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- EMDB-13831: Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound... -

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Basic information

Entry
Database: EMDB / ID: EMD-13831
TitleCryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene
Map dataCryo-EM map of Ty3 intasome targeting RNA Pol III transcribed gene
Sample
  • Complex: Ty3 retrotransposon engaged with TFIIIB transcription factor and tRNA promoter
    • Complex: DNA
      • DNA: DNA (56-MER)
      • DNA: DNA (31-MER)
      • DNA: DNA (34-MER)
      • DNA: DNA (9-MER)
      • DNA: DNA (19-MER)
    • Complex: TFIIIB transcription factor
      • Protein or peptide: Transposon Ty3-G Gag-Pol polyprotein
      • Protein or peptide: Transcription factor TFIIIB component B''
      • Protein or peptide: TATA-box-binding protein
      • Protein or peptide: Transcription factor IIIB 70 kDa subunit
Function / homology
Function and homology information


retrotransposon nucleocapsid / RNA polymerase III core binding / retrotransposition / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding ...retrotransposon nucleocapsid / RNA polymerase III core binding / retrotransposition / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity / regulation of transcription by RNA polymerase III / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / DNA binding, bending / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / RNA polymerase II transcribes snRNA genes / ribonuclease H / 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 / RNA Polymerase II Pre-transcription Events / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / RNA nuclease activity / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / DNA-templated transcription initiation / DNA integration / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / disordered domain specific binding / RNA-DNA hybrid ribonuclease activity / peptidase activity / DNA-binding transcription factor binding / DNA recombination / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Peptidase A2B, Ty3 transposon peptidase / Ty3 transposon peptidase / Ty3 transposon capsid-like protein / Ty3 transposon capsid-like protein / Transcription factor TFIIIB component B'', fungi / Brf1, TBP-binding domain / Brf1-like TBP-binding domain / Transcription factor TFIIIB component B'', Myb domain / Myb DNA-binding like / Integrase zinc-binding domain ...Peptidase A2B, Ty3 transposon peptidase / Ty3 transposon peptidase / Ty3 transposon capsid-like protein / Ty3 transposon capsid-like protein / Transcription factor TFIIIB component B'', fungi / Brf1, TBP-binding domain / Brf1-like TBP-binding domain / Transcription factor TFIIIB component B'', Myb domain / Myb DNA-binding like / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Homeobox-like domain superfamily / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
TATA-box-binding protein / Transcription factor IIIB 70 kDa subunit / Transcription factor TFIIIB component B'' / Transposon Ty3-G Gag-Pol polyprotein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsAbascal-Palacios G / Jochem L / Pla-Prats C / Beuron F / Vannini A
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Cancer Research UKCR-UK C47547/A21536 United Kingdom
Wellcome Trust200818/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of Ty3 retrotransposon integration at RNA Polymerase III-transcribed genes.
Authors: Guillermo Abascal-Palacios / Laura Jochem / Carlos Pla-Prats / Fabienne Beuron / Alessandro Vannini /
Abstract: Retrotransposons are endogenous elements that have the ability to mobilise their DNA between different locations in the host genome. The Ty3 retrotransposon integrates with an exquisite specificity ...Retrotransposons are endogenous elements that have the ability to mobilise their DNA between different locations in the host genome. The Ty3 retrotransposon integrates with an exquisite specificity in a narrow window upstream of RNA Polymerase (Pol) III-transcribed genes, representing a paradigm for harmless targeted integration. Here we present the cryo-EM reconstruction at 4.0 Å of an active Ty3 strand transfer complex bound to TFIIIB transcription factor and a tRNA gene. The structure unravels the molecular mechanisms underlying Ty3 targeting specificity at Pol III-transcribed genes and sheds light into the architecture of retrotransposon machinery during integration. Ty3 intasome contacts a region of TBP, a subunit of TFIIIB, which is blocked by NC2 transcription regulator in RNA Pol II-transcribed genes. A newly-identified chromodomain on Ty3 integrase interacts with TFIIIB and the tRNA gene, defining with extreme precision the integration site position.
History
DepositionNov 3, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateJan 26, 2022-
Current statusJan 26, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7q5b
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13831.png

Downloads & links

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Map

FileDownload / File: emd_13831.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Ty3 intasome targeting RNA Pol III transcribed gene
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 304 pix.
= 322.24 Å		1.06 Å/pix.
x 304 pix.
= 322.24 Å		1.06 Å/pix.
x 304 pix.
= 322.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.044251382 - 0.10186844
Average (Standard dev.)0.00025617518 (±0.0025739507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 322.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z322.240322.240322.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-0.0440.1020.000

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Supplemental data

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Sample components

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Entire : Ty3 retrotransposon engaged with TFIIIB transcription factor and ...

EntireName: Ty3 retrotransposon engaged with TFIIIB transcription factor and tRNA promoter
Components
  • Complex: Ty3 retrotransposon engaged with TFIIIB transcription factor and tRNA promoter
    • Complex: DNA
      • DNA: DNA (56-MER)
      • DNA: DNA (31-MER)
      • DNA: DNA (34-MER)
      • DNA: DNA (9-MER)
      • DNA: DNA (19-MER)
    • Complex: TFIIIB transcription factor
      • Protein or peptide: Transposon Ty3-G Gag-Pol polyprotein
      • Protein or peptide: Transcription factor TFIIIB component B''
      • Protein or peptide: TATA-box-binding protein
      • Protein or peptide: Transcription factor IIIB 70 kDa subunit

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Supramolecule #1: Ty3 retrotransposon engaged with TFIIIB transcription factor and ...

SupramoleculeName: Ty3 retrotransposon engaged with TFIIIB transcription factor and tRNA promoter
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#9

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Supramolecule #2: DNA

SupramoleculeName: DNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #9
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: TFIIIB transcription factor

SupramoleculeName: TFIIIB transcription factor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#8
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: DNA (56-MER)

MacromoleculeName: DNA (56-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 17.165039 KDa
SequenceString: (DG)(DA)(DG)(DC)(DC)(DC)(DG)(DT)(DA)(DA) (DT)(DA)(DC)(DA)(DA)(DC)(DA)(DG)(DA)(DT) (DT)(DT)(DT)(DT)(DT)(DC)(DT)(DC)(DT) (DT)(DA)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DA) (DT) (DT)(DT)(DT)(DT)(DA)(DT) ...String:
(DG)(DA)(DG)(DC)(DC)(DC)(DG)(DT)(DA)(DA) (DT)(DA)(DC)(DA)(DA)(DC)(DA)(DG)(DA)(DT) (DT)(DT)(DT)(DT)(DT)(DC)(DT)(DC)(DT) (DT)(DA)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DA) (DT) (DT)(DT)(DT)(DT)(DA)(DT)(DA)(DT) (DT)(DT)(DC)(DG)(DT)(DC)(DG)(DA)

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Macromolecule #2: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 9.484193 KDa
SequenceString:
(DG)(DA)(DG)(DC)(DC)(DC)(DG)(DT)(DA)(DA) (DT)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DA)(DA) (DT)(DC)(DC)(DA)(DA)(DC)(DA)(DA)(DA) (DT)(DA)

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Macromolecule #3: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 10.532895 KDa
SequenceString:
(DT)(DC)(DG)(DA)(DC)(DG)(DA)(DA)(DA)(DT) (DA)(DT)(DA)(DA)(DA)(DA)(DA)(DT)(DT)(DT) (DA)(DA)(DA)(DA)(DC)(DT)(DA)(DA)(DG) (DA)(DG)(DA)(DA)(DA)

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Macromolecule #4: DNA (9-MER)

MacromoleculeName: DNA (9-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 2.751818 KDa
SequenceString:
(DT)(DA)(DT)(DT)(DT)(DG)(DT)(DT)(DG)

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Macromolecule #9: DNA (19-MER)

MacromoleculeName: DNA (19-MER) / type: dna / ID: 9 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 5.882792 KDa
SequenceString:
(DG)(DG)(DT)(DG)(DT)(DT)(DG)(DT)(DA)(DT) (DT)(DA)(DC)(DG)(DG)(DG)(DC)(DT)(DC)

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Macromolecule #5: Transposon Ty3-G Gag-Pol polyprotein

MacromoleculeName: Transposon Ty3-G Gag-Pol polyprotein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 178.556016 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML NMSMISWPND ASRIVYCRRH LLNPAAQWAN DFVQEQGIL EITFDTFIQG LYQHFYKPPD INKIFNAITQ LSEAKLGIER LNQRFRKIWD RMPPDFMTEK AAIMTYTRLL T KETYNIVR ...String:
MSFMDQIPGG GNYPKLPVEC LPNFPIQPSL TFRGRNDSHK LKNFISEIML NMSMISWPND ASRIVYCRRH LLNPAAQWAN DFVQEQGIL EITFDTFIQG LYQHFYKPPD INKIFNAITQ LSEAKLGIER LNQRFRKIWD RMPPDFMTEK AAIMTYTRLL T KETYNIVR MHKPETLKDA MEEAYQTTAL TERFFPGFEL DADGDTIIGA TTHLQEEYDS DYDSEDNLTQ NGYVHTVRTR RS YNKPMSN HRNRRNNNPS REECIKNRLC FYCKKEGHRL NECRARKAVL TDLELESKDQ QTPFIKTLPI VHYIAIPEMD NTA EKTIKI QNTKVKTLFD SGSPTSFIRR DIVELLKYEI YETPPLRFRG FVATKSAVTS EAVTIDLKIN DLHITLAAYI LDNM DYQLL IGNPILRRYP KILHTVLNTR ESPDSLKPKT YRSETVNNVR TYSAGNRGNP RNIKLSFAPT ILEATDPKSA GNRGD SRTK TLSLATTTPA AIDPLTTLDN PGSTQSTFAQ FPIPEEASIL EEDGKYSNVV STIQSVEPNA TDHSNKDTFC TLPVWL QQK YREIIRNDLP PRPADINNIP VKHDIEIKPG ARLPRLQPYH VTEKNEQEIN KIVQKLLDNK FIVPSKSPCS SPVVLVP KK DGTFRLCVDY RTLNKATISD PFPLPRIDNL LSRIGNAQIF TTLDLHSGYH QIPMEPKDRY KTAFVTPSGK YEYTVMPF G LVNAPSTFAR YMADTFRDLR FVNVYLDDIL IFSESPEEHW KHLDTVLERL KNENLIVKKK KCKFASEETE FLGYSIGIQ KIAPLQHKCA AIRDFPTPKT VKQAQRFLGM INYYRRFIPN CSKIAQPIQL FICDKSQWTE KQDKAIDKLK DALCNSPVLV PFNNKANYR LTTDASKDGI GAVLEEVDNK NKLVGVVGYF SKSLESAQKN YPAGELELLG IIKALHHFRY MLHGKHFTLR T DHISLLSL QNKNEPARRV QRWLDDLATY DFTLEYLAGP KNVVADAISR AVYTITPETS RPIDTESWKS YYKSDPLCSA VL IHMKELT QHNVTPEDMS AFRSYQKKLE LSETFRKNYS LEDEMIYYQD RLVVPIKQQN AVMRLYHDHT LFGGHFGVTV TLA KISPIY YWPKLQHSII QYIRTCVQCQ LIKSHRPRLH GLLQPLPIAE GRWLDISMDF VTGLPPTSNN LNMILVVVDR FSKR AHFIA TRKTLDATQL IDLLFRYIFS YHGFPRTITS DRDVRMTADK YQELTKRLGI KSTMSSANHP QTDGQSERTI QTLNR LLRA YASTNIQNWH VYLPQIEFVY NSTPTRTLGK SPFEIDLGYL PNTPAIKSDD EVNARSFTAV ELAKHLKALT IQTKEQ LEH AQIEMETNNN QRRKPLLLNI GDHVLVHRDA YFKKGAYMKV QQIYVGPFRV VKKINDNAYE LDLNSHKKKH RVINVQF LK KFVYRPDAYP KNKPISSTER IKRAHEVTAL IGIDTTHKTY LCHMQDVDPT LSVEYSEAEF CQIPERTRRS ILANFRQL Y ETQDNPEREE DVVSQNEICQ YDNTSP

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Macromolecule #6: Transcription factor TFIIIB component B''

MacromoleculeName: Transcription factor TFIIIB component B'' / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 67.801906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSIVNKSGT RFAPKVRQRR AATGGTPTPK PRTPQLFIPE SKEIEEDNSD NDKGVDENET AIVEKPSLVG ERSLEGFTLT GTNGHDNEI GDEGPIDAST QNPKADVIED NVTLKPAPLQ THRDQKVPRS SRLASLSKDN ESRPSFKPSF LDSSSNSNGT A RRLSTISN ...String:
MSSIVNKSGT RFAPKVRQRR AATGGTPTPK PRTPQLFIPE SKEIEEDNSD NDKGVDENET AIVEKPSLVG ERSLEGFTLT GTNGHDNEI GDEGPIDAST QNPKADVIED NVTLKPAPLQ THRDQKVPRS SRLASLSKDN ESRPSFKPSF LDSSSNSNGT A RRLSTISN KLPKKIRLGS ITENDMNLKT FKRHRVLGKP SSAKKPAGAH RISIVSKISP PTAMTDSLDR NEFSSETSTS RE ADENENY VISKVKDIPK KVRDGESAKY FIDEENFTMA ELCKPNFPIG QISENFEKSK MAKKAKLEKR RHLRELRMRA RQE FKPLHS LTKEEQEEEE EKRKEERDKL LNADIPESDR KAHTAIQLKL NPDGTMAIDE ETMVVDRHKN ASIENEYKEK VDEN PFANL YNYGSYGRGS YTDPWTVEEM IKFYKALSMW GTDFNLISQL YPYRSRKQVK AKFVNEEKKR PILIELALRS KLPPN FDEY CCEIKKNIGT VADFNEKLIE LQNEHKHHMK EIEEAKNTAK EEDQTAQRLN DANLNKKGSG GIMTNDLKVY RKTEVV LGT IDDLKRKKLK ERNNDDNEDN EGSEEEPEID Q

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Macromolecule #7: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 27.042275 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF ...String:
MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF PIRLEGLAFS HGTFSSYEPE LFPGLIYRMV KPKIVLLIFV SGKIVLTGAK QREEIYQAFE AIYPVLSEFR KM

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Macromolecule #8: Transcription factor IIIB 70 kDa subunit

MacromoleculeName: Transcription factor IIIB 70 kDa subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 67.011477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPVCKNCHGT EFERDLSNAN NDLVCKACGV VSEDNPIVSE VTFGETSAGA AVVQGSFIGA GQSHAAFGGS SALESREATL NNARRKLRA VSYALHIPEY ITDAAFQWYK LALANNFVQG RRSQNVIASC LYVACRKEKT HHMLIDFSSR LQVSVYSIGA T FLKMVKKL ...String:
MPVCKNCHGT EFERDLSNAN NDLVCKACGV VSEDNPIVSE VTFGETSAGA AVVQGSFIGA GQSHAAFGGS SALESREATL NNARRKLRA VSYALHIPEY ITDAAFQWYK LALANNFVQG RRSQNVIASC LYVACRKEKT HHMLIDFSSR LQVSVYSIGA T FLKMVKKL HITELPLADP SLFIQHFAEK LDLADKKIKV VKDAVKLAQR MSKDWMFEGR RPAGIAGACI LLACRMNNLR RT HTEIVAV SHVAEETLQQ RLNEFKNTKA AKLSVQKFRE NDVEDGEARP PSFVKNRKKE RKIKDSLDKE EMFQTSEEAL NKN PILTQV LGEQELSSKE VLFYLKQFSE RRARVVERIK ATNGIDGENI YHEGSENETR KRKLSEVSIQ NEHVEGEDKE TEGT EEKVK KVKTKTSEEK KENESGHFQD AIDGYSLETD PYCPRNLHLL PTTDTYLSKV SDDPDNLEDV DDEELNAHLL NEEAS KLKE RIWIGLNADF LLEQESKRLK QEADIATGNT SVKKKRTRRR NNTRSDEPTK TVDAAAAIGL MSDLQDKSGL HAALKA AEE SGDFTTADSV KNMLQKASFS KKINYDAIDG LFR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationName
40.0 mMTris-HCl
80.0 mMNaCl
7.0 mMMgCl2
1.0 mMDTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Details: Glow discharged at 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 4974 / Average exposure time: 7.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 2 / Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2437 / Average exposure time: 5.3 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.4 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID2
Particle selectionNumber selected: 628998
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: INSILICO MODEL / In silico model: Generated using Phyre2 modelling webserver
Final reconstructionNumber classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 101469
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.4)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0.4) / Details: Hierarchical Classification Process
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Target criteria: Correlation Coefficient
Output model

PDB-7q5b:
Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene

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