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- PDB-5v8w: Crystal structure of human Integrator IntS9-IntS11 CTD complex -

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Basic information

Entry
Database: PDB / ID: 5v8w
TitleCrystal structure of human Integrator IntS9-IntS11 CTD complex
Components
  • Integrator complex subunit 11
  • Integrator complex subunit 9
KeywordsHYDROLASE / snRNA processing / integrator complex
Function / homology
Function and homology information


snRNA processing / integrator complex / snRNA 3'-end processing / regulation of transcription elongation by RNA polymerase II / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA polymerase II transcribes snRNA genes / RNA endonuclease activity / negative regulation of transforming growth factor beta receptor signaling pathway / blood microparticle / nucleoplasm ...snRNA processing / integrator complex / snRNA 3'-end processing / regulation of transcription elongation by RNA polymerase II / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA polymerase II transcribes snRNA genes / RNA endonuclease activity / negative regulation of transforming growth factor beta receptor signaling pathway / blood microparticle / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Integrator IntS9, C-terminal domain / Integrator IntS11, C-terminal domain / Integrator complex subunit 9 / Integrator complex subunit 11, MBL-fold / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain ...: / : / Integrator IntS9, C-terminal domain / Integrator IntS11, C-terminal domain / Integrator complex subunit 9 / Integrator complex subunit 11, MBL-fold / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Integrator complex subunit 11 / Integrator complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsWu, Y. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
National Institutes of Health/Office of the DirectorS10OD012018 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance.
Authors: Wu, Y. / Albrecht, T.R. / Baillat, D. / Wagner, E.J. / Tong, L.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrator complex subunit 9
B: Integrator complex subunit 11
C: Integrator complex subunit 9
D: Integrator complex subunit 11
E: Integrator complex subunit 9
F: Integrator complex subunit 11
G: Integrator complex subunit 9
H: Integrator complex subunit 11


Theoretical massNumber of molelcules
Total (without water)86,7078
Polymers86,7078
Non-polymers00
Water7,548419
1
A: Integrator complex subunit 9
B: Integrator complex subunit 11


Theoretical massNumber of molelcules
Total (without water)21,6772
Polymers21,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-11 kcal/mol
Surface area10140 Å2
MethodPISA
2
C: Integrator complex subunit 9
D: Integrator complex subunit 11


Theoretical massNumber of molelcules
Total (without water)21,6772
Polymers21,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-12 kcal/mol
Surface area10160 Å2
MethodPISA
3
E: Integrator complex subunit 9
F: Integrator complex subunit 11


Theoretical massNumber of molelcules
Total (without water)21,6772
Polymers21,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-4 kcal/mol
Surface area9280 Å2
MethodPISA
4
G: Integrator complex subunit 9
H: Integrator complex subunit 11


Theoretical massNumber of molelcules
Total (without water)21,6772
Polymers21,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-9 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.010, 67.780, 98.585
Angle α, β, γ (deg.)90.00, 100.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Integrator complex subunit 9 / / Int9 / Protein related to CPSF subunits of 74 kDa / RC-74


Mass: 9003.422 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 582-658)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS9, RC74 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NV88
#2: Protein
Integrator complex subunit 11 / / Int11 / Cleavage and polyadenylation-specific factor 3-like protein / CPSF3-like protein / Protein ...Int11 / Cleavage and polyadenylation-specific factor 3-like protein / CPSF3-like protein / Protein related to CPSF subunits of 68 kDa / RC-68


Mass: 12673.415 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 491-600)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF3L, INTS11, RC68 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5TA45, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis-Tris pH 6.5, 21-24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 51362 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 5038 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→24.83 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.03
RfactorNum. reflection% reflection
Rfree0.2203 1861 3.9 %
Rwork0.1665 --
obs0.1686 47760 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5636 0 0 419 6055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125727
X-RAY DIFFRACTIONf_angle_d1.2997733
X-RAY DIFFRACTIONf_dihedral_angle_d15.3912151
X-RAY DIFFRACTIONf_chiral_restr0.056926
X-RAY DIFFRACTIONf_plane_restr0.005977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0979-2.15460.29661370.2153362X-RAY DIFFRACTION96
2.1546-2.21790.2451410.19953507X-RAY DIFFRACTION100
2.2179-2.28950.26911420.19443498X-RAY DIFFRACTION100
2.2895-2.37120.30931430.19473534X-RAY DIFFRACTION100
2.3712-2.46610.26971430.19013522X-RAY DIFFRACTION100
2.4661-2.57820.23441440.17683545X-RAY DIFFRACTION100
2.5782-2.7140.261430.18033537X-RAY DIFFRACTION100
2.714-2.88380.25991440.18853533X-RAY DIFFRACTION100
2.8838-3.10610.24911430.18723546X-RAY DIFFRACTION100
3.1061-3.41790.24491440.17453553X-RAY DIFFRACTION100
3.4179-3.91090.2031430.15343538X-RAY DIFFRACTION100
3.9109-4.9210.16451460.12413587X-RAY DIFFRACTION100
4.921-24.83190.15791480.14933637X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.5022-0.3923-0.35633.00252.74063.8725-0.42110.3307-0.96230.27620.26730.72470.6465-0.11290.18180.3392-0.12340.07440.3491-0.03520.474310.893558.660763.58
25.16990.03883.52857.2115-1.20092.9060.2094-0.73310.27050.67620.02490.6304-0.3298-0.7954-0.20510.2645-0.03860.11650.33610.00350.259311.113271.65974.3172
33.4902-3.68094.17734.2373-5.64489.31750.1116-0.83631.02620.38180.00330.0621-0.75240.70580.11660.2142-0.07860.02620.3641-0.07160.330218.713974.956775.8176
44.1851.18153.1433.21471.83833.3110.2864-0.2589-0.1824-0.2367-0.08550.8918-0.1227-1.15320.10830.23580.02640.00410.29710.00210.35059.54778.50761.4166
53.4375-2.759-1.82753.2283-0.34254.06350.11050.0848-0.09210.02630.00040.2029-0.1321-0.1703-0.12590.1838-0.0328-0.0010.15820.01050.17918.758272.10962.9982
63.5116-0.1675-0.5784.45862.09755.21120.0289-0.2918-0.52760.411-0.28860.35850.6048-0.28820.1040.3132-0.04370.06660.22750.00810.244717.820561.727469.1724
79.7553-4.09778.24381.7374-3.52837.3768-0.09412.1861-2.3196-1.58120.59012.22491.84631.2028-0.4780.8929-0.1096-0.07250.7132-0.24621.15284.654847.791457.5802
82.51671.6444-2.05833.5614-1.73343.8088-0.22480.181-0.1934-0.3060.1389-0.02720.10560.09610.08840.2611-0.0159-0.00850.1676-0.05850.18426.819966.953756.3373
98.61481.61290.95013.43720.70987.75170.13950.0522-0.17370.0005-0.0383-0.23380.01070.6481-0.06540.18120.0411-0.00110.2109-0.03730.1535.298560.093248.9125
108.82466.9836-3.92035.9116-3.88193.86640.24590.08091.8268-0.91370.0250.8550.28850.6357-0.3580.9346-0.37530.15120.6152-0.08240.571636.732179.158551.6967
118.4021.0306-1.39095.3926-0.13024.15-0.1025-0.2276-0.41530.3725-0.0361-0.190.12960.23160.12890.22130.0311-0.00920.1754-0.04040.157332.192462.129558.8592
129.68872.31550.94534.096-4.86037.38260.21950.21640.4413-0.1808-0.3639-0.1863-0.19430.22280.15870.31410.03460.06630.2830.00710.323642.641762.962127.4767
139.176-1.2966-0.63442.29212.2772.33930.15811.70090.8043-1.5145-0.4236-0.828-0.6455-0.22170.27940.66560.0840.02370.83970.2110.491436.119469.718213.2305
145.45412.85413.19634.8616-1.45715.029-0.45122.2860.5571-2.0361-0.30470.78590.7114-0.34790.54790.77480.10750.05571.42660.19360.695327.059870.604412.276
155.36273.18053.28266.51365.08254.1523-0.8796-0.39080.81620.16840.7234-0.1262-0.355-0.26160.2060.69370.0523-0.03850.62210.21190.680132.165980.229124.1332
167.51310.7443-0.2557.99410.01853.39730.22641.13341.7761-0.81780.051.1927-1.1261-0.7866-0.15440.54680.19240.0920.57290.28190.758728.286472.134922.9252
176.17881.1307-1.95265.7469-0.85373.2112-0.05720.88760.3931-0.46920.07420.2509-0.3147-0.2062-0.01940.32290.05330.02090.32730.09160.196933.631562.619423.8641
187.82281.0144-2.1553.19690.19243.78170.0108-0.23580.01250.120.00780.0981-0.1070.1684-0.04110.33270.02960.03920.21580.06380.221932.986461.792833.8143
193.5315-3.3742-2.28043.80862.20532.4145-0.1310.5347-0.31720.0202-0.19231.2777-0.4892-0.97720.33920.35020.03030.02340.3863-0.04970.411514.18753.9342.2759
203.08890.5927-0.66232.4930.76484.5617-0.02370.17510.2787-0.1515-0.05730.2073-0.2684-0.59840.03460.22410.0586-0.01890.21580.02260.234621.543357.150936.6686
215.6609-3.5233-1.18292.53941.31762.38890.12190.56670.12860.1947-0.24980.4165-0.0511-0.19650.1120.235-0.02220.06850.15790.05250.301-10.471959.597817.277
225.0944-2.92265.31973.2702-1.29218.0882-0.3639-1.1778-0.64241.4170.29010.8367-0.4513-0.4598-0.00220.53310.01260.0860.3657-0.00030.304-6.976872.012828.0571
236.7434-6.10575.74915.5476-5.2044.913-0.0522-0.18580.90380.9688-0.0117-1.29850.2780.8980.03970.37150.0468-0.03360.453-0.01620.43970.673177.154127.0976
242.0715-0.76541.5255.9067-1.20437.151-0.0825-0.06540.1419-0.07560.30820.4683-0.0605-0.2574-0.23380.25720.03860.03460.17580.02930.262-6.778178.501416.3325
257.02496.56860.62938.39760.85872.8663-0.8984-0.4630.4353-0.09320.36990.266-0.1182-0.0110.27980.2120.0426-0.02180.16830.01830.163-1.061673.682615.8023
267.56975.1222-3.44215.6319-0.51523.3678-0.0486-0.14491.0423-0.02290.05510.33720.14870.0377-0.03340.25740.0615-0.03240.1461-0.00740.1366-1.181468.355313.5607
272.41060.7725-1.89674.5413-1.14234.3683-0.3204-0.5265-0.21140.29590.19190.26150.4211-0.06180.12040.35560.09870.04530.27360.06980.1989-2.378461.884521.581
287.42442.0316-4.79085.7125-1.6195.1413-0.38930.2639-0.3395-0.12010.3254-0.09110.4909-0.10120.05370.25410.0028-0.02440.11340.02990.1306-1.767564.731311.061
293.135-0.9083-0.47823.7597-4.79077.0217-0.8224-0.91672.0064-0.25090.1369-0.8804-1.99681.53190.64820.3448-0.35030.13730.9569-0.28931.20222.431871.39172.627
308.0384-2.69232.27142.04170.26698.4195-0.2760.4270.5080.13060.3758-0.6443-0.320.98830.02020.2402-0.0176-0.00320.3769-0.05710.331417.259262.1555-1.2689
312.37420.12372.90791.14610.69054.84340.1923-0.8996-1.1611.05020.2654-0.74971.21090.459-0.12570.45980.0946-0.12320.39740.02550.515312.137949.30552.6737
327.03481.07260.51582.3830.95415.8022-0.03190.02020.253-0.08780.18070.1039-0.32260.4907-0.03740.164-0.01790.01620.1244-0.01560.15118.09963.0088-1.2328
335.55471.4212-1.81985.65130.16084.5502-0.1203-0.337-0.23530.19920.1155-0.17250.30310.56410.01310.23770.1074-0.03320.2218-0.02940.16268.995660.413610.22
344.6395-2.11733.3765.2809-2.01264.5873-0.19040.53810.264-0.3838-0.1876-0.273-0.12230.27070.24050.2547-0.05990.03990.27940.04530.22478.799169.931-30.4665
357.16292.39925.94025.19512.61776.3039-0.7718-0.43940.92180.66280.0629-0.0499-0.4877-0.67820.48010.4323-0.0015-0.08260.2298-0.0250.37254.048780.456-22.5731
362.89921.73812.36628.93110.99339.2037-0.2461-0.52310.6156-0.64660.09630.6152-0.5149-1.0180.06980.2759-0.0162-0.0250.26540.04820.21450.899773.7055-24.1983
377.2754-0.5106-0.31653.95060.77724.7542-0.10110.2479-0.2302-0.25250.1167-0.09940.2314-0.2199-0.02270.2316-0.04760.00760.16290.0390.1296.68463.662-25.0876
384.97491.3449-1.60591.52-0.28462.3554-0.3264-0.601-0.66710.01910.1109-0.09770.0659-0.00880.17710.20830.00240.0210.17850.05930.22727.09761.5741-15.227
395.08970.2759-0.056.07193.01766.695-0.0902-0.0889-0.07340.13420.09770.62980.1348-0.5964-0.04410.2151-0.03720.02780.23680.08530.177-6.046453.4297-4.2515
402.9999-0.83930.33414.538-0.12343.214-0.07020.03540.168-0.0310.09380.38-0.1171-0.5259-0.00420.1981-0.004-0.00550.22850.03660.1891-4.795758.0896-13.9477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 582 through 590 )
2X-RAY DIFFRACTION2chain 'A' and (resid 591 through 600 )
3X-RAY DIFFRACTION3chain 'A' and (resid 601 through 606 )
4X-RAY DIFFRACTION4chain 'A' and (resid 607 through 614 )
5X-RAY DIFFRACTION5chain 'A' and (resid 615 through 640 )
6X-RAY DIFFRACTION6chain 'A' and (resid 641 through 658 )
7X-RAY DIFFRACTION7chain 'B' and (resid 493 through 502 )
8X-RAY DIFFRACTION8chain 'B' and (resid 503 through 522 )
9X-RAY DIFFRACTION9chain 'B' and (resid 523 through 560 )
10X-RAY DIFFRACTION10chain 'B' and (resid 561 through 568 )
11X-RAY DIFFRACTION11chain 'B' and (resid 569 through 597 )
12X-RAY DIFFRACTION12chain 'C' and (resid 582 through 590 )
13X-RAY DIFFRACTION13chain 'C' and (resid 591 through 601 )
14X-RAY DIFFRACTION14chain 'C' and (resid 602 through 606 )
15X-RAY DIFFRACTION15chain 'C' and (resid 607 through 613 )
16X-RAY DIFFRACTION16chain 'C' and (resid 614 through 629 )
17X-RAY DIFFRACTION17chain 'C' and (resid 630 through 658 )
18X-RAY DIFFRACTION18chain 'D' and (resid 493 through 522 )
19X-RAY DIFFRACTION19chain 'D' and (resid 523 through 537 )
20X-RAY DIFFRACTION20chain 'D' and (resid 538 through 596 )
21X-RAY DIFFRACTION21chain 'E' and (resid 582 through 590 )
22X-RAY DIFFRACTION22chain 'E' and (resid 591 through 601 )
23X-RAY DIFFRACTION23chain 'E' and (resid 602 through 606 )
24X-RAY DIFFRACTION24chain 'E' and (resid 607 through 620 )
25X-RAY DIFFRACTION25chain 'E' and (resid 621 through 629 )
26X-RAY DIFFRACTION26chain 'E' and (resid 630 through 640 )
27X-RAY DIFFRACTION27chain 'E' and (resid 641 through 658 )
28X-RAY DIFFRACTION28chain 'F' and (resid 504 through 516 )
29X-RAY DIFFRACTION29chain 'F' and (resid 517 through 522 )
30X-RAY DIFFRACTION30chain 'F' and (resid 523 through 537 )
31X-RAY DIFFRACTION31chain 'F' and (resid 538 through 542 )
32X-RAY DIFFRACTION32chain 'F' and (resid 543 through 570 )
33X-RAY DIFFRACTION33chain 'F' and (resid 571 through 596 )
34X-RAY DIFFRACTION34chain 'G' and (resid 582 through 605 )
35X-RAY DIFFRACTION35chain 'G' and (resid 606 through 613 )
36X-RAY DIFFRACTION36chain 'G' and (resid 614 through 629 )
37X-RAY DIFFRACTION37chain 'G' and (resid 630 through 658 )
38X-RAY DIFFRACTION38chain 'H' and (resid 493 through 522 )
39X-RAY DIFFRACTION39chain 'H' and (resid 523 through 550 )
40X-RAY DIFFRACTION40chain 'H' and (resid 551 through 597 )

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