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- PDB-9bvt: RNA Pol II - High Mn(+2) concentration -

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Basic information

Entry
Database: PDB / ID: 9bvt
TitleRNA Pol II - High Mn(+2) concentration
Components
  • (DNA-directed RNA polymerase II subunit ...) x 6
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 3
  • (DNA-directed RNA polymerases II subunit ...) x 2
  • DNA (5'-D(P*AP*CP*GP*TP*CP*CP*CP*TP*CP*TP*CP*GP*A)-3')
  • DNA-directed RNA polymerase subunit beta
  • RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')
KeywordsTRANSCRIPTION / RNA Pol II - High Mn(+2) concentration
Function / homology
Function and homology information


: / : / : / : / : / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex ...: / : / : / : / : / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / ribosome biogenesis / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily ...DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RPB4 isoform 1 / RPC10 isoform 1 / RPB3 isoform 1 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase subunit beta ...: / DNA / DNA (> 10) / RNA / RPB4 isoform 1 / RPC10 isoform 1 / RPB3 isoform 1 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase subunit beta / RPB11 isoform 1 / RPB10 isoform 1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCalero, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)112686 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.
Authors: Lin, G. / Barnes, C.O. / Weiss, S. / Dutagaci, B. / Qiu, C. / Feig, M. / Song, J. / Lyubimov, A. / Cohen, A.E. / Kaplan, C.D. / Calero, G.
History
DepositionMay 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases II subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases II subunit RPABC4
X: RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')
W: DNA (5'-D(P*AP*CP*GP*TP*CP*CP*CP*TP*CP*TP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,03525
Polymers521,31014
Non-polymers72511
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)221.190, 393.970, 283.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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DNA-directed RNA polymerase II subunit ... , 6 types, 6 molecules ACDGIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0Z3
#4: Protein DNA-directed RNA polymerase II subunit RPB4


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTI6
#7: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q270
#9: Protein DNA-directed RNA polymerase II subunit RPB9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9EWC2
#11: Protein DNA-directed RNA polymerase II subunit RPB11


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7A1

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DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules EFH

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q456
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8C2

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DNA-directed RNA polymerases II subunit ... , 2 types, 2 molecules JL

#10: Protein DNA-directed RNA polymerases II subunit RPABC5


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7Q6
#12: Protein DNA-directed RNA polymerases II subunit RPABC4


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PY05

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Protein / RNA chain / DNA chain , 3 types, 3 molecules BXW

#13: RNA chain RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')


Mass: 3264.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA transcript / Source: (synth.) synthetic construct (others)
#14: DNA chain DNA (5'-D(P*AP*CP*GP*TP*CP*CP*CP*TP*CP*TP*CP*GP*A)-3')


Mass: 3887.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template / Source: (synth.) synthetic construct (others)
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q4H2, DNA-directed RNA polymerase

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Non-polymers , 4 types, 153 molecules

#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#16: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#17: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 5.92 Å3/Da / Density % sol: 76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Tacsimate Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.35→197 Å / Num. obs: 175204 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.92 / Net I/σ(I): 6.2
Reflection shellResolution: 3.35→3.65 Å / Num. unique obs: 10487 / CC1/2: 0.28

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→49.25 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 7425 4.94 %
Rwork0.2201 --
obs0.2215 150237 89.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30107 477 16 142 30742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331182
X-RAY DIFFRACTIONf_angle_d0.6742182
X-RAY DIFFRACTIONf_dihedral_angle_d17.5611886
X-RAY DIFFRACTIONf_chiral_restr0.0434758
X-RAY DIFFRACTIONf_plane_restr0.0055369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.440.4798410.4591851X-RAY DIFFRACTION16
3.44-3.480.42231440.41272643X-RAY DIFFRACTION50
3.48-3.520.48291070.47281909X-RAY DIFFRACTION36
3.52-3.570.42221500.40012783X-RAY DIFFRACTION53
3.57-3.610.38511820.39623434X-RAY DIFFRACTION65
3.61-3.660.43071620.39073587X-RAY DIFFRACTION67
3.66-3.710.41412050.37614925X-RAY DIFFRACTION91
3.71-3.770.37053050.35365270X-RAY DIFFRACTION99
3.77-3.830.37252860.34185303X-RAY DIFFRACTION100
3.83-3.890.33012740.32665306X-RAY DIFFRACTION100
3.89-3.960.39472740.33615277X-RAY DIFFRACTION100
3.96-4.030.28132740.27145316X-RAY DIFFRACTION100
4.03-4.110.33442780.28895335X-RAY DIFFRACTION100
4.11-4.190.28842800.27715247X-RAY DIFFRACTION99
4.19-4.280.28892600.2375338X-RAY DIFFRACTION100
4.28-4.380.25532910.21715287X-RAY DIFFRACTION100
4.38-4.490.22692920.2055329X-RAY DIFFRACTION100
4.49-4.610.22052820.20155315X-RAY DIFFRACTION100
4.61-4.750.22872800.20445311X-RAY DIFFRACTION100
4.75-4.90.23922990.20445339X-RAY DIFFRACTION100
4.9-5.080.22592750.20665321X-RAY DIFFRACTION100
5.08-5.280.24962790.20345301X-RAY DIFFRACTION99
5.28-5.520.24733170.21165319X-RAY DIFFRACTION100
5.52-5.810.26542630.21465374X-RAY DIFFRACTION100
5.81-6.180.2263090.21725318X-RAY DIFFRACTION100
6.18-6.650.26992400.21725438X-RAY DIFFRACTION100
6.65-7.320.23892560.20685394X-RAY DIFFRACTION100
7.32-8.370.21042670.17315440X-RAY DIFFRACTION100
8.37-10.530.17582870.14575407X-RAY DIFFRACTION99
10.53-49.250.20172660.1825395X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 108.0648 Å / Origin y: 51.3677 Å / Origin z: -1.3089 Å
111213212223313233
T0.9767 Å20.0205 Å20.058 Å2-0.9448 Å20.0312 Å2--1.1091 Å2
L0.4571 °2-0.0335 °2-0.0019 °2-0.5858 °2-0.0147 °2--0.3117 °2
S0.024 Å °0.0127 Å °0.2633 Å °0.2309 Å °-0.0373 Å °0.1251 Å °-0.1115 Å °-0.0365 Å °-0.0109 Å °
Refinement TLS groupSelection details: all

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