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- PDB-5m3j: Influenza B polymerase bound to four heptad repeats of serine 5 p... -

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Basic information

Entry
Database: PDB / ID: 5m3j
TitleInfluenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD
Components
  • DNA-directed RNA polymerase subunit
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*C)-3')
  • RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')
  • RNA-directed RNA polymerase catalytic subunit
KeywordsVIRAL PROTEIN / influenza B virus RNA-dependent RNA polymerase / vRNA promoter / Pol II serine 5 phosphorylated CTD peptide
Function / homology
Function and homology information


microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / cap snatching / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / PIWI-interacting RNA (piRNA) biogenesis / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / 7-methylguanosine mRNA capping / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / host cell mitochondrion / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / Inhibition of DNA recombination at telomere / positive regulation of RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / DNA-templated transcription termination / virion component / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / kinase binding / Formation of TC-NER Pre-Incision Complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-directed RNA polymerase activity / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / endonuclease activity / Estrogen-dependent gene expression / Hydrolases; Acting on ester bonds / transcription by RNA polymerase II / host cell cytoplasm / hydrolase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / host cell nucleus / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / 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 Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / 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, 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 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus
Similarity search - Domain/homology
RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLukarska, M. / Pflug, A. / Cusack, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council322586 France
CitationJournal: Nature / Year: 2017
Title: Structural basis of an essential interaction between influenza polymerase and Pol II CTD.
Authors: Lukarska, M. / Fournier, G. / Pflug, A. / Resa-Infante, P. / Reich, S. / Naffakh, N. / Cusack, S.
History
DepositionOct 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / ndb_struct_na_base_pair / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
R: RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*C)-3')
V: RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')
X: DNA-directed RNA polymerase subunit


Theoretical massNumber of molelcules
Total (without water)274,9706
Polymers274,9706
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41500 Å2
ΔGint-259 kcal/mol
Surface area90880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.160, 200.160, 250.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Polymerase acidic protein


Mass: 85822.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag C-terminal linker and TEV site / Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Strain: B/Memphis/13/2003 / Gene: PA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Z9
#2: Protein RNA-directed RNA polymerase catalytic subunit


Mass: 86207.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal linker C-terminal linker and TEV site / Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Strain: B/Memphis/13/2003 / Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2


Mass: 90844.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal linker C-terminal linker and TEV site / Source: (gene. exp.) Influenza B virus / Strain: B/Memphis/13/2003 / Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8X3

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RNA chain , 2 types, 2 molecules RV

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


Mass: 4321.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3' end vRNA promoter / Source: (synth.) Influenza B virus
#5: RNA chain RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')


Mass: 4557.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5' end vRNA promoter / Source: (synth.) Influenza B virus

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Protein/peptide , 1 types, 1 molecules X

#6: Protein/peptide DNA-directed RNA polymerase subunit


Mass: 3216.893 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Four heptad repeats of serine 5 phosphorylated Pol II CTD
Source: (synth.) Homo Sapiens (human)
References: UniProt: P24928*PLUS, DNA-directed RNA polymerase

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Details

Has protein modificationY

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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: 5.27 Å3/Da / Density % sol: 76.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: FluB polymerase in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP) was mixed with 5' and 3' ends of vRNA promoter and CTD ...Details: FluB polymerase in a buffer containing 500 mM NaCl, 50 mM Hepes pH 7.5, 5% glycerol and 2mM Tris(2-carboxyethyl)phosphine (TCEP) was mixed with 5' and 3' ends of vRNA promoter and CTD peptide. Reservoir solution contained 0.1 M bicine pH 9.0, 10% MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 73405 / % possible obs: 99.9 % / Redundancy: 8.54 % / CC1/2: 0.998 / Rmerge(I) obs: 0.191 / Net I/σ(I): 8.38
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 8.63 % / Rmerge(I) obs: 2.22 / Mean I/σ(I) obs: 1.02 / CC1/2: 0.547 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSA

4wsa


Resolution: 3.5→49.07 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 3520 4.8 %
Rwork0.2387 --
obs0.2401 73405 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17424 589 0 0 18013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218412
X-RAY DIFFRACTIONf_angle_d0.47224935
X-RAY DIFFRACTIONf_dihedral_angle_d12.38611201
X-RAY DIFFRACTIONf_chiral_restr0.0382762
X-RAY DIFFRACTIONf_plane_restr0.0033100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.54790.42771340.43422764X-RAY DIFFRACTION100
3.5479-3.59860.44541590.412733X-RAY DIFFRACTION100
3.5986-3.65230.42171420.38572771X-RAY DIFFRACTION100
3.6523-3.70930.40591650.37422746X-RAY DIFFRACTION100
3.7093-3.77010.41621240.35532776X-RAY DIFFRACTION100
3.7701-3.83510.34461510.33962753X-RAY DIFFRACTION100
3.8351-3.90480.32891210.32862801X-RAY DIFFRACTION100
3.9048-3.97990.34591380.30822767X-RAY DIFFRACTION100
3.9799-4.06110.30091360.28852772X-RAY DIFFRACTION100
4.0611-4.14930.30941420.28012775X-RAY DIFFRACTION100
4.1493-4.24580.25391510.26812783X-RAY DIFFRACTION100
4.2458-4.35190.33481350.25032754X-RAY DIFFRACTION100
4.3519-4.46950.23641410.2382775X-RAY DIFFRACTION100
4.4695-4.60090.23711420.21412770X-RAY DIFFRACTION100
4.6009-4.74930.22651590.20422777X-RAY DIFFRACTION100
4.7493-4.91890.25051230.20492818X-RAY DIFFRACTION100
4.9189-5.11570.25281160.20642803X-RAY DIFFRACTION100
5.1157-5.34820.22871360.20492819X-RAY DIFFRACTION100
5.3482-5.62980.22761390.20712819X-RAY DIFFRACTION100
5.6298-5.9820.23761410.21852796X-RAY DIFFRACTION100
5.982-6.44290.28671200.24382833X-RAY DIFFRACTION100
6.4429-7.08960.27771380.22042826X-RAY DIFFRACTION100
7.0896-8.11140.21551390.20552854X-RAY DIFFRACTION100
8.1114-10.20440.19341600.16242862X-RAY DIFFRACTION100
10.2044-49.07440.2641680.22272938X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5484-0.2068-0.57071.0320.54850.6850.34210.5343-0.6731-0.0079-0.65140.76510.7593-0.67540.35282.2914-0.2858-0.07762.2109-0.18231.6068-75.075626.6639-70.5096
22.70890.6816-0.7490.6289-0.6571.81880.81530.9683-1.85620.232-0.2513-0.89291.42491.493-1.04742.9368-0.3083-0.10482.8635-0.92591.9583-77.868318.474-80.3674
31.10640.5088-0.36660.38150.13331.35660.2237-0.03170.44540.2146-0.1310.0916-0.27330.2339-0.0741.2428-0.29620.05320.92250.00110.9441-51.4951.3187-14.2737
40.93740.4165-0.00340.0334-0.59281.11660.3167-0.27470.36380.4022-0.18190.4347-0.0629-0.0492-0.12571.8976-0.5810.36771.0297-0.25921.2401-67.022356.48042.7528
50.7226-0.4324-0.33430.20590.08961.32510.256-0.1173-0.16120.489-0.36660.45340.34360.21420.12241.4618-0.27390.04730.986-0.07061.2648-51.691628.672-14.8567
61.8882-0.1972-0.01051.8976-0.67822.01160.17290.9360.6411-0.13170.16070.20660.576-0.0572-0.28361.5476-0.18890.15541.44110.00661.0269-48.123543.8127-46.4969
71.1212-0.7336-0.50660.6561-0.07110.5550.1718-0.0936-0.3377-0.0312-0.34790.45740.4324-0.16220.12441.7514-0.33570.13821.2965-0.13521.138-58.694426.1542-18.3648
81.63881.2497-0.02922.64010.45981.0230.10760.01070.19590.0105-0.192-0.06380.38880.52840.09181.598-0.20210.13061.37080.03590.8224-37.535140.1781-24.1271
91.3981-0.1413-0.2970.013-0.09760.03960.3884-0.22890.30490.409-0.0880.65690.29920.1032-0.22932.1297-0.36890.12140.9671-0.14371.2794-61.054824.2755-6.3037
101.71341.04590.81971.5755-0.16261.66240.23220.0934-0.1710.6977-0.08540.36070.2492-0.6324-0.21741.4261-0.31720.36371.1002-0.00661.1958-83.89759.7785-22.7255
111.4757-0.242-1.12150.57870.86321.8683-0.10410.29020.499-0.3390.21080.4579-0.27140.3164-0.13061.5749-0.40010.01221.3620.21691.2747-70.49149.1727-52.0746
120.20180.1217-0.30631.0207-0.45720.88890.04560.190.11340.165-0.02670.53260.2696-0.1707-0.03091.4633-0.40560.141.1491-0.02041.2283-86.770137.42-29.6391
130.3187-0.4481-0.04521.1030.79740.70940.4547-0.15710.088-0.3657-0.5583-0.14220.05580.41730.04912.3308-0.32340.31791.32360.15011.2541-96.37843.7487-31.3191
141.45620.34270.84681.8293-0.81841.70960.3282-0.22450.06390.1489-0.22380.3116-0.07520.1893-0.07532.0382-0.69480.29351.2401-0.04441.1154-84.592716.924915.7197
153.81342.1912-1.59232.0813-1.64312.09230.5494-0.42521.6818-0.2028-0.4909-0.04640.66060.2967-0.04191.8085-0.34770.29621.70890.08392.1924-47.411469.7091-34.5202
160.4523-0.2235-0.29330.85620.35520.13370.4724-0.22840.45380.78-0.72660.1471-0.65430.76840.20421.7314-0.47420.10421.2002-0.08331.361-44.870662.7465-16.4348
173.24710.23283.25092.0010.4483.2796-0.1572-0.7116-0.44770.2212-1.0270.8725-0.6813-0.72051.00622.28-0.37060.69411.6637-0.52071.3182-81.734561.285213.065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 392 )
4X-RAY DIFFRACTION4chain 'A' and (resid 393 through 722 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 116 )
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 222 )
7X-RAY DIFFRACTION7chain 'B' and (resid 223 through 330 )
8X-RAY DIFFRACTION8chain 'B' and (resid 331 through 413 )
9X-RAY DIFFRACTION9chain 'B' and (resid 414 through 517 )
10X-RAY DIFFRACTION10chain 'B' and (resid 518 through 633 )
11X-RAY DIFFRACTION11chain 'B' and (resid 634 through 749 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 360 )
13X-RAY DIFFRACTION13chain 'C' and (resid 361 through 529 )
14X-RAY DIFFRACTION14chain 'C' and (resid 530 through 740 )
15X-RAY DIFFRACTION15chain 'R' and (resid 1 through 14 )
16X-RAY DIFFRACTION16chain 'V' and (resid 1 through 14 )
17X-RAY DIFFRACTION17chain 'X' and (resid 21 through 29 )

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