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- PDB-7dkh: Crystal structure of the Ctr9/Paf1/Cdc73/Rtf1 quaternary complex -

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Basic information

Entry
Database: PDB / ID: 7dkh
TitleCrystal structure of the Ctr9/Paf1/Cdc73/Rtf1 quaternary complex
Components
  • Cell division control protein 73
  • RNA polymerase II-associated protein 1
  • RNA polymerase-associated protein CTR9
  • RNA polymerase-associated protein RTF1
KeywordsGENE REGULATION / Paf1 complex / H2B mono-ubiquitination / Rad6/Bre1 / ubiquitin discharge
Function / homology
Function and homology information


: / : / : / snoRNA transcription by RNA polymerase II / : / : / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / sno(s)RNA 3'-end processing / regulation of transcription initiation by RNA polymerase II ...: / : / : / snoRNA transcription by RNA polymerase II / : / : / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / sno(s)RNA 3'-end processing / regulation of transcription initiation by RNA polymerase II / meiotic DNA double-strand break formation / RNA polymerase II C-terminal domain phosphoserine binding / triplex DNA binding / global genome nucleotide-excision repair / Cdc73/Paf1 complex / negative regulation of DNA recombination / rDNA heterochromatin formation / mRNA 3'-end processing / negative regulation of mitophagy / : / RNA polymerase II complex binding / transcription by RNA polymerase I / transcription by RNA polymerase III / transcription elongation by RNA polymerase I / transcription elongation by RNA polymerase II / DNA-templated transcription termination / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / euchromatin / rRNA processing / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleus
Similarity search - Function
Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal ...Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / RNA polymerase II associated factor Paf1 / Paf1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
RNA polymerase II-associated protein 1 / RNA polymerase-associated protein RTF1 / RNA polymerase-associated protein CTR9 / Cell division control protein 73
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsChen, F.L. / Liu, B.B. / Guo, L. / Li, D.F. / Zhou, H. / Long, J.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670758 China
National Natural Science Foundation of China (NSFC)31870750 China
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Crystal Structure of the Core Module of the Yeast Paf1 Complex.
Authors: Chen, F.L. / Liu, B.B. / Zeng, J.W. / Guo, L. / Ge, X. / Feng, W. / Li, D.F. / Zhou, H. / Long, J.F.
History
DepositionNov 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase-associated protein CTR9
B: RNA polymerase II-associated protein 1
C: Cell division control protein 73
D: RNA polymerase-associated protein RTF1
E: RNA polymerase-associated protein CTR9
F: RNA polymerase II-associated protein 1
G: Cell division control protein 73
H: RNA polymerase-associated protein RTF1
I: RNA polymerase-associated protein CTR9
J: RNA polymerase II-associated protein 1
K: Cell division control protein 73
L: RNA polymerase-associated protein RTF1


Theoretical massNumber of molelcules
Total (without water)420,73012
Polymers420,73012
Non-polymers00
Water00
1
A: RNA polymerase-associated protein CTR9
B: RNA polymerase II-associated protein 1
C: Cell division control protein 73
D: RNA polymerase-associated protein RTF1


Theoretical massNumber of molelcules
Total (without water)140,2434
Polymers140,2434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21220 Å2
ΔGint-135 kcal/mol
Surface area52890 Å2
MethodPISA
2
E: RNA polymerase-associated protein CTR9
F: RNA polymerase II-associated protein 1
G: Cell division control protein 73
H: RNA polymerase-associated protein RTF1


Theoretical massNumber of molelcules
Total (without water)140,2434
Polymers140,2434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20890 Å2
ΔGint-134 kcal/mol
Surface area53270 Å2
MethodPISA
3
I: RNA polymerase-associated protein CTR9
J: RNA polymerase II-associated protein 1
K: Cell division control protein 73
L: RNA polymerase-associated protein RTF1


Theoretical massNumber of molelcules
Total (without water)140,2434
Polymers140,2434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20960 Å2
ΔGint-137 kcal/mol
Surface area53100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.195, 190.195, 216.423
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein RNA polymerase-associated protein CTR9 / Centromere-binding factor 1-dependent protein 1 / Cln three-requiring protein 9


Mass: 113746.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: CTR9, CDP1, YOL145C / Production host: Escherichia coli (E. coli) / References: UniProt: P89105
#2: Protein RNA polymerase II-associated protein 1 / Protein PAF1


Mass: 11956.307 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PAF1, YBR279W, YBR2016 / Production host: Escherichia coli (E. coli) / References: UniProt: P38351
#3: Protein Cell division control protein 73 / RNA polymerase-associated protein CDC73


Mass: 6333.072 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: CDC73, YLR418C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06697
#4: Protein RNA polymerase-associated protein RTF1


Mass: 8207.274 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RTF1, CSL3, YGL244W, HRA458 / Production host: Escherichia coli (E. coli) / References: UniProt: P53064
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 8% tascimate, pH 6.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 97 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 2.9→48.96 Å / Num. obs: 100181 / % possible obs: 99.9 % / Redundancy: 31.2 % / Biso Wilson estimate: 73.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.044 / Rrim(I) all: 0.178 / Net I/σ(I): 17
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 1.756 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9841 / CC1/2: 0.794 / Rpim(I) all: 0.455 / Rrim(I) all: 1.815

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→48.96 Å / SU ML: 0.4021 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0631 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 5119 5.11 %
Rwork0.1926 95013 -
obs0.1954 100132 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.01 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27198 0 0 0 27198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004327674
X-RAY DIFFRACTIONf_angle_d0.936137277
X-RAY DIFFRACTIONf_chiral_restr0.04914167
X-RAY DIFFRACTIONf_plane_restr0.00624768
X-RAY DIFFRACTIONf_dihedral_angle_d23.688910648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.930.36721620.31013065X-RAY DIFFRACTION96.76
2.93-2.970.32481660.26983150X-RAY DIFFRACTION100
2.97-30.33421610.27023136X-RAY DIFFRACTION100
3-3.040.33731670.27463126X-RAY DIFFRACTION100
3.04-3.080.35491820.27793127X-RAY DIFFRACTION100
3.08-3.120.39471890.26583128X-RAY DIFFRACTION100
3.12-3.170.31932120.26863143X-RAY DIFFRACTION100
3.17-3.220.36521580.26843112X-RAY DIFFRACTION100
3.22-3.270.28751310.2543181X-RAY DIFFRACTION100
3.27-3.320.30221550.24623171X-RAY DIFFRACTION100
3.32-3.380.34091770.24453142X-RAY DIFFRACTION100
3.38-3.440.2691690.22723153X-RAY DIFFRACTION99.97
3.44-3.50.29121670.22953145X-RAY DIFFRACTION99.85
3.5-3.580.30351540.21423164X-RAY DIFFRACTION99.91
3.58-3.650.27061860.21433174X-RAY DIFFRACTION99.97
3.65-3.740.26661690.20553130X-RAY DIFFRACTION99.94
3.74-3.830.28071640.19163164X-RAY DIFFRACTION99.97
3.83-3.940.21871520.18133178X-RAY DIFFRACTION100
3.94-4.050.23431940.1783149X-RAY DIFFRACTION100
4.05-4.180.22181640.17133178X-RAY DIFFRACTION99.97
4.18-4.330.19771780.17173167X-RAY DIFFRACTION99.97
4.33-4.50.25211990.1693146X-RAY DIFFRACTION99.94
4.5-4.710.21181810.15473151X-RAY DIFFRACTION100
4.71-4.960.20331890.15133159X-RAY DIFFRACTION100
4.96-5.270.2321870.17093193X-RAY DIFFRACTION100
5.27-5.670.2741610.19463194X-RAY DIFFRACTION99.97
5.67-6.240.25621370.20483251X-RAY DIFFRACTION99.97
6.24-7.150.25391620.18163243X-RAY DIFFRACTION99.97
7.15-8.990.17491800.15263259X-RAY DIFFRACTION99.88
8.99-48.960.1871660.15873334X-RAY DIFFRACTION98.29
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)
15.27674820412-1.81129239866-0.687488033344.244840300973.589459356027.662439306090.1393199623360.3753733100540.04782727120540.252222911284-0.4621901587720.827541784170.504833776002-1.257370582760.2934791554170.621066969984-0.1026067690230.1220386791690.721419750149-0.1575449404011.31079788277-15.663585675771.547207090415.6300989559
22.047177823050.387624866150.1799738053353.186297676040.816795997731.231758437280.01804568996660.194451302997-0.5461297160460.132831454584-0.121786413550.3571834803140.199740228392-0.06436422381180.09750712704990.381721977490.03342076771240.0398763716960.438316014343-0.06517903714770.412329376718.8037336922196.265718877225.8377960083
32.783170891072.09538630479-0.09783631512254.952754968670.4766082379451.44748031148-0.1273724417860.4340035677210.439733871215-0.2930754192930.218730120736-0.263104642467-0.294637960120.267990515641-0.1069875524150.341505552333-0.0419189229222-0.0523100793090.5542257076950.1538778917730.54286404394540.926425327138.07217706933.9792462851
48.492737770880.358905142151.064656624221.009194280130.5240282097731.00223370859-0.0149315391509-0.2954116536390.5643795514030.430178895690.164722305965-0.3144590451690.1517259233720.181304850905-0.1613516534560.609007471363-0.0697015091465-0.1157151433260.510178767527-0.04358748784650.55279237880561.540177901140.05317164959.8822140824
51.24025909786-0.841972556918-1.579602900364.603082116891.543364042632.3616000515-0.418505103952-0.5226744492090.614474837950.5118265284920.833580086561-0.8274405197760.1554229952820.453166645373-0.4073606755940.724041012790.116823798618-0.4149708936790.933594934566-0.3873084262271.0155540211694.8007855669141.8930790666.3439746946
65.103247113065.296391658323.297768720558.792288321342.303700874622.42227030345-1.00033702737-1.201389881192.600160161270.4571135038360.1236362088040.370109726385-0.272023299139-0.2391952434230.6211234154510.716491881525-0.1684427698050.02657180607680.79431451406-0.2137017937860.76170683747765.8096705466143.05380304363.6867935236
72.754624345562.542932150055.004370193722.279024363434.451678710318.8954942839-0.7346393826210.4172103697130.233949574365-0.03117081818640.1038992795730.666645151124-0.1407831695381.314467954040.4135189657060.405826035684-0.138216813588-0.07761203416190.694514673340.1358170842880.80668874792546.506503314141.76600850742.9296743555
82.012344700962.1647494468-0.8306087822342.13673847707-0.9223320135910.347865542577-0.9474724658710.629572125921.10266246202-1.417036972680.5013184354160.881240638837-0.1135619873520.04946595472420.3163055024280.531242855335-0.0827195074879-0.1277251250950.5495513385010.1253039763120.48214110641226.56922077127.60249285925.8298470902
97.515268074965.425601025732.563541888477.041169025812.678809953921.362574982160.4257486553550.603610289797-0.5675966132170.976298800896-0.04332381624260.2753343696250.3781246438280.126798389345-0.363254200730.442430357629-0.001533445156690.01768313682140.499549828663-0.1262782778190.38537132149611.535326029198.808464500723.0688721079
104.459804883725.255929313022.833015641886.087754691853.306573493692.082863279260.4979225512490.290435290263-1.01226302561-0.28853924179-0.447429088932-0.2722070677420.5051474781640.0519552052959-0.02775751810710.799935539874-0.05173534395350.134628397860.59338540131-0.1123668858151.26830961898-3.5448316319367.883920318120.8276853704
115.63177180321-0.768276322168-0.9672733357127.316510165450.9054245022758.77259697863-0.4348855766490.377105877427-2.07166430463-0.3041617943551.02048462442-1.465746513650.8454682087551.09685846716-0.6438654393280.6495523236290.224920026498-0.08921904992340.767897066714-0.3374959117921.3526056086919.606993802873.240536883719.780541494
125.039982575133.61977912517-2.577487629133.19734887577-2.217072912217.151459087610.910313563322-0.0561891409071.80548700246-1.692423565390.3713928830510.999345748223-0.246121842877-1.43516399788-1.038133309351.204727377340.161211764420.05653568918861.135148867620.7727445143742.0421330689330.2408673742157.93529641132.35315584
133.443240325744.03005826853-3.800441626694.72390891202-4.441284909454.178971680670.1260151544460.707205110754-0.8308367816770.5443911438080.08054006920870.0973614754414-1.28038937609-0.68654675854-0.3972630988660.914362254736-0.00902474670126-0.1380524610830.9257733081910.251982311330.96877869069629.6726554628146.31580309626.6811288233
147.75354270623-0.6435902479874.758959612841.1162002361-0.7721596443.052387091670.04861683173660.3235010171070.6770786342480.298837054414-0.3067327291580.243279688794-0.01186508366460.235512959170.152729668460.477099761472-0.0935246003012-0.006328542616050.452650304354-0.0165068221120.57087278341940.0327985076133.63708994142.534237668
156.311965637852.64750205362.132984363044.886396947864.771156002954.722148633330.0242715085718-1.1259531439-0.4124620713312.4993044197-1.135450616650.8385069150271.34623563735-0.117038608950.8481321588920.98403687499-0.1841102799840.05369707153830.785282311320.1341992404950.67722788599741.955690684128.31148845365.3980079504
166.50262169863-6.10736951692-5.040440449755.769060701934.75005100133.903597413960.09703619613-2.321934364520.066801220662.54536322318-0.3838536984970.8074197956551.312273674380.3148350869940.2151428922721.19447791477-0.4564954560210.0751510385521.33443232984-0.01161867040640.67877361294243.7019291046136.08185600475.2403225273
173.64339275794-1.937677612-1.08226398391.0329277320.5806846277530.3123044483030.0922487089698-0.5848060171880.739887252179-1.3158358949-0.111714254836-1.20352836907-0.05227189922030.745607000673-0.04726038928611.124032825810.1063199335720.2329461689481.395096084-0.121847720741.4204456521358.752470336688.76745326118.39753903246
185.22624876298-7.411767339440.5877250069822.0194098551-0.8495800187470.5746994526470.656317384476-2.655626977690.222173692638-0.8779017886830.346485624789-0.8681540679630.3487404018261.76664226141-0.8179224619060.702765264460.08057432180990.02428495659031.37369370441-0.06192939265291.0974886464141.847659038100.29083241611.9161389152
195.171213880293.562897649632.214775172023.384428977911.64354942585.64009002444-0.1292257591091.679471336340.258007669739-0.7926634055810.1214841276050.220142681113-0.277152752984-0.0169332973610.02580119635990.6750475354410.111964055343-0.04007019048930.896370870856-0.03658452995950.35599593061616.2912831707110.2370229929.22979449579
203.9837870921-0.2545582253671.303828772158.790248608142.128276652342.48030608665-0.252329448382-0.3802896910980.817596394343-1.29003019673-0.1159659817271.24800273997-0.801011725618-0.2507061197750.2680484872080.77566511563-0.0218468931848-0.2921572442670.6179072657610.00319817533840.8896626152962.4981203734190.38628901126.644849531
211.84494818115-0.6824599033870.8762986744334.22955467475-1.415442934942.82339680012-0.09529182060450.1881129483070.40812153502-0.269345400386-0.0250753520846-0.109073655355-0.1107657348710.1944494871520.122814490220.383878356345-0.1188052898640.009636324741620.5201130096980.03940414319690.43289916572582.0991240132156.47406984425.3327861781
223.06186740909-2.656533548710.6193503135466.4870660397-0.4161938933951.381632597120.2081368201950.433642783206-0.333096402002-1.22646608608-0.0449335384385-0.2387139421240.4992386095590.102144010727-0.1377754922150.836198928064-0.134510504110.1316560315510.609177879687-0.06340519540010.5067134613893.2439019521116.01816097727.882623714
233.630320443410.52533848068-3.290378024721.249338092880.2517068337473.52375712394-0.0142795357123-0.7589600162910.040706071163-0.1515729078430.376949118462-0.7919480464610.4456641696870.702204646717-0.3413534257060.7658028364620.1338370184110.01644752163060.75673553659-0.2590823639130.919770931461108.454722245110.16042056148.6780085446
242.535758149461.44876139759-0.4692862804574.28781205302-0.1908422697070.9423403032340.211532023928-0.708415804102-0.6597714698390.515349639714-0.05999016529940.141532727210.389890014123-0.0182538482798-0.1217207315660.95429341455-0.0517533266513-0.03059289054340.706734029950.1927001697190.65312571361481.700914051688.188022478961.824206087
253.68283453369-0.1629023635430.7383808039532.20602733515-1.276989741510.8787845348160.1599774322740.273003633072-0.4744745223390.04085467871920.209704686973-0.184017315487-0.5286084795960.32381227065-0.3983483517011.054440250770.0767032506111-0.09048249208950.617653187216-0.09111566377570.61151709987887.958900862994.908560122362.6211537941
262.32199725884-2.97985434385-0.5430157412353.549125957720.5922209378760.322428315848-0.03504442597620.4281278011020.132024460472-1.04239637266-0.477890119233-1.59867692250.614270944133-0.1645083451140.5156224441530.716122612233-0.147587509150.07857086425290.4679621779750.004182884528830.57331405279694.0159985401126.19753891431.2474019576
274.807961387234.46229421141-1.828480354775.78563869799-1.290888516320.846940711585-0.216801352360.677514967309-0.136920708118-0.7285007470720.05011538388740.451445977726-0.00103132150832-0.1717039348360.1184451014310.458135222237-0.0757644764811-0.07029976304680.4720589390.05002078173970.44028331023578.5719993006154.15348306623.2420973964
286.61594450036-4.83329869318-5.294005587213.768279512524.226661441364.78078134388-0.612010707023-0.3761871728060.727706624526-0.6880061290440.4839983793441.10036014859-0.5806687235450.377445840705-0.02729226135980.513759760211-0.0371364765442-0.102782432960.5708487354410.1981740163320.68965356762572.7648240633172.02817211325.4735520249
294.37695866786-4.981462532334.766058121215.66641137999-5.426802524365.19931995164-0.384197708014-0.1692135793050.973739239088-0.407337824134-0.1113604097771.46824633631-0.524498416488-0.780553620010.3035447655560.585146217203-0.334243096292-0.2313310471190.5649603182830.1914499025521.3573667644167.2503550919176.70064869325.3928978505
309.07992505645-5.63941735793-0.9900282661863.912135579752.268304309266.608477747160.1115601204020.7991243305870.878674087159-1.67775666572-0.7838523566311.46970988054-1.32773098694-0.5308245816910.6225824999621.076666069370.0252720707423-0.5203355570080.6792276470160.08191003510751.6362679350157.6019854668191.95928392624.1026838558
316.751809511694.04517445893-0.5411346269926.43931256739-4.384455235754.13737580082-0.381282611669-0.6645555691541.51199571455-1.11377421707-0.45220654832.85245196528-1.62548394802-2.793085209820.8744765416830.7567696512940.281099994243-0.4424555631740.957678918406-0.1965697221831.7107966890150.3303840287186.61944894627.9650452435
328.949673233231.17071476423-1.875094964023.267272939770.7409231670228.52801706361-0.451555003457-0.973357677204-0.479108787736-1.03257174672-0.213953785821.794179437540.24937690802-1.679149317560.4424664757070.686684599043-0.132761118267-0.3785950636110.9589714169390.09070826266341.5609687442248.791713069167.7573519822.2643910674
332.5963111988-1.699380372153.367304664472.23616116507-1.922536356384.613656363390.2966214402271.78057227533-0.1833722994910.195165151703-1.020488243280.00661194869362-0.224550187683-0.7611224884110.574153027051.473880130890.2103788813031.192926385091.686966677810.08687966492732.30687722515116.587091365117.11115333531.0485701364
346.75415585624-0.783879090328-4.998464583682.943466327831.648233233589.12487536036-0.455980098541.26599101489-0.0421092203855-0.672072059665-0.0469593314843-0.761047695290.502641610280.5885879784270.5965656513061.07100813665-0.219764983690.5569737246040.9391984780110.0819928999731.19336616533109.836073498122.76103814624.9098016986
357.383116756876.93097133887-6.932571340116.42449520201-6.515943970516.53145454836-0.652952959523-0.216891603363-0.572604759532-1.69733984676-0.101012914815-1.423224284341.25222876740.9123561806380.7143918934550.9084359312940.007144225428810.2164758044560.5198207415050.03408221888130.83183260878399.5883957456121.87503661334.2886901194
367.436871485-1.943029500213.22780307127.771375689325.010762771469.036419571250.251209040598-0.7029515990450.9579425483080.8359771007970.04570262836110.4828293202980.0919829000768-0.740632076196-0.2950575902250.638782234505-0.1799649122760.2223155388850.465585886236-0.05898249381720.60973386647486.7052063367119.63248661156.7280548234
373.56135471058-2.010929517795.67024375031.24843401113-3.204793630689.00264212125-0.211414049056-1.992401231250.4799073634222.587725759060.0246720094308-0.577313715561-1.37314217949-1.867734416430.17880693021.87394715350.00406028484904-0.07235195825411.05850614924-0.1065807068410.82453744897393.6504608445115.9168721274.8092210422
382.92493660979-2.22414318599-4.294445132859.81483124859-0.6146061102898.1282464499-0.03718425028041.39627563314-1.737216555110.391979988624-0.735164973119-0.07515365361290.900360774541-0.9150553144280.5190511512732.122571902010.06105734374160.07559432617421.59666019015-0.521467856131.7049483495543.0020708819128.7568830778.6069569301
398.228805013290.169288721039-3.145923787361.57956847859-1.33390189232.199607369620.6931398587590.744911529769-1.338218947871.37182868221-0.1878140693010.03712011391160.5881256364-0.684204324626-0.3130780834821.15111733992-0.296877100054-0.1768763172111.003895555330.06251672003771.102760466560.7638666331135.76913797312.3845557245
408.52215309671.769918412081.416766259174.15471362157-3.44485952883.88032459928-0.7001792903220.524633991545-0.251386458256-1.877632720640.4080668188230.1016821123490.5975981691170.2641917415710.133280143430.804385055689-0.117277220080.002730558973530.5998523711280.002915372251670.53304297691680.1370383729145.89593775312.6820341346
410.4791498056190.903680426222-1.166492560037.77535676898-3.491905462823.13006038792-0.8019116731681.455727346210.408638080315-2.501653779151.46801448534-0.0167187168707-0.8831279001450.870860352988-0.5840930537281.2123710523-0.33975804390.08572793788671.034039173020.3024993902070.8281342550284.8883414166163.3618129684.73044357801
426.138156407360.604176767445-1.922500982345.18902061917-1.872446315086.05702238333-0.198328249222-0.206779907528-1.20653940075-0.543048108421-0.119395210705-0.2866773690980.9472744449190.8577560026760.2921008821080.7002150792030.1579898669520.22118153530.5998302600530.07705192520661.05994579119136.08269629164.984914357517.2878963056
435.475953899130.489069944938-1.105238143251.31332023379-0.08777547554730.9768255979530.0915630687733-0.209014412375-0.246638850104-0.157371533769-0.137766887009-0.31995520370.08416206642120.1694842144020.050358700360.557770026875-0.01393521915940.05985358649020.3700389319490.06996880509440.33585329937102.38002882474.450384905326.3437830731
448.528044769210.387984565264-0.3470471748720.7081080176760.2163896720891.337746146640.2115545792520.7973322853350.586303850474-0.172156181377-0.1036899623410.530606933995-0.271011584028-0.255467361617-0.109606842910.6047337311510.0681757155318-0.01959939141690.474856030605-0.00245720027070.73363804512853.229227436483.567693902929.1510850282
450.934571665566-0.204784139666-0.6980034848512.8869278430.8767784910265.10071517572-0.156210067449-0.185152191508-0.1034778080240.915603694926-0.238323068726-0.369435420352-0.110052772096-0.1868848933160.429553028720.8075488521090.0409003170995-0.2666468806930.512181460320.09928268075670.99156183050440.952849236980.206435865256.3011614988
463.20697490492-1.576832745680.08677040762454.131916048091.214885706741.790478138910.164471672857-0.386115443711-0.2855960495770.793375982097-0.1639260725760.02337560819870.443928785994-0.210192758152-0.005936074387640.848171434436-0.02150907742620.07191945781460.5755407438930.1370730676390.38747519271625.5439339307108.09232006358.65153002
476.215140346386.00216360359-1.373613173136.47357842035-2.16172934321.726388262360.373786254-0.02993599475691.406588161171.941958666560.4077044663351.86604238061-0.243024845031-0.222505428083-0.7271316468350.9446001320360.06944617424930.3454251591810.816677906454-0.009262936633720.74270017227819.2753131504135.70438848265.1065334228
488.38568812136-2.099064546845.275465390719.93278855049-3.887779424064.491946831460.406498336729-0.375265481147-0.5837113003341.695969272160.698589419615-0.03213813200220.464427384746-0.123337499053-0.8927067758461.079175752290.0624307877288-0.1481915740280.6304107361090.2034717278270.68129849307830.300726008998.738356696762.1164075733
497.45691618347-0.860678570056-0.4098464345991.141947457530.5783075773062.70384064933-0.2163365333820.991376200920.103229599750.110040232636-0.7087693673610.223414893671-0.260758225048-0.2773918992250.8448833275950.5294351334240.129620917067-0.03555406740690.5475449992070.05015575841151.2081520338348.072646047181.491714926336.7473400855
504.56801170829-3.267863214934.269768455135.60598980045-0.2133787924926.52006156191-0.4526472585742.9274350954-0.997690303278-0.283043892322-0.3809563143591.01933513748-0.284974807084-0.8629941250930.6860843550310.596577094875-0.0811133465613-0.03495247559910.982366460483-0.1057764782930.50838461134572.097457363172.667166630624.1413122691
516.28154893477-0.107110985666-0.3227414875611.09251967350.3496915175920.5284762525990.3123073946780.126724457326-0.151621736039-0.135107643125-0.204365952517-0.353981213429-0.01713365588860.0905602412181-0.1450547467780.4951609677580.0005848301101430.1010126537940.4575450270040.06064015652410.379838764143103.86075861975.302210242523.0120833154
525.37515280401-6.81634689441-1.379858700359.026875721531.052269711762.442799843020.325455682013-0.7331803114771.32755218565-0.212764048367-0.274951014742-1.93974731185-0.214088822811.220273131480.01372695568070.516449154978-0.1037248131370.07228196173150.6542000116370.04500173951390.924455843899135.79629909378.778374795623.3084596382
536.55204357062-0.1769423965290.4566249855642.64182916854-0.6217722145817.896677953270.7457714763930.4800273564822.59761853910.12575839865-0.282207279277-0.619886392037-1.35347223544-0.0662244915385-0.4385181952660.774727337107-0.1371170085170.2386898972130.443790782352-0.04597247207731.14598097723117.70843733595.177393105621.2895400309
543.00232461017-1.221344573582.202938857983.41383936028-2.993764764293.13428723858-0.4039324480670.145648108973-0.803701251709-0.8485075699710.5924724061150.9974127931160.658939471023-0.139446804395-0.2683322443570.657186214411-0.0263844507321-0.1325451004860.652758372215-0.2229525304871.4196722033643.482474106364.459855200226.5577579808
551.89307436036-1.09245204181-2.86396928542.483095269431.80799408777.13004643330.3503154305230.623667612241-0.54016088430.0272828386669-0.132754773514-0.4072774223750.769764766017-0.391950651065-0.1636022917630.6221343385410.12893544762-0.1005377060250.6357809871110.05732343845661.2298641691151.610574824675.008329862433.8010785345
561.89050193835-0.2992653446760.09354102642612.741066273221.075390524532.79751858191-0.43261274712-0.374438902283-0.07905686316561.23194671643-0.517139218749-1.08327626142-0.1072747433571.353945139890.7645444729191.05222727269-0.0313796983259-0.5379818328210.7276178437140.2252637654991.2166120341652.860386890185.469702949961.259091973
57-0.07674423876030.0897426172546-0.06382051231330.0490225040201-0.0900143384985-0.160030975242-0.0650324074006-0.380142851388-0.0796639410827-2.05525446684-0.2341196900990.736356417131-0.21543764403-0.177172751060.2759677573951.44722373764-0.00810772959594-0.156343703911.246678136420.2342434768940.90224314643483.8363212738108.08249527410.7916191893
582.57406317008-3.39231965563-1.44954458157.69959599632-2.810658336598.906795378310.2069980646011.02233402052-1.00628800552-1.87470281124-0.3544272157760.2939271222830.22601261082-0.4416761183090.1931766473770.792168345499-0.1095780924510.05071196732650.885078031527-0.1108378517980.5622805384786.727696305275.10310185829.23037191249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 430 )
3X-RAY DIFFRACTION3chain 'A' and (resid 431 through 646 )
4X-RAY DIFFRACTION4chain 'A' and (resid 647 through 834 )
5X-RAY DIFFRACTION5chain 'A' and (resid 835 through 922 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 14 )
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 24 )
8X-RAY DIFFRACTION8chain 'B' and (resid 25 through 39 )
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 84 )
11X-RAY DIFFRACTION11chain 'B' and (resid 85 through 103 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 7 )
13X-RAY DIFFRACTION13chain 'C' and (resid 8 through 15 )
14X-RAY DIFFRACTION14chain 'C' and (resid 16 through 35 )
15X-RAY DIFFRACTION15chain 'C' and (resid 36 through 45 )
16X-RAY DIFFRACTION16chain 'C' and (resid 46 through 53 )
17X-RAY DIFFRACTION17chain 'D' and (resid 18 through 26 )
18X-RAY DIFFRACTION18chain 'D' and (resid 27 through 43 )
19X-RAY DIFFRACTION19chain 'D' and (resid 44 through 68 )
20X-RAY DIFFRACTION20chain 'E' and (resid 10 through 233 )
21X-RAY DIFFRACTION21chain 'E' and (resid 234 through 454 )
22X-RAY DIFFRACTION22chain 'E' and (resid 455 through 600 )
23X-RAY DIFFRACTION23chain 'E' and (resid 601 through 646 )
24X-RAY DIFFRACTION24chain 'E' and (resid 647 through 922 )
25X-RAY DIFFRACTION25chain 'F' and (resid 5 through 15 )
26X-RAY DIFFRACTION26chain 'F' and (resid 16 through 39 )
27X-RAY DIFFRACTION27chain 'F' and (resid 40 through 55 )
28X-RAY DIFFRACTION28chain 'F' and (resid 56 through 60 )
29X-RAY DIFFRACTION29chain 'F' and (resid 61 through 65 )
30X-RAY DIFFRACTION30chain 'F' and (resid 66 through 80 )
31X-RAY DIFFRACTION31chain 'F' and (resid 81 through 85 )
32X-RAY DIFFRACTION32chain 'F' and (resid 86 through 103 )
33X-RAY DIFFRACTION33chain 'G' and (resid 3 through 7 )
34X-RAY DIFFRACTION34chain 'G' and (resid 8 through 12 )
35X-RAY DIFFRACTION35chain 'G' and (resid 13 through 24 )
36X-RAY DIFFRACTION36chain 'G' and (resid 25 through 45 )
37X-RAY DIFFRACTION37chain 'G' and (resid 46 through 53 )
38X-RAY DIFFRACTION38chain 'H' and (resid 18 through 26 )
39X-RAY DIFFRACTION39chain 'H' and (resid 27 through 43 )
40X-RAY DIFFRACTION40chain 'H' and (resid 44 through 59 )
41X-RAY DIFFRACTION41chain 'H' and (resid 60 through 68 )
42X-RAY DIFFRACTION42chain 'I' and (resid 10 through 133 )
43X-RAY DIFFRACTION43chain 'I' and (resid 134 through 430 )
44X-RAY DIFFRACTION44chain 'I' and (resid 431 through 600 )
45X-RAY DIFFRACTION45chain 'I' and (resid 601 through 730 )
46X-RAY DIFFRACTION46chain 'I' and (resid 731 through 875 )
47X-RAY DIFFRACTION47chain 'I' and (resid 876 through 923 )
48X-RAY DIFFRACTION48chain 'J' and (resid 5 through 14 )
49X-RAY DIFFRACTION49chain 'J' and (resid 15 through 29 )
50X-RAY DIFFRACTION50chain 'J' and (resid 30 through 39 )
51X-RAY DIFFRACTION51chain 'J' and (resid 40 through 70 )
52X-RAY DIFFRACTION52chain 'J' and (resid 71 through 84 )
53X-RAY DIFFRACTION53chain 'J' and (resid 85 through 103 )
54X-RAY DIFFRACTION54chain 'K' and (resid 3 through 12 )
55X-RAY DIFFRACTION55chain 'K' and (resid 13 through 24 )
56X-RAY DIFFRACTION56chain 'K' and (resid 25 through 53 )
57X-RAY DIFFRACTION57chain 'L' and (resid 18 through 43 )
58X-RAY DIFFRACTION58chain 'L' and (resid 44 through 68 )

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  • 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

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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

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