[English] 日本語
Yorodumi
- PDB-5i9e: Crystal structure of a nuclear actin ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i9e
TitleCrystal structure of a nuclear actin ternary complex
Components
  • Actin-related protein 4
  • Actin
  • Helicase SWR1
KeywordsHYDROLASE / nuclear actin / Arp4 / chromatin remodeling
Function / homology
Function and homology information


Swr1 complex / Ino80 complex / kinetochore assembly / recombinational repair / SWI/SNF complex / ATP-dependent chromatin remodeler activity / NuA4 histone acetyltransferase complex / helicase activity / chromatin organization / histone binding ...Swr1 complex / Ino80 complex / kinetochore assembly / recombinational repair / SWI/SNF complex / ATP-dependent chromatin remodeler activity / NuA4 histone acetyltransferase complex / helicase activity / chromatin organization / histone binding / DNA helicase / molecular adaptor activity / cytoskeleton / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / structural molecule activity / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 ...domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / helicase superfamily c-terminal domain / Nucleotidyltransferase; domain 5 / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin / Actin-related protein 4 / Helicase SWR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces bayanus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, Z. / Cao, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation31270762 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystal structure of a nuclear actin ternary complex.
Authors: Cao, T. / Sun, L. / Jiang, Y. / Huang, S. / Wang, J. / Chen, Z.
History
DepositionFeb 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_struct_oper_list
Item: _audit_author.name / _citation.journal_id_CSD ..._audit_author.name / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin-related protein 4
B: Actin
C: Actin-related protein 4
D: Actin
H: Helicase SWR1
E: Helicase SWR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,01512
Polymers211,9046
Non-polymers1,1126
Water0
1
A: Actin-related protein 4
B: Actin
E: Helicase SWR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5086
Polymers105,9523
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-59 kcal/mol
Surface area33960 Å2
MethodPISA
2
C: Actin-related protein 4
D: Actin
H: Helicase SWR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5086
Polymers105,9523
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-54 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.260, 202.220, 87.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Actin-related protein 4 / Actin-like protein ARP4 / Actin-like protein 4


Mass: 54991.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ARP4, ACT3, YJL081C, J1012 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P80428
#2: Protein Actin /


Mass: 41735.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces bayanus (yeast) / Gene: ACT1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60011
#3: Protein Helicase SWR1 / Swi2/Snf2-related 1


Mass: 9224.541 Da / Num. of mol.: 2 / Fragment: UNP residues 340-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SWR1, YDR334W, D9651.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05471, DNA helicase
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 291 K / Method: evaporation
Details: polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→48.403 Å / Num. obs: 48531 / % possible obs: 99.7 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.4
Reflection shellResolution: 2.8→2.87 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000V705data reduction
HKL-2000V705data scaling
PHASER5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QB0, 1YAG

3qb0

1yag


Resolution: 2.8→48.403 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.97
RfactorNum. reflection% reflection
Rfree0.2844 1999 4.12 %
Rwork0.2317 --
obs0.2338 48531 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12589 0 66 0 12655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712940
X-RAY DIFFRACTIONf_angle_d0.70817524
X-RAY DIFFRACTIONf_dihedral_angle_d10.6297782
X-RAY DIFFRACTIONf_chiral_restr0.0461957
X-RAY DIFFRACTIONf_plane_restr0.0042230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.41581390.3593237X-RAY DIFFRACTION99
2.87-2.94760.38561400.35353256X-RAY DIFFRACTION99
2.9476-3.03430.3771400.33473261X-RAY DIFFRACTION99
3.0343-3.13220.41811410.32953276X-RAY DIFFRACTION100
3.1322-3.24420.36471420.30183324X-RAY DIFFRACTION100
3.2442-3.3740.33651420.27513289X-RAY DIFFRACTION100
3.374-3.52750.29871410.26053277X-RAY DIFFRACTION100
3.5275-3.71350.32791430.25593328X-RAY DIFFRACTION100
3.7135-3.9460.28521430.24183323X-RAY DIFFRACTION100
3.946-4.25050.2781420.2093334X-RAY DIFFRACTION100
4.2505-4.6780.2431440.18893347X-RAY DIFFRACTION100
4.678-5.35410.24111450.20123372X-RAY DIFFRACTION100
5.3541-6.74270.30051450.22523397X-RAY DIFFRACTION100
6.7427-48.40980.23751520.20013511X-RAY DIFFRACTION98
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)
11.647-0.0314-0.14892.2479-0.63262.622-0.0307-1.00031.55280.7288-0.1468-0.0894-0.9143-0.1735-0.1570.7339-0.0355-0.05540.8891-0.00040.944226.474227.291398.821
26.23352.7208-2.81551.1789-0.98163.16250.03120.69961.1739-0.27940.3118-0.5057-0.1142-0.055-0.41910.6039-0.10370.13050.9406-0.06770.608517.087215.5523100.6498
31.8996-0.2251-0.22293.4424-3.72812.97550.2606-0.6361-0.57450.3803-0.27950.28940.16920.16310.13260.6861-0.03950.01580.66620.08510.593419.9613195.3795112.5874
44.0987-0.04481.68652.7837-0.95131.41950.02340.081-0.32650.3299-0.02480.429-0.0212-0.5821-0.0140.5292-0.02240.09140.4901-0.00730.397413.3112202.1938101.3071
53.2583-1.38330.68392.8728-0.98742.10170.05420.5454-0.2735-0.13610.4760.2378-0.09160.0398-0.44490.55580.10580.02670.7935-0.04360.521431.5147201.466390.5342
61.65450.2679-0.71912.23860.61643.11560.0569-0.3588-0.41980.34880.1155-0.22360.78190.275-0.240.77890.1675-0.1940.82070.10980.856938.0642186.7999115.686
72.83170.52782.72361.25990.56712.65390.1750.2929-0.0255-0.64370.8013-0.3554-0.5880.2455-0.22020.83360.17410.60651.24450.14811.505160.3917189.41797.4194
83.155-1.39670.19331.3473-1.89145.29450.1513-0.148-0.76220.0557-0.0113-0.36020.66470.8921-0.28310.73510.2373-0.04490.8443-0.050.940447.0183186.8187105.7369
92.1875-0.5957-0.00952.3965-0.13752.74850.38230.8566-0.0066-0.6091-0.2706-0.77180.02920.5566-0.05540.66320.14390.09921.0754-0.14470.74942.0287200.096786.6016
104.0413-2.5192-2.51736.1756-0.45165.68670.1906-0.63420.3534-0.33730.0269-1.39250.63431.1958-0.04110.55560.01310.01890.6981-0.04550.783932.8273209.232102.2672
119.51124.63981.90585.53210.69293.1896-0.47781.09670.6242-0.40340.43521.2872-0.3723-0.45760.11280.57370.0226-0.01910.6010.07880.5159.4942211.264790.893
121.32720.352-0.25840.074-0.07140.04640.26360.6656-0.8687-0.35970.5711.8068-0.014-0.752-0.57460.5876-0.1604-0.06060.77340.00720.841315.4154206.001584.7322
133.759-0.0173-0.34335.1631-1.36172.7336-0.6058-1.47310.53661.3030.37930.13861.1608-0.86130.19371.89520.2195-0.07231.2187-0.00440.627124.5292227.8437134.0825
144.76142.140.56231.13480.41120.21680.0301-1.68051.4301-0.0541-0.44230.51471.5702-0.8346-0.00531.60510.29060.33311.91750.31240.70739.1497223.6939136.7276
152.3012-0.5364-0.37530.15140.60543.3631-0.1409-0.30660.20710.91250.58480.2442-0.024-0.7067-0.20541.50130.12160.38631.26270.07610.980810.0091223.5701131.0261
165.19520.43560.89491.9738-0.78021.668-0.1168-0.7810.3721.23490.2235-0.0118-0.8663-0.4464-0.15091.2020.08220.05160.7007-0.18760.580723.5673227.2763122.4378
172.8981-0.2298-0.08273.2644-0.33283.3133-0.3335-0.8781-0.3120.54160.02310.2104-0.17060.12710.0270.89630.1523-0.03140.85520.03110.618328.9717210.3475123.9553
182.2063-0.43520.2011.77981.07571.84050.19950.9678-0.232.3126-0.55760.71470.8262-0.96070.26112.1099-0.03170.06971.54870.10730.774317.2287203.5958144.8417
190.66610.6833-0.38810.7447-0.53220.3981.03560.1915-0.42770.11920.3070.27130.5838-0.1968-0.64582.41550.3405-0.16461.19640.40981.334130.9172191.1486148.9318
200.5811-0.3532-1.09030.10610.47541.8613-0.8214-1.3933-0.47280.76470.06530.51671.80281.1710.14031.88730.48580.34531.68360.19480.99820.1379201.4547151.8308
218.2617-0.1427-1.22660.40970.6451.108-0.61270.9638-1.88470.55740.3162-0.37450.0261-0.88930.86481.33030.03320.11751.40990.07040.403124.548196.9452131.1968
222.8425-0.34250.0323.33650.85231.6267-0.14-0.7382-0.53540.64080.063-0.1645-0.27150.7982-0.05250.9647-0.0139-0.15921.0710.13550.627336.6492205.638127.4701
232.02970.04260.47875.34741.66392.6971-0.2437-0.94460.39810.8714-0.1469-0.866-0.65950.66060.2361.18910.1085-0.36131.27390.07090.832141.4605203.7538132.2246
242.2834-0.8572-0.05361.0697-0.90762.486-0.3297-0.27231.08590.52720.0251-0.3208-0.45240.38330.18780.95060.0330.01120.925-0.24840.832928.6573230.8171121.2806
255.449-1.1580.71481.1994-0.31461.6417-0.20910.27090.48490.9919-0.072-0.88580.04460.75160.02150.91720.18480.1320.65860.27031.3225.0719243.921798.8988
260.02190.20450.02771.587-0.37712.0555-0.2265-0.954-0.818-0.44810.91571.27450.174-1.0035-0.58360.61840.07930.22680.85890.25311.4009-3.5798246.185993.2966
271.0659-1.893-0.90663.41371.43634.8245-0.89380.13280.0837-0.0521-0.61080.50511.2438-0.63370.43111.2418-0.0471-0.08841.3379-0.00242.6447-28.2314243.763889.7788
282.0532-1.12990.48491.5549-0.93281.38250.3403-0.15760.43270.056-0.17480.72380.17110.0029-0.30070.64920.05580.20120.96030.52051.9202-16.0083246.313293.2678
292.32490.14490.98550.6882-1.25112.93040.2417-0.24150.46970.42060.37620.73850.0161-0.8266-0.71260.74710.08660.24490.6520.21011.446-8.3122239.6491107.0271
300.7358-0.49690.15110.9031-0.06570.97140.2477-0.42370.67120.23790.18760.5649-0.2635-0.313-0.21690.91230.19410.39260.85520.21331.9616-2.9198261.1008106.7977
312.16311.4986-0.88621.4158-0.25256.25530.14681.0195-0.1945-0.49440.66521.0287-0.9812-1.6308-0.22830.79380.198-0.00751.45080.66432.4641-18.3599267.556676.3512
320.924-0.7863-0.15761.69020.01362.5439-0.12710.32631.3256-0.4471-0.16310.5976-0.6635-0.45340.03430.80670.14230.1011.14770.65832.218-15.7542264.083485.9229
330.6506-0.11230.00011.36640.0690.7265-0.6334-0.0846-0.2666-0.5341.0618-0.4457-1.61771.0498-0.04431.5654-0.15210.30151.65380.36772.44290.5174286.7997.1693
341.8368-0.11320.65392.1940.64191.99920.14640.1831.24910.56320.22940.5635-0.488-0.7114-0.21320.98710.18520.48480.81310.08442.2571-6.4745273.3165101.3167
350.92590.82160.77340.86660.21120.4921-0.43610.2640.09190.22250.63080.3893-0.36450.59-0.37580.98820.09030.47340.68670.10912.03576.7177265.4835103.9332
363.4040.31210.16213.0115-0.31263.1968-0.0776-0.6026-0.15151.35880.76790.71280.6512-0.5257-0.75911.07970.09930.3910.70480.20611.3239-0.9077235.4931111.8261
373.24052.2636-0.42612.3527-0.16740.57170.6224-0.01650.43-0.5019-0.53420.43040.1948-0.3187-0.19221.03310.1921-0.22151.73530.170.92537.7314231.3165.9778
381.0261.26241.65371.44122.23313.38560.05850.3092-0.7983-1.2674-0.0650.4651-0.3597-0.4866-0.04241.0081-0.0821-0.24581.07980.04251.1011-3.9642224.096670.7121
396.49111.57590.57664.85980.79332.86840.4951.5502-0.7158-1.8673-0.33640.26770.5680.3483-0.16851.0110.2019-0.17430.95410.13280.750611.4764224.080769.9264
403.9234-1.60880.77454.6-2.22331.91450.1251.08680.1969-0.313-0.40740.8601-0.1252-0.55230.19850.7502-0.0114-0.04840.84810.17640.6669.4456232.343781.6865
412.6455-1.64680.31952.373-1.04690.75450.03531.10490.5944-0.3707-0.07450.47270.2472-0.0042-0.06830.7130.0113-0.07420.93430.47080.95315.321246.150675.5859
421.0173-0.09650.84060.8066-0.22361.32960.44270.43650.8315-0.75360.14680.47961.1835-0.9582-0.18061.26770.2353-0.36941.8992-0.0591.5383-16.2099236.706260.6097
433.5745-0.46891.24581.3191-1.4941.8365-0.07661.5248-0.2666-0.33460.2647-0.2995-0.7534-0.1867-0.14311.2127-0.0609-0.45391.41510.87931.837-18.0083254.258155.9423
440.148-0.3357-0.19110.87570.46840.2861-0.4022-0.7520.3327-1.0087-0.0940.1768-0.3888-0.62030.08771.22870.2462-0.46172.09730.28081.4346-19.2586248.383651.9916
451.76150.32690.29660.91711.63442.57980.2270.2979-0.0493-0.9227-0.69921.6526-0.2604-1.3088-0.08950.83460.1158-0.17531.15890.49011.9331-13.9407250.641271.5843
461.5348-0.68-1.2163.37280.11380.8688-0.24070.91750.9877-0.23640.19240.1244-0.09050.88120.18170.89930.06780.03051.20180.56981.3170.6332257.717775.2528
471.2223-1.2548-0.24971.92860.70791.97660.37420.75011.0868-0.8186-0.02070.40080.2717-0.5023-0.110.6337-0.0213-0.15691.2320.73961.20385.2193250.888866.8723
484.6762-0.69650.91044.9613-1.01814.0799-0.41340.61790.93821.04640.170.1301-0.78450.40360.17070.6972-0.03250.1060.98210.26280.742519.77234.066485.8472
490.84040.92790.47921.01920.52010.2572-0.52370.09270.0785-0.8567-0.03420.15761.18080.13030.08421.3510.13340.0592.2160.05871.427121.679216.707479.7385
500.902-0.86710.61110.8305-0.59790.47210.5029-0.43130.310.29320.17080.3003-0.26480.8019-0.1410.72310.04430.06720.92540.15860.591325.4344220.254387.7228
515.8381.5928-0.99233.6714.80488.28220.1146-0.2673-0.1690.5241-0.1293-0.6606-0.79650.9889-0.27760.67250.0237-0.0330.99660.20450.758131.2534221.475999.0602
524.0787-0.3457-0.25764.12810.58173.71210.70580.89170.18280.494-0.9245-0.0590.84770.04990.19310.6911-0.1572-0.04480.9129-0.07010.686236.5276223.5623111.3521
535.1325-1.91914.4923.2324-2.39374.1424-0.5683-0.07680.42032.168-0.4088-1.0651.57091.2981-0.09391.4390.1071-0.03391.3621-0.27410.788340.7738227.6017120.668
540.0328-0.0003-0.0719-0.00330.00770.1426-0.78580.3552-0.05610.3546-0.0102-0.0457-1.4424-0.0840.15181.43610.2524-0.60291.1779-0.08861.659745.7079228.5509127.9789
550.3807-0.247-0.10910.20140.01410.0372-0.2316-0.33541.066-0.0036-0.0573-0.2731-1.03560.3113-0.1261.2202-0.0155-0.13760.9909-0.25991.362612.4438243.7009118.393
560.63780.3371.12341.7467-0.61963.12490.30140.4699-0.15931.4107-0.44990.8674-0.43251.21550.01180.91180.13960.20050.65830.13731.048215.0101246.2832107.0756
572.7031.43771.53452.5477-2.44346.8505-0.29650.15511.0368-0.4342-0.75141.0515-1.0969-0.23310.21920.7650.2242-0.10560.94460.58391.324514.289247.921695.6927
583.8391-2.275-2.89164.52382.27272.3582-0.9763-0.5424-0.56780.7677-0.59190.7686-0.3818-0.39550.71620.6441-0.00780.02120.96140.39781.051617.2778249.803884.7848
590.77320.7713-1.99960.7915-1.85165.9059-0.29160.31640.89840.49850.6465-0.4045-2.2011-0.39160.09740.24450.6897-0.99760.9792.25980.517420.7145251.745172.0122
600.1698-0.2572-0.19260.36930.26370.20520.4199-0.3810.55660.49460.8354-0.7207-0.9330.5528-0.34971.0479-0.32830.09842.1270.57381.277522.1309255.456962.9868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:9)
2X-RAY DIFFRACTION2(chain A and resid 10:20)
3X-RAY DIFFRACTION3(chain A and resid 21:76)
4X-RAY DIFFRACTION4(chain A and resid 77:140)
5X-RAY DIFFRACTION5(chain A and resid 141:189)
6X-RAY DIFFRACTION6(chain A and resid 190:255)
7X-RAY DIFFRACTION7(chain A and resid 256:260)
8X-RAY DIFFRACTION8(chain A and resid 261:306)
9X-RAY DIFFRACTION9(chain A and resid 307:440)
10X-RAY DIFFRACTION10(chain A and resid 441:457)
11X-RAY DIFFRACTION11(chain A and resid 458:482)
12X-RAY DIFFRACTION12(chain A and resid 483:489)
13X-RAY DIFFRACTION13(chain B and resid 5:28)
14X-RAY DIFFRACTION14(chain B and resid 29:58)
15X-RAY DIFFRACTION15(chain B and resid 59:95)
16X-RAY DIFFRACTION16(chain B and resid 96:148)
17X-RAY DIFFRACTION17(chain B and resid 149:183)
18X-RAY DIFFRACTION18(chain B and resid 184:220)
19X-RAY DIFFRACTION19(chain B and resid 221:236)
20X-RAY DIFFRACTION20(chain B and resid 237:260)
21X-RAY DIFFRACTION21(chain B and resid 261:275)
22X-RAY DIFFRACTION22(chain B and resid 276:312)
23X-RAY DIFFRACTION23(chain B and resid 313:334)
24X-RAY DIFFRACTION24(chain B and resid 335:375)
25X-RAY DIFFRACTION25(chain C and resid 1:29)
26X-RAY DIFFRACTION26(chain C and resid 30:44)
27X-RAY DIFFRACTION27(chain C and resid 45:54)
28X-RAY DIFFRACTION28(chain C and resid 55:99)
29X-RAY DIFFRACTION29(chain C and resid 100:139)
30X-RAY DIFFRACTION30(chain C and resid 140:199)
31X-RAY DIFFRACTION31(chain C and resid 200:216)
32X-RAY DIFFRACTION32(chain C and resid 217:250)
33X-RAY DIFFRACTION33(chain C and resid 251:265)
34X-RAY DIFFRACTION34(chain C and resid 266:401)
35X-RAY DIFFRACTION35(chain C and resid 402:454)
36X-RAY DIFFRACTION36(chain C and resid 455:482)
37X-RAY DIFFRACTION37(chain D and resid 5:52)
38X-RAY DIFFRACTION38(chain D and resid 53:79)
39X-RAY DIFFRACTION39(chain D and resid 80:103)
40X-RAY DIFFRACTION40(chain D and resid 104:127)
41X-RAY DIFFRACTION41(chain D and resid 128:180)
42X-RAY DIFFRACTION42(chain D and resid 181:214)
43X-RAY DIFFRACTION43(chain D and resid 215:232)
44X-RAY DIFFRACTION44(chain D and resid 233:256)
45X-RAY DIFFRACTION45(chain D and resid 257:279)
46X-RAY DIFFRACTION46(chain D and resid 280:304)
47X-RAY DIFFRACTION47(chain D and resid 305:357)
48X-RAY DIFFRACTION48(chain D and resid 358:375)
49X-RAY DIFFRACTION49(chain E and resid 350:353)
50X-RAY DIFFRACTION50(chain E and resid 354:360)
51X-RAY DIFFRACTION51(chain E and resid 361:370)
52X-RAY DIFFRACTION52(chain E and resid 371:378)
53X-RAY DIFFRACTION53(chain E and resid 379:384)
54X-RAY DIFFRACTION54(chain E and resid 385:390)
55X-RAY DIFFRACTION55(chain H and resid 350:354)
56X-RAY DIFFRACTION56(chain H and resid 355:364)
57X-RAY DIFFRACTION57(chain H and resid 365:370)
58X-RAY DIFFRACTION58(chain H and resid 371:379)
59X-RAY DIFFRACTION59(chain H and resid 380:387)
60X-RAY DIFFRACTION60(chain H and resid 388:393)

+
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