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- PDB-3u61: Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp,... -

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Basic information

Entry
Database: PDB / ID: 3u61
TitleStructure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and ADP
Components
  • (DNA polymerase accessory protein ...) x 2
  • DNA polymerase processivity component
  • Primer DNA strand
  • Template DNA strand
KeywordsDNA BINDING PROTEIN/DNA / AAA+ / ATP hydrolase / clamp loader / sliding clamp / primer-template DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / DNA clamp loader activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication ...Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / DNA clamp loader activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication / DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Bacteriophage clamp loader A subunit, A domain / Bacteriophage clamp loader A subunit, A' domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1260 / Sliding-clamp-loader small subunit gp62 / Sliding-clamp-loader large subunit / : / : / Bacteriophage clamp loader A subunit / Sliding-clamp-loader large subunit, AAA+ ATPase lid domain / Sliding-clamp-loader large subunit, C-terminal domain ...Bacteriophage clamp loader A subunit, A domain / Bacteriophage clamp loader A subunit, A' domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1260 / Sliding-clamp-loader small subunit gp62 / Sliding-clamp-loader large subunit / : / : / Bacteriophage clamp loader A subunit / Sliding-clamp-loader large subunit, AAA+ ATPase lid domain / Sliding-clamp-loader large subunit, C-terminal domain / Sliding clamp, C-terminal / Sliding clamp / gp45 sliding clamp, C terminal / DNA polymerase processivity factor / DNA polymerase processivity factor / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Helicase, Ruva Protein; domain 3 - #60 / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / Helix non-globular / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Special / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-08T / ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Sliding clamp / Sliding-clamp-loader large subunit / Sliding-clamp-loader small subunit
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 3.2 Å
AuthorsKelch, B.A. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
CitationJournal: Science / Year: 2011
Title: How a DNA polymerase clamp loader opens a sliding clamp.
Authors: Kelch, B.A. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA polymerase accessory protein 44
C: DNA polymerase accessory protein 44
D: DNA polymerase accessory protein 44
E: DNA polymerase accessory protein 44
A: DNA polymerase accessory protein 62
G: DNA polymerase processivity component
H: DNA polymerase processivity component
F: DNA polymerase processivity component
I: Template DNA strand
J: Primer DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,80416
Polymers252,31910
Non-polymers1,4856
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28370 Å2
ΔGint-150 kcal/mol
Surface area89760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.303, 137.272, 222.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
14
24
15
25
35
16
26
36
46

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain F and resid 1001:1101
211chain G and resid 2001:2101
311chain H and resid 3001:3101
112chain F and resid 1102:1220
212chain G and resid 2102:2220
312chain H and resid 3102:3220
113chain B and resid 6:159
213chain C and resid 6:159
114chain B and resid 160:208
214chain C and resid 160:208
115chain A and resid 209:218
215chain B and resid 209:218
315chain C and resid 209:218
116chain A and resid 234:316
216chain B and resid 234:316
316chain C and resid 234:316
416chain D and resid 234:316

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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DNA polymerase accessory protein ... , 2 types, 5 molecules BCDEA

#1: Protein
DNA polymerase accessory protein 44 / Clamp loader large subunit / Protein Gp44


Mass: 36189.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 44, gp44 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04526
#2: Protein DNA polymerase accessory protein 62 / Clamp loader small subunit / Protein Gp62


Mass: 22941.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 62, gp62 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04527

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Protein , 1 types, 3 molecules GHF

#3: Protein DNA polymerase processivity component / DNA polymerase accessory protein 45 / Gp45


Mass: 25162.592 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 45, gp45 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04525

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DNA chain , 2 types, 2 molecules IJ

#4: DNA chain Template DNA strand


Mass: 6117.943 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain Primer DNA strand


Mass: 3013.995 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 6 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-08T / [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium


Mass: 492.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14BeF3N5O10P2

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG4k, 0.1M MES pH 6.5, 20mM NaCl, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 44596 / Num. obs: 44464 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.7 % / Rsym value: 0.123 / Net I/σ(I): 18.9
Reflection shellResolution: 3.2→3.32 Å / Redundancy: 17.2 % / Mean I/σ(I) obs: 6 / Rsym value: 0.483 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacementSAD / Resolution: 3.2→47.646 Å / SU ML: 0.94 / σ(F): 1 / Phase error: 30.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3051 2913 7.13 %random
Rwork0.2392 ---
obs0.2439 40848 96.16 %-
all-42479 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.859 Å2 / ksol: 0.294 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-25.0351 Å2-0 Å2-0 Å2
2---8.4104 Å2-0 Å2
3----16.6247 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16331 325 92 0 16748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01117060
X-RAY DIFFRACTIONf_angle_d1.56823119
X-RAY DIFFRACTIONf_dihedral_angle_d18.1466372
X-RAY DIFFRACTIONf_chiral_restr0.1012649
X-RAY DIFFRACTIONf_plane_restr0.0062894
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11F762X-RAY DIFFRACTIONPOSITIONAL
12G762X-RAY DIFFRACTIONPOSITIONAL0.067
13H762X-RAY DIFFRACTIONPOSITIONAL0.074
21F923X-RAY DIFFRACTIONPOSITIONAL
22G923X-RAY DIFFRACTIONPOSITIONAL0.069
23H923X-RAY DIFFRACTIONPOSITIONAL0.088
31B1190X-RAY DIFFRACTIONPOSITIONAL
32C1190X-RAY DIFFRACTIONPOSITIONAL0.094
41B395X-RAY DIFFRACTIONPOSITIONAL
42C395X-RAY DIFFRACTIONPOSITIONAL0.065
51A72X-RAY DIFFRACTIONPOSITIONAL
52B72X-RAY DIFFRACTIONPOSITIONAL0.088
53C72X-RAY DIFFRACTIONPOSITIONAL0.162
61A668X-RAY DIFFRACTIONPOSITIONAL
62B668X-RAY DIFFRACTIONPOSITIONAL0.053
63C668X-RAY DIFFRACTIONPOSITIONAL0.056
64D660X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.25250.38021300.31141618X-RAY DIFFRACTION88
3.2525-3.30850.36861370.3171704X-RAY DIFFRACTION92
3.3085-3.36870.3751490.31111674X-RAY DIFFRACTION93
3.3687-3.43350.35331300.30411766X-RAY DIFFRACTION93
3.4335-3.50350.34151140.28761722X-RAY DIFFRACTION94
3.5035-3.57970.36271490.29031770X-RAY DIFFRACTION96
3.5797-3.66290.33411410.28521749X-RAY DIFFRACTION96
3.6629-3.75450.29751260.27251796X-RAY DIFFRACTION95
3.7545-3.8560.31571400.25831759X-RAY DIFFRACTION96
3.856-3.96940.31831470.24451797X-RAY DIFFRACTION96
3.9694-4.09740.2781370.24381807X-RAY DIFFRACTION97
4.0974-4.24380.31561400.22861783X-RAY DIFFRACTION96
4.2438-4.41360.31291300.20721838X-RAY DIFFRACTION98
4.4136-4.61430.26561600.20351822X-RAY DIFFRACTION98
4.6143-4.85730.26521380.19291867X-RAY DIFFRACTION98
4.8573-5.16130.30421310.22011845X-RAY DIFFRACTION98
5.1613-5.55930.34391440.26181855X-RAY DIFFRACTION99
5.5593-6.11770.37351500.2631875X-RAY DIFFRACTION99
6.1177-7.00060.32941350.24211912X-RAY DIFFRACTION99
7.0006-8.81090.25641350.17921948X-RAY DIFFRACTION100
8.8109-47.65150.25551500.22862028X-RAY DIFFRACTION99
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)
13.05030.04720.91415.8956-1.27022.6659-0.1870.11890.3595-0.1622-0.13060.39240.1140.119-0.00010.83850.08290.270.93560.1181.28523.17351.90964.0109
21.27261.76170.48442.9175-0.95472.5283-0.2655-0.86450.03760.1650.40690.0407-0.1658-0.8490.00011.2458-0.0976-0.0831.33720.1581.47344.616127.80341.1236
32.5018-0.13780.8483.30181.99793.7706-0.20060.27270.2564-0.11610.0401-0.35070.22840.032-0.00011.05070.118-0.05261.1303-0.13581.1715-3.540623.156635.3209
42.9563-0.289-0.34185.42840.24963.9628-0.07370.2360.1479-0.57430.1555-0.5014-0.120.2830.00030.70520.10710.10890.72750.03930.8059-26.799120.660613.3292
52.91490.29110.34492.72611.17582.55650.4468-0.67290.35290.0464-0.3669-0.0945-0.8361-0.2865-0.00021.19560.1415-0.08950.8273-0.09831.0854-36.263137.454233.1165
62.7712-0.36431.02812.5224-1.40642.4964-0.5124-0.40710.70110.32320.53560.11860.0844-0.2628-0.00011.04660.3308-0.11371.6006-0.4221.3122-14.217634.123852.0998
71.65450.787-2.47714.3497-0.48017.13450.16440.02550.07130.05620.05870.21640.0256-0.5725-0.00090.51320.13730.02250.84860.00890.7251-39.54212.304439.5827
83.3377-0.6024-0.93892.33082.60854.4970.1486-0.6868-0.68861.05280.1577-0.51450.0339-0.4601.10260.1537-0.03451.1053-0.05760.9429-40.583113.250467.0077
90.8470.05270.20240.68070.34981.4974-0.2857-0.34380.37240.6604-0.1806-0.0101-0.0636-0.7160.00041.82230.3829-0.08242.1104-0.22751.2297-9.618521.705770.8237
100.7405-2.30880.38796.2425-2.00275.0170.2082-0.1721-0.2470.1059-0.4836-0.32430.4533-0.00210.00010.9686-0.0895-0.12370.90210.040.884-28.3084-8.048458.511
110.5388-1.3132-0.00391.00460.01360.32940.1632-0.2873-0.08341.24550.153-0.5476-0.1366-0.246-0.00021.7224-0.0982-0.37281.2272-0.08871.3484-14.9961-18.154778.4353
121.8329-1.4678-0.94741.7787-0.5011.6627-0.7239-1.0258-0.34910.75140.64750.15850.9890.34180.00012.14660.58820.00251.90990.03351.33713.63.857463.6497
133.0389-0.13470.03851.6258-1.47971.29470.39680.1772-0.3092-0.05780.08780.0016-0.39340.06540.00011.05260.03740.15130.87990.2231.14691.0711-20.857112.83
141.1987-0.4137-0.38471.45250.68130.7616-0.21510.1247-0.47220.39380.1722-0.71280.0792-0.005601.45410.23050.1211.3169-0.08581.2327.79513.278439.395
151.7768-0.3428-0.3293-0.11820.14921.03960.2390.5413-0.4264-0.56720.462-0.16540.06410.4099-0.00051.5899-0.0002-0.27251.3473-0.00711.7177-10.9409-23.47348.5746
162.2892-1.027-2.39430.4870.20734.56640.0567-0.03220.3290.1039-0.03660.5344-0.2842-0.8795-0.00010.74220.1157-0.00441.09770.05590.8754-50.9392-1.389811.4926
174.285-1.4065-0.10295.22560.0973.88430.0890.33940.1497-0.6272-0.1235-0.5427-0.0232-0.0289-0.00011.00780.08780.25590.79160.09970.8053-31.4764-0.1629-10.6216
184.2003-1.8084-0.66564.5519-0.29212.1056-0.3129-0.5242-0.22021.101-0.1747-0.17810.85560.3429-0.00011.1652-0.20230.02981.12550.17930.9-31.5843-37.682635.2973
194.4737-0.77071.14055.1729-0.41693.5003-0.1854-0.0653-0.1650.83390.07650.62450.0629-0.0836-0.00040.8858-0.22040.1491.09960.05330.9033-52.2695-17.085437.4079
202.2058-1.5125-0.07085.5417-0.94052.81781.07250.51090.3198-0.9373-0.5927-0.690.17410.45440.00031.04490.14110.1650.8749-0.03411.0558-14.0341-25.4949-7.6031
214.3667-0.63680.59152.13250.10924.90620.2304-0.2691-0.6914-0.0748-0.1576-0.01050.74240.52270.00041.13070.12670.02730.970.20881.1806-10.9648-44.145114.4007
220.8459-0.4614-0.16340.18040.1920.71420.1464-2.6795-0.73290.5984-0.27690.20671.39890.70790.0021.24220.13670.28251.6347-0.11391.6172-13.4035-1.084828.9066
230.7589-0.3836-0.07170.8588-0.33410.0933-0.0861-0.07410.08840.0544-0.0502-0.59222.28020.60960.00151.09270.3546-0.10511.3749-0.04190.9968-17.6616-1.054229.8358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 2:159 )B2 - 159
2X-RAY DIFFRACTION2( CHAIN B AND RESID 160:187 )B160 - 187
3X-RAY DIFFRACTION3( CHAIN B AND RESID 234:318 )B234 - 318
4X-RAY DIFFRACTION4( CHAIN C AND RESID 2:159 )C2 - 159
5X-RAY DIFFRACTION5( CHAIN C AND RESID 160:221 )C160 - 221
6X-RAY DIFFRACTION6( CHAIN C AND RESID 234:318 )C234 - 318
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:159 )D - C1 - 159
8X-RAY DIFFRACTION8( CHAIN D AND RESID 160:232 )D - C160 - 232
9X-RAY DIFFRACTION9( CHAIN D AND RESID 233:318 )D - C233 - 318
10X-RAY DIFFRACTION10( CHAIN E AND RESID 3:159 )E3 - 159
11X-RAY DIFFRACTION11( CHAIN E AND RESID 160:213 )E160 - 213
12X-RAY DIFFRACTION12( CHAIN E AND RESID 233:315 )E233 - 315
13X-RAY DIFFRACTION13( CHAIN A AND RESID 3:37 )A3 - 37
14X-RAY DIFFRACTION14( CHAIN A AND RESID 38:108 )A38 - 108
15X-RAY DIFFRACTION15( CHAIN A AND RESID 117:187 )A117 - 187
16X-RAY DIFFRACTION16( CHAIN G AND RESID 1001:1106 )G1001 - 1106
17X-RAY DIFFRACTION17( CHAIN G AND RESID 1107:1228 )G1107 - 1228
18X-RAY DIFFRACTION18( CHAIN H AND RESID 2001:2106 )H2001 - 2106
19X-RAY DIFFRACTION19( CHAIN H AND RESID 2107:2228 )H2107 - 2228
20X-RAY DIFFRACTION20( CHAIN F AND RESID 3001:3106 )F3001 - 3106
21X-RAY DIFFRACTION21( CHAIN F AND RESID 3107:3222 )F3107 - 3222
22X-RAY DIFFRACTION22chain I
23X-RAY DIFFRACTION23chain J

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