.31139554X-RAY DIFFRACTION96
5.6672-5.99060.33541900.29619691X-RAY DIFFRACTION97
5.9906-6.40320.34811930.2769741X-RAY DIFFRACTION97
6.4032-6.95970.31021810.25819665X-RAY DIFFRACTION97
6.9597-7.77970.28111770.22629584X-RAY DIFFRACTION96
7.7797-9.20730.15451820.18579436X-RAY DIFFRACTION94
9.2073-13.16170.17521840.14249735X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refinement-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)
11.16522.24130.09545.35851.4111.0458-0.0485-0.2944-0.3506-0.59170.6885-0.2841-0.2834-0.29840.00061.1446-0.0649-0.02932.05940.12111.505-72.454-42.3122-14.532
23.7717-3.69251.35663.3713-1.02544.6788-0.2891-1.1222-0.2306-1.26620.8829-0.99270.2613-0.3597-0.00111.1416-0.2787-0.04391.6581-0.1871.3383-77.009-34.1066-11.9282
31.7848-1.82420.49252.2540.05192.49860.1143-0.34180.3002-0.03250.1881-0.48660.32120.0197-0.00021.26550.2187-0.08921.5877-0.05731.4645-74.9706-23.164116.6247
43.5422-1.9044-1.25266.2922-1.7832.95760.00290.7943-0.3530.63441.2156-0.7282-0.593-1.57980.08571.13-0.0284-0.38631.4682-0.06471.4415-76.0752-14.80612.48
54.54012.2265-0.46763.96631.65352.77010.17470.5778-0.84651.32210.5586-0.98520.1026-0.19040.01481.11570.0956-0.47932.0449-0.27921.6685-55.2092-42.090216.3679
65.16560.4875-1.25924.92941.75722.7628-0.11190.92950.32681.69920.83252.05270.68220.49350.08311.32170.4468-0.61761.75760.12471.3996-51.7818-33.902713.5968
70.42971.2242-0.22223.0519-0.41551.07430.07450.0260.2677-0.18460.2333-0.9378-0.0422-0.066901.3201-0.22890.03251.8066-0.2461.9654-52.5869-23.2082-15.6361
82.43640.110.19144.28021.0272.2332-0.0613-0.8861-0.804-0.35541.23730.41810.03311.3116-0.00051.28090.1202-0.26121.7606-0.03981.8213-51.2637-15.5976-10.8624
91.0556-0.099-0.08022.12760.27881.29720.04910.052-0.10690.07540.013-0.3259-0.0396-0.078501.5301-0.0468-0.15071.9945-0.03291.8305-64.1244-28.87711.2039
101.09540.3483-0.03851.99860.13331.51610.02260.0206-0.0005-0.01760.0152-0.4758-0.0957-0.0445-01.50410.1233-0.24451.96790.07551.8035-63.5443-29.08020.8369
112.2061-0.95260.42614.1283-0.2883-0.05910.28970.35860.9055-0.58160.52170.20860.04990.80150.00122.02930.01940.11431.6190.14291.627.9674-10.407677.5316
121.4446-0.283-1.14523.58640.13974.9114-0.2590.55570.94230.9596-0.47870.82040.6660.52710.00011.30540.00180.13741.2560.2831.66310.4523-14.862973.7653
130.9766-0.16941.58311.8220.43232.5226-0.0477-0.2705-0.3993-0.2546-0.17740.6779-0.32480.0406-0.00031.6996-0.1144-0.13761.5114-0.01441.7871-27.0797-12.948186.5148
143.6108-0.77460.2144.7963-1.60113.1331-0.5581-0.39190.0191-0.59270.1467-0.79430.8398-0.3849-0.00061.58590.1622-0.08680.9176-0.19981.8302-30.2555-14.315378.0929
155.1122-2.16221.82683.73341.94013.17550.4073-0.49870.40080.0765-0.31870.19420.6-0.67650.00011.6897-0.09630.12111.3051-0.11081.7793-13.89836.909598.9786
165.61880.9526-2.30084.6034-2.23621.55940.6738-1.7230.8508-1.6489-0.5226-0.65842.5357-2.2349-0.11882.1927-0.7036-0.11921.7562-0.12451.1658-17.25139.965891.7308
172.2782-0.6368-1.13531.00311.17491.5370.19590.55250.0144-0.8212-0.0764-0.0173-0.12380.192702.0962-0.0489-0.10051.4790.22491.5304-5.17129.544863.3425
183.761.08440.30341.6299-1.040.83311.50.57481.17070.0267-0.83970.3347-0.0737-0.24490.02542.22040.2612-0.21891.2806-0.1971.4202-13.607110.348861.1754
190.77190.01690.47661.4708-0.29890.98750.12980.16540.0716-0.1225-0.15050.0784-0.1086-0.0275-01.85460.0779-0.05022.11760.01121.7401-12.32-2.249779.3405
200.96560.01310.55471.1752-0.21211.33290.0420.10980.0945-0.0977-0.02740.0748-0.289-0.068801.9896-0.05220.05381.9826-0.15871.8168-11.9315-1.687379.1528
213.0241-0.3462-0.8561.8849-1.45692.1142-0.1347-0.36530.3091-0.0533-0.06060.0833-0.13650.12560.00011.38440.09180.03791.57960.15351.7894-121.3942-5.378315.6115
223.5142-0.1808-2.12263.1223-1.31023.34790.1835-0.09071.4262-1.3550.0643-0.73240.4871-0.17960.00031.7455-0.03650.44351.33370.35862.4697-134.928416.958316.0906
231.74470.3315-0.59254.5313-0.286-0.1414-0.2638-0.87430.43541.07670.0493-0.03920.26890.9436-0.11951.5467-0.2-0.04522.2534-0.20361.4153-110.8583-0.17725.6854
242.08260.4338-0.23342.2192-0.5452.48811.10452.396-1.09350.0890.2825-0.02140.4365-1.84380.14131.50340.31320.27832.4730.13691.7563-110.8878-20.6314-8.1776
251.82352.277-1.00723.1157-2.21673.22-0.2924-0.09361.2285-0.7514-0.34510.1170.9643-0.6027-0.0871.1783-0.04340.15852.3642-0.25331.9564-136.7874-5.508622.3862
260.91920.2704-0.37742.06670.88443.0829-0.10660.36990.3408-0.1858-0.0330.0692-0.1406-0.060801.4253-0.10490.18581.7828-0.14212.3754-5.6793-5.8061-16.5308
273.4467-0.4964-3.03360.52861.35543.84970.78330.5072.66671.3317-0.24621.18620.77260.19820.00182.10270.01610.3291.34540.02162.7847.583316.9524-18.9223
280.22720.7756-0.38211.3016-1.10610.5613-0.23890.4302-0.1628-1.8172-0.596-0.50270.0518-0.6543-0.01522.0320.16710.11122.2751-0.00672.3388-17.3852-1.2844-26.7244
290.90330.4823-0.63131.43340.18742.53151.3711-0.8814-0.5041-0.10740.2992-0.06632.0216-0.23230.08261.3649-0.36880.03611.8614-0.25442.428-15.3016-19.79698.7924
300.09690.31390.6512.3748-0.10322.8814-0.54191.20741.2814-0.041-0.0917-0.57131.23381.3147-0.26261.1729-0.27910.31122.1251-0.06632.832610.359-4.1798-22.9857
311.18110.83860.18933.6404-0.79852.1533-0.01340.24970.1029-0.1250.07130.6953-0.3194-0.2112-0.00021.59460.021-0.41151.6636-0.13091.6126-39.5447-60.120972.6962
323.6668-0.10311.12451.73921.11222.3086-1.5027-0.17520.4010.08640.31370.5531-0.24542.1963-0.0182.2792-0.1016-0.77862.30340.03482.0327-56.7027-72.916457.2458
332.3607-0.88870.86761.721-0.93520.6160.80390.3189-0.97520.45040.52840.9732-1.6605-0.7230.80131.4563-0.0055-0.19882.12890.28162.4109-50.4147-49.424177.1521
341.96251.38740.97671.72080.61220.516-0.01590.08771.4293-0.7477-0.2927-1.4127-0.25910.70210.0011.94290.0864-0.41092.1624-0.02432.1839-12.2342-48.952265.724
352.6330.1727-0.77190.0346-0.52432.6144-0.3445-0.5442-0.8386-0.07760.13742.03241.081.1742-0.17141.8658-0.1561-0.49411.13540.0292.8541-45.149-76.335275.0431
361.3880.54490.22261.35680.1080.7978-0.2810.06870.1944-0.45380.1980.54960.0751-0.07610.00011.79610.1173-0.28881.66040.40221.9203-16.645855.534849.879
374.4518-0.1160.78652.172-1.51191.75051.3242-1.6209-0.0046-0.8573-0.36610.24350.9921-1.01940.00171.9076-0.2825-0.56362.3990.56652.1224-30.44667.079931.7764
381.03090.77380.25461.2592-1.51662.2731-0.18730.901-0.2409-0.6969-0.28370.06890.30120.4993-0.00072.3916-0.2086-0.06571.85610.01521.5534-13.7345.448939.0107
392.81991.3046-0.0791.68730.43630.6958-0.3618-1.74380.90251.1760.76090.34240.49610.56880.01812.01240.1755-0.43311.340.29452.1877-24.934346.442877.8844
401.75911.0441-1.04630.4589-0.52861.28530.1880.94351.547-0.89060.2980.64140.48130.41120.68822.5065-0.0966-0.31561.02260.57132.5254-13.617471.082343.8789
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 38 through 134)
2X-RAY DIFFRACTION2(chain 'B' and resid 20 through 102)
3X-RAY DIFFRACTION3(chain 'C' and resid 16 through 118)
4X-RAY DIFFRACTION4(chain 'D' and resid 28 through 122)
5X-RAY DIFFRACTION5(chain 'E' and resid 39 through 135)
6X-RAY DIFFRACTION6(chain 'F' and resid 25 through 102)
7X-RAY DIFFRACTION7(chain 'G' and resid 14 through 118)
8X-RAY DIFFRACTION8(chain 'H' and resid 29 through 121)
9X-RAY DIFFRACTION9(chain 'I' and resid -72 through 72)
10X-RAY DIFFRACTION10(chain 'J' and resid -72 through 72)
11X-RAY DIFFRACTION11(chain 'K' and resid 38 through 134)
12X-RAY DIFFRACTION12(chain 'L' and resid 20 through 102)
13X-RAY DIFFRACTION13(chain 'M' and resid 16 through 118)
14X-RAY DIFFRACTION14(chain 'N' and resid 28 through 122)
15X-RAY DIFFRACTION15(chain 'O' and resid 39 through 135)
16X-RAY DIFFRACTION16(chain 'P' and resid 25 through 102)
17X-RAY DIFFRACTION17(chain 'Q' and resid 14 through 118)
18X-RAY DIFFRACTION18(chain 'R' and resid 29 through 121)
19X-RAY DIFFRACTION19(chain 'S' and resid -72 through 72)
20X-RAY DIFFRACTION20(chain 'T' and resid -72 through 72)
21X-RAY DIFFRACTION21(chain 'U' and resid 0 through 471)
22X-RAY DIFFRACTION22(chain 'V' and resid 5 through 93)
23X-RAY DIFFRACTION23(chain 'W' and resid 6 through 95)
24X-RAY DIFFRACTION24(chain 'X' and resid 1 through 76)
25X-RAY DIFFRACTION25(chain 'Y' and resid 11 through 98)
26X-RAY DIFFRACTION26(chain 'Z' and resid 0 through 471)
27X-RAY DIFFRACTION27(chain 'a' and resid 5 through 95)
28X-RAY DIFFRACTION28(chain 'b' and resid 7 through 95)
29X-RAY DIFFRACTION29(chain 'c' and resid 1 through 76)
30X-RAY DIFFRACTION30(chain 'd' and resid 5 through 98)
31X-RAY DIFFRACTION31(chain 'e' and resid 0 through 471)
32X-RAY DIFFRACTION32(chain 'f' and resid 10 through 95)
33X-RAY DIFFRACTION33(chain 'g' and resid 6 through 95)
34X-RAY DIFFRACTION34(chain 'h' and resid 1 through 76)
35X-RAY DIFFRACTION35(chain 'i' and resid 5 through 98)
36X-RAY DIFFRACTION36(chain 'j' and resid 0 through 471)
37X-RAY DIFFRACTION37(chain 'k' and resid 5 through 90)
38X-RAY DIFFRACTION38(chain 'l' and resid 3 through 95)
39X-RAY DIFFRACTION39(chain 'm' and resid 1 through 76)
40X-RAY DIFFRACTION40(chain 'n' and resid 5 through 98)

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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