[English] 日本語
Yorodumi
- PDB-5j9w: Crystal structure of the NuA4 core complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j9w
TitleCrystal structure of the NuA4 core complex
Components
  • Chromatin modification-related protein EAF6
  • Chromatin modification-related protein YNG2
  • Enhancer of polycomb-like protein 1
  • Histone acetyltransferase ESA1
KeywordsTRANSFERASE / NuA4 / nucleosome / histone / acetylation
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / SUMOylation of transcription cofactors / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / histone H4 acetyltransferase activity / rDNA heterochromatin formation / peptide N-acetyltransferase activity / NuA4 histone acetyltransferase complex / peptide-lysine-N-acetyltransferase activity / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / methylated histone binding / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / nucleosome / regulation of cell cycle / chromatin remodeling / cell cycle / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus / cytosol
Similarity search - Function
Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / Enhancer of polycomb protein / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type ...Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / Enhancer of polycomb protein / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / Zinc finger, PHD-type, conserved site / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / Chromatin modification-related protein YNG2 / Enhancer of polycomb-like protein 1 / Chromatin modification-related protein EAF6 / Histone acetyltransferase ESA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, Z.C. / Xu, P.
CitationJournal: Mol Cell / Year: 2016
Title: The NuA4 Core Complex Acetylates Nucleosomal Histone H4 through a Double Recognition Mechanism.
Authors: Peng Xu / Chengmin Li / Zhihong Chen / Shuanying Jiang / Shilong Fan / Jiawei Wang / Junbiao Dai / Ping Zhu / Zhucheng Chen /
Abstract: NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal ...NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal structures of the NuA4 core complex and a cryoelectron microscopy structure with the nucleosome. The structures show that the histone-binding pocket of the enzyme is rearranged, suggesting its activation. The enzyme binds the histone tail mainly through the target lysine residue, with a preference for a small residue at the -1 position. The complex engages the nucleosome at the dish face and orients its catalytic pocket close to the H4 tail to achieve selective acetylation. The combined data reveal a space-sequence double recognition mechanism of the histone tails by a modifying enzyme in the context of the nucleosome.
History
DepositionApr 11, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Histone acetyltransferase ESA1
F: Chromatin modification-related protein EAF6
G: Enhancer of polycomb-like protein 1
H: Chromatin modification-related protein YNG2
A: Histone acetyltransferase ESA1
B: Chromatin modification-related protein EAF6
C: Enhancer of polycomb-like protein 1
D: Chromatin modification-related protein YNG2
I: Histone acetyltransferase ESA1
J: Chromatin modification-related protein EAF6
K: Enhancer of polycomb-like protein 1
L: Chromatin modification-related protein YNG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,48514
Polymers289,86612
Non-polymers1,6192
Water0
1
E: Histone acetyltransferase ESA1
F: Chromatin modification-related protein EAF6
G: Enhancer of polycomb-like protein 1
H: Chromatin modification-related protein YNG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4325
Polymers96,6224
Non-polymers8101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17340 Å2
ΔGint-91 kcal/mol
Surface area37690 Å2
MethodPISA
2
A: Histone acetyltransferase ESA1
B: Chromatin modification-related protein EAF6
C: Enhancer of polycomb-like protein 1
D: Chromatin modification-related protein YNG2


Theoretical massNumber of molelcules
Total (without water)96,6224
Polymers96,6224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15650 Å2
ΔGint-89 kcal/mol
Surface area37780 Å2
MethodPISA
3
I: Histone acetyltransferase ESA1
J: Chromatin modification-related protein EAF6
K: Enhancer of polycomb-like protein 1
L: Chromatin modification-related protein YNG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4325
Polymers96,6224
Non-polymers8101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17610 Å2
ΔGint-94 kcal/mol
Surface area37670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 138.570, 167.868
Angle α, β, γ (deg.)90.00, 97.11, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Histone acetyltransferase ESA1


Mass: 36556.883 Da / Num. of mol.: 3 / Fragment: UNP residues 141-445 / Mutation: E338Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ESA1, YOR244W, O5257 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08649, histone acetyltransferase
#2: Protein Chromatin modification-related protein EAF6 / ESA1-associated factor 6


Mass: 12915.704 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: EAF6, YJR082C, J1854 / Production host: Escherichia coli (E. coli) / References: UniProt: P47128
#3: Protein Enhancer of polycomb-like protein 1


Mass: 33320.547 Da / Num. of mol.: 3 / Fragment: UNP residues 121-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: EPL1, YFL024C / Production host: Escherichia coli (E. coli) / References: UniProt: P43572
#4: Protein Chromatin modification-related protein YNG2 / ESA1-associated factor 4 / ING1 homolog 2


Mass: 13828.894 Da / Num. of mol.: 3 / Fragment: UNP residues 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YNG2, EAF4, NBN1, YHR090C / Production host: Escherichia coli (E. coli) / References: UniProt: P38806
#5: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C23H38N7O17P3S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.15 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 100 mM HEPES (pH 7.5), 9% PEG 20000, 8% glycerol, 7% 2-Propanol, 10% 1,6-Hexanediol, 10 mM DTT

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 30, 2015
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 80437 / % possible obs: 83.1 % / Redundancy: 3 % / Net I/σ(I): 6.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.878 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.43
RfactorNum. reflection% reflection
Rfree0.2711 1989 2.47 %
Rwork0.2269 --
obs0.228 80437 82.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18691 0 0 0 18691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319075
X-RAY DIFFRACTIONf_angle_d0.6525691
X-RAY DIFFRACTIONf_dihedral_angle_d13.37711681
X-RAY DIFFRACTIONf_chiral_restr0.0412742
X-RAY DIFFRACTIONf_plane_restr0.0033308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8005-2.87040.3821280.30655122X-RAY DIFFRACTION76
2.8704-2.9480.32641370.30045329X-RAY DIFFRACTION79
2.948-3.03460.33481390.29825530X-RAY DIFFRACTION82
3.0346-3.13250.35861470.28685772X-RAY DIFFRACTION85
3.1325-3.24430.36151450.27545809X-RAY DIFFRACTION86
3.2443-3.37410.31821480.26745799X-RAY DIFFRACTION86
3.3741-3.52740.31421460.26025760X-RAY DIFFRACTION85
3.5274-3.7130.28051470.23335762X-RAY DIFFRACTION85
3.713-3.94520.26971450.21185722X-RAY DIFFRACTION85
3.9452-4.2490.21371440.19625683X-RAY DIFFRACTION84
4.249-4.67510.22551430.1795634X-RAY DIFFRACTION83
4.6751-5.34830.22981430.1915598X-RAY DIFFRACTION82
5.3483-6.72560.27111400.23435547X-RAY DIFFRACTION81
6.7256-29.88010.20441370.17785381X-RAY DIFFRACTION78
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)
12.6882-0.4450.4722.9335-0.11541.94770.1234-1.34260.2885-0.08620.26490.2835-0.4633-0.2555-0.05480.43290.00480.16060.0848-0.29090.3323-24.810824.0848155.9638
20.7303-0.22560.22731.56220.29440.8085-0.0686-0.1099-0.018-0.02030.04330.0920.0204-0.0730.00840.2207-0.00130.0390.1574-0.03530.2384-22.758712.906147.2022
32.0039-3.3281-0.12612.87241.67081.3256-0.0001-0.4995-0.15550.55060.1719-0.22470.39390.30120.02490.51610.01280.12660.39190.02180.2727-19.8903-1.0164158.4712
41.7423-0.15270.85711.6195-0.24541.5457-0.05130.16670.07270.02580.005-0.1506-0.27770.43180.05550.2256-0.02180.04290.2285-0.0430.1965-4.935815.8933148.4112
51.69031.2658-0.51061.0269-0.03482.3718-0.00470.8187-0.07410.1099-0.0394-0.3449-0.17491.29920.13250.3048-0.24220.09590.5705-0.11780.422215.070618.2737148.4329
62.10140.7367-1.53382.2301-1.51362.8120.14810.06360.20290.1591-0.0614-0.0199-0.2544-0.2421-0.02880.3434-0.110.03280.5187-0.02490.313415.622317.6961157.876
72.3569-0.24040.09962.5062-0.02794.3196-0.28320.3935-0.3765-0.0188-0.1679-0.1754-0.5573-0.15410.24730.29120.0079-0.06720.4292-0.10010.286-3.10623.6341144.8426
80.0515-0.0683-0.05990.0220.00580.0334-0.2231-0.0674-0.29790.7320.08580.5176-0.0721-0.6245-0.00280.6548-0.0958-0.02780.72420.22160.5081-51.9876-43.7137163.1515
93.37161.3405-1.57891.1679-0.57461.45220.36520.14440.0917-0.15180.5190.27860.3096-0.7103-0.42050.5906-0.0543-0.12970.39120.12870.4892-40.6344-39.0447151.8879
102.17640.1547-0.46552.1099-0.26623.3814-0.6432-0.3653-0.5646-0.51590.1404-0.4240.35010.04080.06250.4477-0.0441-0.05130.26270.01210.3394-26.3934-32.3486139.7409
110.9994-0.4707-0.05592.6311-0.77212.12410.0740.6025-0.0066-0.65170.0226-0.19870.1352-0.21810.00470.6842-0.09660.03770.3394-0.08930.2497-15.6345-22.9274127.3436
122.837-0.7529-0.18742.82391.48061.01440.09030.02430.5084-0.3013-0.0786-0.97550.39110.1982-0.00010.4554-0.08960.06640.42140.0090.4113-10.1856-14.2544129.1043
131.8306-1.57921.62523.06430.09472.520.03970.0618-0.0930.22670.0452-0.29010.09710.7102-0.01130.57290.10650.00190.27720.08620.3396-14.2525-21.9457138.1476
140.6955-1.3611.99252.5648-3.82075.71120.2302-0.0731-0.72660.0423-0.1304-0.56680.74580.657-0.01630.99880.28130.10121.3674-0.10920.7282-10.1919-29.1636142.0974
151.0276-0.4174-0.68540.490.08841.3816-0.0573-0.1536-0.31950.2369-0.01060.40040.0656-0.31660.06250.2981-0.05840.10440.1966-0.09720.5653-38.0613.9719149.9987
161.44260.6290.20712.30430.02981.208-0.3220.6498-0.4575-1.27950.29030.3509-0.1645-0.55850.03850.63850.0527-0.15770.7107-0.19120.7432-49.043712.6965129.589
172.25460.37960.76612.6030.58362.28960.1811-0.23360.1488-0.10640.13470.6838-0.1518-0.5374-0.30950.3628-0.07270.0310.430.01340.4707-36.0628-11.223137.993
181.33681.0926-0.80662.19320.30531.0571-0.05970.3966-0.4508-0.02690.03360.70490.32360.32770.05990.36480.0669-0.03160.522-0.19480.8053-49.97937.5797140.6178
192.4465-0.2224-1.431.54011.41152.38620.30940.68750.431-0.9501-0.41230.8178-0.6753-0.11220.00080.4765-0.008-0.1240.339-0.0440.3169-29.067726.3563134.9579
203.06040.0618-0.73632.218-0.98051.87490.36860.0424-0.22420.44740.282-0.5091-0.8723-0.4158-0.07040.676-0.03840.28680.4210.03920.1394-16.71644.9402112.8874
210.96141.1768-0.68732.1362-1.79851.6437-0.12880.0878-0.1293-0.22550.28920.09340.388-0.6293-0.08390.3271-0.0867-0.01490.2580.08090.2805-31.0498-29.7802147.7079
221.44721.428-2.25716.94870.9095.23710.06560.59950.2185-0.11510.26650.3393-0.2455-0.3078-0.03370.4806-0.18370.06930.450.02690.2027-21.90113.7015116.1295
231.6810.10680.78590.741-0.61044.0327-0.0492-0.17150.6565-0.0879-0.3977-1.0651-0.19951.09460.1430.2899-0.43430.0242-1.6513-0.12970.4508-17.2421-4.1946132.2167
241.30630.1159-0.47451.7385-2.57395.0254-0.1821-0.3667-0.48270.7722-0.6822-1.1195-0.71050.20480.44430.3079-0.0024-0.01470.42130.05380.2147-18.4153-23.7299152.7283
252.68871.4116-0.30261.7571-0.67561.191-0.0750.46930.2705-0.12470.13850.06190.2570.0477-0.00880.3522-0.0083-0.01470.34090.18620.2783-27.2873-42.8227165.8786
260.0871-0.16140.11142.6389-2.96323.1598-0.1192-0.0548-0.27250.1878-0.3525-0.5158-0.3838-0.02370.26440.42390.012-0.05350.31310.09510.313-28.16-30.6917167.0423
270.9834-0.2721-0.58311.4438-0.9061.32510.10520.1335-0.05580.09530.40370.3191-0.255-0.61-0.27620.32770.0255-0.00920.21190.0530.2153-27.2021-11.234137.266
280.77811.05450.57531.59491.83145.57440.05651.3316-0.3199-1.4308-0.1515-0.19980.3649-0.12480.0060.68370.0501-0.0740.52250.26671.0963-29.5699-1.9943110.4497
292.1547-0.19370.04522.1327-1.07653.6087-0.1331-0.1992-0.54580.29690.2079-0.12630.3062-0.4111-0.02480.48610.06090.02660.39830.07590.5063.2186-5.506196.0744
301.4880.3088-0.27621.4962-0.51771.3829-0.03050.053-0.1548-0.0183-0.0783-0.17790.0310.02250.05360.2551-0.00640.04120.22170.05040.19555.67977.904789.525
312.21870.07590.11540.7305-0.44221.8329-0.0368-0.0634-0.20540.2176-0.0996-0.32030.01130.26410.03240.23630.01250.01080.36460.08460.43422.88285.150792.9241
321.0792-0.54180.17880.77580.67620.92370.1336-0.2278-0.3076-0.089-0.283-0.2956-0.10950.64780.02740.3194-0.0064-0.02510.76430.14420.655939.73562.873892.4598
332.76492.06621.11791.5080.82580.4414-0.22550.30160.1093-0.39030.1021-0.5518-0.20890.1906-0.03420.5779-0.07760.24831.45510.13261.154553.082.9437103.1158
341.1480.16091.34570.10010.26962.43790.00590.0642-0.4609-0.16230.087-0.40540.1290.2837-0.01250.70030.05270.08711.0654-0.04940.773842.3911-5.399587.7434
351.9343-0.5246-0.2092.76440.38921.8257-0.145-0.17560.16350.18470.1679-0.44520.14880.47230.14890.43520.01040.13410.58730.18970.513524.564613.484182.7851
360.8958-0.1779-1.25150.0320.24981.7358-0.08380.18360.4469-0.0689-0.12850.0482-0.2947-0.20860.01421.0907-0.1497-0.20451.23980.03090.7424-22.781930.007941.0066
371.53480.38741.84730.43440.51972.3341-0.10680.28060.586-0.1246-0.16890.4245-0.0798-0.24920.04030.6081-0.0375-0.13580.36230.14340.4066-7.742437.070653.1967
380.96590.264-1.2752.3770.74922.1831-0.0505-0.90640.860.1131-0.07540.1065-1.10420.3297-0.04460.7347-0.5670.0772-0.03280.46830.33459.325844.019168.7083
390.20040.34280.59330.61431.02071.69910.1455-0.21520.4280.39850.2743-0.3936-0.15960.5166-0.07730.505-0.1971-0.0021.08450.07130.442314.865837.256580.428
400.3421-0.12970.45510.17810.49222.8782-0.026-0.293-0.0705-0.01040.2507-0.1451-0.07070.3698-0.02030.8570.0043-0.03241.21840.14941.041519.070137.930371.8037
410.544-0.3367-0.31010.5575-0.4941.6394-0.0225-0.0528-0.4126-0.3533-0.4970.2079-0.1523-0.15690.03720.6791-0.5058-0.0261-0.02140.84530.11511.204234.595766.33
420.69331.0044-0.02942.49751.68982.70160.22180.40910.1497-0.53320.1012-0.7057-0.56120.6581-0.08180.7637-0.26140.00361.3630.17270.585513.603234.654856.7857
431.60150.6645-0.3860.5844-0.3070.7271-0.12910.328-0.1233-0.07470.10980.05160.207-0.1505-0.00310.3916-0.07920.01140.38450.0340.23-5.15967.245981.4638
440.7749-0.3734-0.13351.583-0.27112.5392-0.0060.25540.2632-0.06790.02660.1428-0.3874-0.41740.0560.37870.0622-0.00480.49080.180.3846-21.979519.398992.4857
451.258-1.5744-0.16542.4567-0.4950.8160.36160.5853-0.313-0.1205-0.43111.346-0.10490.1844-0.04710.40570.08980.07350.66580.05360.4809-9.10328.052275.0822
461.18560.01750.70311.83-0.68991.94550.10190.47280.0578-0.01040.01460.5334-0.5031-0.0219-0.06460.35520.07590.05040.37490.13710.3605-23.276115.734790.3745
470.0613-0.01940.29510.19420.35782.498-0.0571-1.290.42321.01330.57090.51990.13410.0586-0.18150.44330.00050.08320.43950.08120.2748-1.478211.1926108.4085
481.6607-0.64320.70.63850.75572.4592-0.1081-0.01720.22090.23690.13570.01360.34290.20770.05630.5371-0.1667-0.10460.4962-0.02620.466410.660341.756797.9176
490.68990.53140.37590.2826-0.39682.316-0.13020.24080.2767-0.45650.14470.1434-0.2129-0.3058-0.02510.6782-0.0602-0.13150.52430.07670.3637-7.462631.189450.9253
501.17091.68620.85632.36850.77444.49210.0484-0.3838-0.43950.2709-0.111-0.03860.07480.1399-0.06250.52320.0092-0.12010.42820.04260.36548.127635.57496.2327
511.0716-0.30.7820.7688-0.80040.9092-0.4977-0.14510.2435-0.47280.1539-1.0710.6175-0.09280.12040.3094-0.10990.03050.46340.22260.318710.196427.229475.128
522.9983-0.40083.39441.101-1.184.38130.10890.0822-0.2047-0.4205-0.342-0.0090.45870.4055-0.01120.6831-0.09080.06590.5456-0.00220.4367.463223.466657.6096
531.2083-0.25031.46540.0763-0.33121.7643-0.10180.070.1075-0.9297-0.3736-0.3461-0.18140.30020.15921.03120.0358-0.01680.53270.07010.52520.931523.449543.8452
542.0655-1.04240.59431.1169-0.04851.2651-0.00220.0669-0.1795-0.23840.0743-0.33620.48630.2335-0.05531.31460.0307-0.09240.8533-0.01920.4446-6.596222.176432.6383
551.3102-0.06130.3240.4977-0.22951.3525-0.0114-0.023-0.1664-0.2823-0.039-0.07340.4676-0.09260.08170.5189-0.0815-0.02260.25860.03980.302-1.661223.757764.3262
563.8877-0.5516-0.98875.26610.66824.5857-0.0024-0.2830.91550.7732-0.77260.6669-0.45730.04290.3150.7534-0.0215-0.06250.2453-0.06130.5319-0.91142.199695.1585
573.17120.5307-0.32521.82480.41913.5485-0.09160.8621-0.1118-0.6058-0.1749-0.01140.1420.11490.17240.93180.1108-0.0190.8394-0.01180.451230.607955.594397.997
581.2354-0.02460.5421.39780.60761.8279-0.12630.2330.1722-0.17450.12830.0804-0.21250.2846-0.00030.2604-0.0943-0.02090.28750.0160.22934.308560.9463115.1392
591.8267-0.00510.23770.42630.6391.2803-0.11130.22670.0007-0.20860.19-0.2449-0.05720.4512-0.01070.3389-0.16010.02590.7921-0.0640.435653.981860.3359111.8136
601.10690.0366-0.11980.216-0.05860.0448-0.80470.0143-0.03-0.38760.0839-1.4138-0.63650.4880.0989-1.2963-0.58890.12831.62970.00030.775569.991159.9635111.7299
611.0275-0.75310.53240.5222-0.38230.2707-0.2863-0.0306-0.23020.1787-0.1924-0.51860.23080.28360.06680.7390.15220.16472.0928-0.01251.385580.808952.8013106.1715
621.4739-1.1675-0.241.75920.46480.45590.05190.6138-0.1289-0.3274-0.1828-0.7279-0.71270.81390.0250.6695-0.42560.06811.3701-0.03670.83269.957571.1733106.3818
632.27810.0113-0.00361.51330.54932.3273-0.514-0.3413-0.14280.22340.7634-0.28910.57811.1675-0.04830.2766-0.4782-0.1690.879-0.20590.471852.740263.0018125.5014
641.0431-0.95550.88240.9091-0.82190.71490.1609-0.0440.09910.02930.150.23260.0634-0.1346-0.08020.74110.1499-0.05591.052-0.20371.18721.08687.5185157.2386
652.1344-0.59940.26213.9063-0.77451.5683-0.1771-0.05530.03470.0254-0.22090.5883-0.1399-0.73630.09730.56110.2838-0.1630.535-0.13810.878411.586179.5162159.2897
661.016-0.41640.99551.6751-1.11641.3367-0.3202-0.56840.38270.72360.24780.41390.63540.23890.04950.43970.1332-0.00550.46610.09360.420224.421772.2909159.4052
670.30360.46010.73183.3010.29252.31310.2046-0.3126-0.15640.36870.0719-0.07190.7403-0.06-0.16310.51170.058-0.04420.50350.0160.335938.065659.0998157.1154
682.23440.06890.23541.36330.08742.70760.2557-0.0039-0.53120.0469-0.0409-0.6927-0.48620.706-0.07190.36630.0344-0.08950.636-0.13650.839645.252758.2008148.9009
690.8531-0.744-0.25360.68860.05820.22230.30330.07790.0529-0.32580.0181-0.07520.01120.0205-0.10070.32790.0212-0.03210.408-0.09930.331338.284769.4036152.2282
701.9559-0.38754.17268.545-2.51159.24560.063-0.47740.3050.36780.21-0.2912-0.0790.3962-0.04120.62550.1485-0.02781.0454-0.07830.514741.499676.6156.8783
710.89410.47270.69620.56480.11030.6416-0.2347-0.03230.3195-0.2860.04990.1498-0.252-0.06640.12930.3425-0.0115-0.07240.3994-0.02140.413821.584367.4229119.0931
720.60610.234-0.05932.18520.26651.62850.0355-0.02460.09960.3657-0.14850.26080.3246-0.41150.01210.3802-0.13440.01730.7062-0.04510.46727.708749.2381124.5111
731.13780.5965-1.13880.867-1.41222.79790.12430.1415-0.01020.0580.42620.967-0.0195-1.5801-0.31170.3943-0.05190.01060.57320.02820.580918.996961.6303139.8857
741.1648-0.5481-0.2610.7210.44971.19760.0059-0.42160.01170.1579-0.21420.21850.0401-0.41430.16180.355-0.1125-0.02390.6115-0.11970.50547.5653.7306120.6236
750.7585-0.39070.3232.5832-0.87222.2674-0.2619-0.1927-1.1203-0.90590.29910.02691.4578-0.61070.09950.5444-0.04650.0180.33750.00770.548229.626640.13109.2368
761.7392-0.9452-0.52192.79110.63780.7250.18120.041-0.263-0.30740.0838-0.384-0.0010.0394-0.24770.42070.1246-0.09390.4886-0.08010.396440.482236.3468141.1685
770.2617-0.1315-0.21960.58170.43581.2372-0.112-0.03390.04910.03260.00610.2746-0.2313-0.4070.00410.38290.172-0.05840.4042-0.04310.533718.264180.6347155.1185
780.2291-0.45770.28951.0113-0.06953.8073-0.31010.0098-0.1676-0.26260.02510.37640.2131-0.37170.03690.3720.0207-0.01180.4415-0.03510.396137.363936.6448137.8958
791.85012.24620.21873.5712-0.56190.55480.598-0.156-0.2215-0.69380.4069-0.4981-0.28080.6267-0.1401-2.51381.6635-1.22490.1650.3881-0.142439.289647.9726135.9268
801.27740.70660.05480.8550.45771.9738-0.01470.47150.0929-0.1298-0.0594-0.3588-0.2732-0.08230.06740.1640.0562-0.01210.27190.0310.269737.348867.8674141.8336
810.8899-1.2895-0.21483.18851.40451.0046-0.1016-0.33090.632-0.20760.1879-0.449-0.811-0.0228-0.05510.65690.2576-0.10230.6524-0.08890.640330.091686.6353149.1111
820.9629-0.7401-0.55562.13521.54042.16490.0108-0.52730.78950.20330.2831-0.145-0.53060.2996-0.11480.86070.2461-0.0280.8051-0.08880.845720.756397.88158.9128
831.0935-0.61440.27880.9360.12991.1087-0.11520.2280.27940.2072-0.15990.0443-0.5048-0.22610.08570.44470.0577-0.0940.28230.05240.345723.222881.0197144.7268
843.27870.6652-0.23324.95830.54193.92940.1447-0.371-0.92670.20630.21270.69790.6805-0.1557-0.32690.50680.03710.02930.2790.06590.674429.331438.2234143.3789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 160:180)
2X-RAY DIFFRACTION2(chain A and resid 181:278)
3X-RAY DIFFRACTION3(chain A and resid 279:283)
4X-RAY DIFFRACTION4(chain A and resid 284:356)
5X-RAY DIFFRACTION5(chain A and resid 357:397)
6X-RAY DIFFRACTION6(chain A and resid 398:420)
7X-RAY DIFFRACTION7(chain A and resid 421:437)
8X-RAY DIFFRACTION8(chain B and resid 1:8)
9X-RAY DIFFRACTION9(chain B and resid 9:21)
10X-RAY DIFFRACTION10(chain B and resid 22:35)
11X-RAY DIFFRACTION11(chain B and resid 36:66)
12X-RAY DIFFRACTION12(chain B and resid 67:91)
13X-RAY DIFFRACTION13(chain B and resid 92:101)
14X-RAY DIFFRACTION14(chain B and resid 102:107)
15X-RAY DIFFRACTION15(chain C and resid 128:196)
16X-RAY DIFFRACTION16(chain C and resid 197:227)
17X-RAY DIFFRACTION17(chain C and resid 228:256)
18X-RAY DIFFRACTION18(chain C and resid 257:291)
19X-RAY DIFFRACTION19(chain C and resid 292:315)
20X-RAY DIFFRACTION20(chain C and resid 316:334)
21X-RAY DIFFRACTION21(chain C and resid 335:394)
22X-RAY DIFFRACTION22(chain D and resid 1:7)
23X-RAY DIFFRACTION23(chain D and resid 8:24)
24X-RAY DIFFRACTION24(chain D and resid 25:44)
25X-RAY DIFFRACTION25(chain D and resid 45:61)
26X-RAY DIFFRACTION26(chain D and resid 62:77)
27X-RAY DIFFRACTION27(chain D and resid 78:109)
28X-RAY DIFFRACTION28(chain D and resid 110:119)
29X-RAY DIFFRACTION29(chain E and resid 160:181)
30X-RAY DIFFRACTION30(chain E and resid 182:294)
31X-RAY DIFFRACTION31(chain E and resid 295:349)
32X-RAY DIFFRACTION32(chain E and resid 350:394)
33X-RAY DIFFRACTION33(chain E and resid 395:399)
34X-RAY DIFFRACTION34(chain E and resid 400:419)
35X-RAY DIFFRACTION35(chain E and resid 420:437)
36X-RAY DIFFRACTION36(chain F and resid 7:12)
37X-RAY DIFFRACTION37(chain F and resid 13:33)
38X-RAY DIFFRACTION38(chain F and resid 34:45)
39X-RAY DIFFRACTION39(chain F and resid 66:73)
40X-RAY DIFFRACTION40(chain F and resid 74:92)
41X-RAY DIFFRACTION41(chain F and resid 93:99)
42X-RAY DIFFRACTION42(chain F and resid 100:107)
43X-RAY DIFFRACTION43(chain G and resid 125:175)
44X-RAY DIFFRACTION44(chain G and resid 176:230)
45X-RAY DIFFRACTION45(chain G and resid 231:258)
46X-RAY DIFFRACTION46(chain G and resid 259:291)
47X-RAY DIFFRACTION47(chain G and resid 292:315)
48X-RAY DIFFRACTION48(chain G and resid 316:340)
49X-RAY DIFFRACTION49(chain G and resid 341:399)
50X-RAY DIFFRACTION50(chain H and resid 1:13)
51X-RAY DIFFRACTION51(chain H and resid 14:29)
52X-RAY DIFFRACTION52(chain H and resid 30:37)
53X-RAY DIFFRACTION53(chain H and resid 38:50)
54X-RAY DIFFRACTION54(chain H and resid 51:68)
55X-RAY DIFFRACTION55(chain H and resid 69:101)
56X-RAY DIFFRACTION56(chain H and resid 102:118)
57X-RAY DIFFRACTION57(chain I and resid 160:170)
58X-RAY DIFFRACTION58(chain I and resid 171:294)
59X-RAY DIFFRACTION59(chain I and resid 295:361)
60X-RAY DIFFRACTION60(chain I and resid 362:393)
61X-RAY DIFFRACTION61(chain I and resid 394:400)
62X-RAY DIFFRACTION62(chain I and resid 401:420)
63X-RAY DIFFRACTION63(chain I and resid 421:437)
64X-RAY DIFFRACTION64(chain J and resid 5:14)
65X-RAY DIFFRACTION65(chain J and resid 15:21)
66X-RAY DIFFRACTION66(chain J and resid 22:34)
67X-RAY DIFFRACTION67(chain J and resid 35:66)
68X-RAY DIFFRACTION68(chain J and resid 67:92)
69X-RAY DIFFRACTION69(chain J and resid 93:102)
70X-RAY DIFFRACTION70(chain J and resid 103:107)
71X-RAY DIFFRACTION71(chain K and resid 123:181)
72X-RAY DIFFRACTION72(chain K and resid 182:228)
73X-RAY DIFFRACTION73(chain K and resid 229:259)
74X-RAY DIFFRACTION74(chain K and resid 260:296)
75X-RAY DIFFRACTION75(chain K and resid 297:315)
76X-RAY DIFFRACTION76(chain K and resid 316:340)
77X-RAY DIFFRACTION77(chain K and resid 341:399)
78X-RAY DIFFRACTION78(chain L and resid 1:7)
79X-RAY DIFFRACTION79(chain L and resid 8:16)
80X-RAY DIFFRACTION80(chain L and resid 17:33)
81X-RAY DIFFRACTION81(chain L and resid 34:44)
82X-RAY DIFFRACTION82(chain L and resid 45:57)
83X-RAY DIFFRACTION83(chain L and resid 58:100)
84X-RAY DIFFRACTION84(chain L and resid 101:119)

+
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