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- EMDB-6817: Cryo-EM structure of the intron-lariat spliceosome ready for disa... -

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Entry
Database: EMDB / ID: 6817
TitleCryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom
Map dataCryo-EM map of the ILS spliceosome from S.cerevisiae at 3.5 angstrom
SampleS. cerevisiae intron lariat spliceosome (ILS)
  • (Pre-mRNA-splicing factor ...) x 16
  • (nucleic-acidNucleic acid) x 5
  • Pre-mRNA-processing protein 45
  • Protein CWC16
  • (Pre-mRNA-processing factor ...) x 2
  • Small nuclear ribonucleoprotein-associated protein B
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (ligand) x 4
Function / homologyHelicase superfamily 1/2, ATP-binding domain / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Myb-like transcription factor / WD40/YVTN repeat-like-containing domain superfamily / Sm-like protein Lsm6/SmF / SKI-interacting protein, SKIP / Myb domain / WD40-repeat-containing domain / BUD31/G10-related, conserved site / DnaJ domain, conserved site ...Helicase superfamily 1/2, ATP-binding domain / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Myb-like transcription factor / WD40/YVTN repeat-like-containing domain superfamily / Sm-like protein Lsm6/SmF / SKI-interacting protein, SKIP / Myb domain / WD40-repeat-containing domain / BUD31/G10-related, conserved site / DnaJ domain, conserved site / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / Trp-Asp (WD) repeats signature. / WD40 repeat, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Pre-mRNA splicing factor component Cdc5p/Cef1 / PRP8 domain IV core / Small nuclear ribonucleoprotein E / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein Sm D2 / P-loop containing nucleoside triphosphate hydrolase / Pre-mRNA-processing-splicing factor 8 / Ribosomal protein S5 domain 2-type fold, subgroup / Pre-mRNA-splicing factor 19 / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / LSM domain superfamily / U box domain / SKI-interacting protein SKIP, SNW domain / Translation elongation factor EFTu-like, domain 2 / Translation elongation factor EFG/EF2, domain IV / Pre-mRNA-splicing factor Cwf15/Cwc15 / Helicase-associated domain / CWC16 protein / Translation protein, beta-barrel domain superfamily / Homeobox-like domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / mRNA splicing factor SYF2 / DEAD/DEAH box helicase domain / Domain of unknown function DUF1605 / Tetratricopeptide-like helical domain superfamily / Ribonuclease H-like superfamily / PRO8NT domain / PROCN domain / Nucleotide-binding alpha-beta plait domain superfamily / PROCT domain / Tetratricopeptide repeat-containing domain / Zinc finger, RING/FYVE/PHD-type / Pre-mRNA-splicing factor Ntr2 / Torus domain / HAT (Half-A-TPR) repeat / PRO8NT (NUC069), PrP8 N-terminal domain / G-patch domain / HAT (Half-A-TPR) repeat / SKIP/SNW domain / Elongation factor Tu domain 2 / Elongation factor G, domain IV / Helicase associated domain (HA2) / Family of unknown function (DUF572) / Cwf15/Cwc15 cell cycle control protein / Oligonucleotide/oligosaccharide-binding (OB)-fold / PROCN (NUC071) domain / G10 protein / PROCT (NUC072) domain / SYF2 splicing factor / Prp19/Pso4-like / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / pre-mRNA splicing factor component / PRP8 domain IV core / Nineteen complex-related protein 2 / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / LSM domain / Elongation factor G C-terminus / Leucine-rich repeat domain superfamily / RNA-binding domain superfamily / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein D1 / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Slt11-like, RNA recognition motif / EF-G domain III/V-like / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / WD40-repeat-containing domain superfamily / WD domain, G-beta repeat / Chaperone J-domain superfamily / MPN domain / Pre-mRNA-processing factor 19 / Pre-mRNA-splicing factor Cwc2/Slt11 / Pre-mRNA-splicing factor Cwc2 / Elongation factor Tu GTP binding domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / DnaJ domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / U2A'/phosphoprotein 32 family A, C-terminal / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.46 Å resolution
AuthorsWan R / Yan C / Bai R / Lei J / Shi Y
CitationJournal: Cell / Year: 2017
Title: Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae.
Authors: Ruixue Wan / Chuangye Yan / Rui Bai / Jianlin Lei / Yigong Shi
Abstract: The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an ...The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an average resolution of 3.5 Å. The intron lariat remains bound in the spliceosome whereas the ligated exon is already dissociated. The step II splicing factors Prp17 and Prp18, along with Cwc21 and Cwc22 that stabilize the 5' exon binding to loop I of U5 small nuclear RNA (snRNA), have been released from the active site assembly. The DEAH family ATPase/helicase Prp43 binds Syf1 at the periphery of the spliceosome, with its RNA-binding site close to the 3' end of U6 snRNA. The C-terminal domain of Ntr1/Spp382 associates with the GTPase Snu114, and Ntr2 is anchored to Prp8 while interacting with the superhelical domain of Ntr1. These structural features suggest a plausible mechanism for the disassembly of the ILS complex.
Validation ReportPDB-ID: 5y88

SummaryFull reportAbout validation report
DateDeposition: Aug 20, 2017 / Header (metadata) release: Aug 1, 2018 / Map release: Aug 1, 2018 / Last update: Aug 1, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5y88
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6817.png

Downloads & links

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Map

Fileemd_6817.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.31 Å/pix.
= 522.4 Å		400 pix
1.31 Å/pix.
= 522.4 Å		400 pix
1.31 Å/pix.
= 522.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.306 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.05 (by author), 0.033 (movie #1):
Minimum - Maximum-0.13988014 - 0.28165865
Average (Standard dev.)0.00027459196 (0.0073554576)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.0.0.
Limit399.399.399.
Spacing400400400
CellA=B=C: 522.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3061.3061.306
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z522.400522.400522.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1400.2820.000

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Supplemental data

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Sample components

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Entire S. cerevisiae intron lariat spliceosome (ILS)

EntireName: S. cerevisiae intron lariat spliceosome (ILS) / Number of components: 39

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Component #1: protein, S. cerevisiae intron lariat spliceosome (ILS)

ProteinName: S. cerevisiae intron lariat spliceosome (ILS) / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: S288c

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Component #2: protein, Pre-mRNA-splicing factor 8

ProteinName: Pre-mRNA-splicing factor 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 279.867469 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: nucleic-acid, U5 snRNA

Nucleic-acidName: U5 snRNAU5 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAGCAGCUUU ACAGAUCAAU GGCGGAGGGA GGUCAACAUC AAGAACUGUG GGCCUUUUAU UGCCUAUAGA ACUUAUAACG AACAUGGUUC UUGCCUUUUA CCAGAACCAU CCGGGUGUUG UCUCCAUAGA AACAGGUAAA GCUGUCCGUU ACUGUGGGCU UGCCAUAUUU UUUGGAACUU UUCUGCCCUU UUUCUCAAUG AGUAAGGAGG GCGU
MassTheoretical: 68.643344 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, Pre-mRNA-splicing factor SNU114

ProteinName: Pre-mRNA-splicing factor SNU114 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 114.174008 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: nucleic-acid, U6 snRNA

Nucleic-acidName: U6 snRNAU6 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUCGCGAAG UAACCCUUCG UGGACAUUUG GUCAAUUUGA AACAAUACAG AGAUGAUCAG CAGUUCCCCU GCAUAAGGAU GAACCGUUUU ACAAAGAGAU UUAUUUCGUU UU
MassTheoretical: 35.883176 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: nucleic-acid, Intron lariat

Nucleic-acidName: Intron lariat / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUAUGUAUUU AUUUUNNNNN NNNNNUAGAU ACUAACAC
MassTheoretical: 10.810159 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: nucleic-acid, U2 snRNA

Nucleic-acidName: U2 snRNAU2 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ACGAAUCUCU UUGCCUUUUG GCUUAGAUCA AGUGUAGUAU CUGUUCUUUU CAGUGUAACA ACUGAAAUGA CCUCAAUGAG GCUCAUUACC UUUUAAUUUG UUACAAUACA CAUUUUUUGG CACCCAAAAU AAUAAAAUGG ACGGGAAGAG ACUUUUUAAG CAAGUUGUUU UCCGCUAAUG UCAGGUCUCA CUACUUUUUG CUGCUAUUUU UCUUCGCUCA UGGUUUCUUC AUAAGGCGUU UUUAUGAUGG UUUUUCGAAA UUGGUUUUUG AGACGACGGU UGCUCAAGGU UAUUGUUUUU GUUUUCUUCU GGUUGUUUUC UAUUUUCUUU UUUUUAGCUU UCUGUUUCUC CCUUAGUUUG GCUUUUUGCU UCAUACUCUU CCCUGUCUUU CCGAGCCGUU UAUGUCCAAC GCGGGAUUUG GUUUUUCUUU AUCGAUGGGA AGAAAUGGUG CUAUAGUAGG UUGGGAGAUA AUAUUUAUGG UAUGGGGUGC UAGUGCGGAU GGGGCGCUCU UAUUGUUGAU UUCUUCGCUC GUCUUCUUUU UCUGGUGGCG CUGCAAGAGG AAGUUUUUCG ACUUUGUUAU GAUUUUUGGU UUGCAAGGAA AGGUGUCUUA CGAUUCUUUU UUUGAUGUAA UAGGAUAAGC UUGCUUAUCC CCCAAGUAUC GGCCAAAGUU GUUGAUUUUC CUUUUGAAGU GUCCUCGGUU UGAGGGGGUG UAGGGUGGGG UUGGUCUACA AUAAGAGUGU UCCAUUGUUA ACGUGCUGGC GUCUUUUACU AUAUUUUUUU UCCCAGUUUA UUUUGUGCUU AUUUUCUCAU UGAGGAGAAG GAGCUCUUCU CGCAGGAUAU AAAUGGAGGU UUGCUAAAGG GGAGGAGAUG UGUUUGUGAG AAUACUGCUG AGAGAGUUCU GGAAGAGAAA AAAAGGAGGC AAUGGAAGGC GUUUGCUGGG AAAAGAGAAG AGCCAUGACU GCAUCUGUUG UUUCAAGGCC AGUUUUAUUA ACCGCCUAUG UCAUAGAGGC GUUUUUUUUG GAGGGAUUUG AAGAAUGCCG GCGGCAUCAA GAAACGGACU UGAUGGUUGA CGCCUGUUUU UAAAGUUAGA GACGUCGCGA CCCUCGCACU UGUGGAGUCG UUCUUGACUU UUACUUUGGU CGCUUGAUGU UUCUCUCGUC UUCCCGUUCG CUCUU
MassTheoretical: 376.267406 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, Pre-mRNA-splicing factor SNT309

ProteinName: Pre-mRNA-splicing factor SNT309 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.741455 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, Pre-mRNA-splicing factor SYF1

ProteinName: Pre-mRNA-splicing factor SYF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.344016 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, Pre-mRNA-splicing factor CLF1

ProteinName: Pre-mRNA-splicing factor CLF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.555859 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, Pre-mRNA-splicing factor CEF1

ProteinName: Pre-mRNA-splicing factor CEF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.837773 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, Pre-mRNA-splicing factor SYF2

ProteinName: Pre-mRNA-splicing factor SYF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.850719 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, Pre-mRNA-splicing factor BUD31

ProteinName: Pre-mRNA-splicing factor BUD31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.484502 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, Pre-mRNA-splicing factor SLT11

ProteinName: Pre-mRNA-splicing factor SLT11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.98859 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, Pre-mRNA-splicing factor CWC2

ProteinName: Pre-mRNA-splicing factor CWC2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.486562 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, Pre-mRNA-splicing factor PRP46

ProteinName: Pre-mRNA-splicing factor PRP46 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.771289 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, Pre-mRNA-splicing factor CWC15

ProteinName: Pre-mRNA-splicing factor CWC15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.975195 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, Pre-mRNA-processing protein 45

ProteinName: Pre-mRNA-processing protein 45 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.548727 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: protein, Protein CWC16

ProteinName: Protein CWC16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.371086 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: protein, Pre-mRNA-processing factor 17

ProteinName: Pre-mRNA-processing factor 17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.128762 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #21: protein, Pre-mRNA-splicing factor CWC23

ProteinName: Pre-mRNA-splicing factor CWC23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.280355 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #22: protein, Pre-mRNA-splicing factor SPP382

ProteinName: Pre-mRNA-splicing factor SPP382 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 83.155453 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: protein, Pre-mRNA-splicing factor NTR2

ProteinName: Pre-mRNA-splicing factor NTR2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.705395 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #24: protein, Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43

ProteinName: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.68275 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #25: protein, Small nuclear ribonucleoprotein-associated protein B

ProteinName: Small nuclear ribonucleoprotein-associated protein B / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.42699 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #26: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.385098 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #27: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.669945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #28: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.490809 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #29: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.240139 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #30: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.296798 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #31: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 12.876066 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #32: protein, U2 small nuclear ribonucleoprotein A'

ProteinName: U2 small nuclear ribonucleoprotein A' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.232252 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #33: protein, U2 small nuclear ribonucleoprotein B''

ProteinName: U2 small nuclear ribonucleoprotein B'' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.850944 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #34: protein, Pre-mRNA-processing factor 19

ProteinName: Pre-mRNA-processing factor 19 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 56.629777 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #35: nucleic-acid, RNA (intron or U6 snRNA)

Nucleic-acidName: RNA (intron or U6 snRNA) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUUUUUU
MassTheoretical: 2.710535 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #36: ligand, INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE

LigandName: INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.660035 kDa

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Component #37: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #38: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #39: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 37.6 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 150363
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

5y88

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