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- PDB-5xjc: Cryo-EM structure of the human spliceosome just prior to exon lig... -

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Entry
Database: PDB / ID: 5xjc
TitleCryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom
Components
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 6
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • ATP-dependent RNA helicase DHX8
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • Homo sapiens small nuclear RNA (U2) gene
  • Intron-binding protein aquarius
  • PRKR-interacting protein 1
  • Peptidyl-prolyl cis-trans isomerase-like 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • Protein CASC3
  • Protein mago nashi homolog 2
  • RNA-binding protein 8A
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • pre-mRNAPrecursor mRNA
KeywordsSPLICING / RNA splicing / human spliceosome / C* complex / atomic structure / step 2 factors / EJC
Function / homologyLeucine-rich repeat / Btz domain / Pre-mRNA splicing Prp18-interacting factor / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Tetratricopeptide repeat / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding ...Leucine-rich repeat / Btz domain / Pre-mRNA splicing Prp18-interacting factor / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Tetratricopeptide repeat / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / BUD31/G10-related, conserved site / PRP8 domain IV core / WD40-repeat-containing domain / Myb domain / SKI-interacting protein, SKIP / Small ribonucleoprotein associated, SmB/SmN / Sm-like protein Lsm6/SmF / Armadillo-type fold / MIF4G-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin E-set / Pre-mRNA splicing factor component Cdc5p/Cef1 / RNA-binding domain, S1 / RNA helicase, DEAD-box type, Q motif / Leucine-rich repeat domain superfamily / EF-G domain III/V-like / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / Small nuclear ribonucleoprotein D1 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / RBM8, RNA recognition motif / Pre-mRNA-processing factor 17 / Intron-binding protein aquarius, N-terminal / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Cyclophilin-like domain superfamily / Protein CASC3 / Pre-mRNA-processing-splicing factor 8 / P-loop containing nucleoside triphosphate hydrolase / Small nuclear ribonucleoprotein Sm D2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein E / CWF11 family / Spt5 C-terminal domain / Ribosomal protein S5 domain 2-type fold, subgroup / Helicase superfamily 1/2, ATP-binding domain / C2 domain superfamily / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Mago nashi protein / SKI-interacting protein SKIP, SNW domain / Initiation factor eIF-4 gamma, MA3 / MIF4G-like, type 3 / U box domain / U2A'/phosphoprotein 32 family A, C-terminal / HAT (Half-A-TPR) repeat / S1 domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / G10 protein / Sec63 domain / WD40 repeat / Helicase, C-terminal / Leucine-rich repeat / LSM domain, eukaryotic/archaea-type / SANT/Myb domain / Transcription factor, GTP-binding domain / Ricin B, lectin domain / ATP-dependent RNA helicase DEAD-box, conserved site / Zinc finger, CCCH-type / Translation elongation factor EFTu-like, domain 2 / Small GTP-binding protein domain / Pre-mRNA-splicing factor 19 / Ribonuclease H-like superfamily / mRNA splicing factor SYF2 / mRNA splicing factor Cwf21 domain / Zinc finger, RING/FYVE/PHD-type / Tetratricopeptide repeat-containing domain / PROCT domain / Nucleotide-binding alpha-beta plait domain superfamily / PROCN domain / PRO8NT domain / Nucleic acid-binding, OB-fold / Tetratricopeptide-like helical domain superfamily / Translation elongation factor EFG/EF2, domain IV / Domain of unknown function DUF1605 / DEAD/DEAH box helicase domain / LSM domain superfamily / Protein of unknown function DUF1168 / Homeobox-like domain superfamily / Translation protein, beta-barrel domain superfamily / Pre-mRNA-splicing factor SPF27 / RNA-binding motif protein 8 / Helicase-associated domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / RNA-binding domain superfamily / RNA recognition motif domain / DEAD-box RNA helicase Q motif profile.
Function and homology information
Specimen sourceHomo sapiens (human)
Human adenovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsZhang, X. / Yan, C. / Hang, J. / Finci, I.L. / Lei, J. / Shi, Y.
CitationJournal: Cell / Year: 2017
Title: An Atomic Structure of the Human Spliceosome.
Authors: Xiaofeng Zhang / Chuangye Yan / Jing Hang / Lorenzo I Finci / Jianlin Lei / Yigong Shi
Abstract: Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the ...Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the human spliceosome just before exon ligation (the C complex) at an average resolution of 3.76 Å. The splicing factor Prp17 stabilizes the active site conformation. The step II factor Slu7 adopts an extended conformation, binds Prp8 and Cwc22, and is poised for selection of the 3'-splice site. Remarkably, the intron lariat traverses through a positively charged central channel of RBM22; this unusual organization suggests mechanisms of intron recruitment, confinement, and release. The protein PRKRIP1 forms a 100-Å α helix linking the distant U2 snRNP to the catalytic center. A 35-residue fragment of the ATPase/helicase Prp22 latches onto Prp8, and the quaternary exon junction complex (EJC) recognizes upstream 5'-exon sequences and associates with Cwc22 and the GTPase Snu114. These structural features reveal important mechanistic insights into exon ligation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 30, 2017 / Release: Jul 5, 2017

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Structure visualization

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: U5 snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: U5 small nuclear ribonucleoprotein 200 kDa helicase
E: U5 small nuclear ribonucleoprotein 40 kDa protein
F: U6 snRNA
G: pre-mRNA
H: Homo sapiens small nuclear RNA (U2) gene
I: Pre-mRNA-splicing factor SYF1
J: Crooked neck-like protein 1
K: Pre-mRNA-splicing factor SPF27
L: Cell division cycle 5-like protein
M: Pre-mRNA-splicing factor SYF2
N: Protein BUD31 homolog
O: Pre-mRNA-splicing factor RBM22
P: Spliceosome-associated protein CWC15 homolog
Q: Intron-binding protein aquarius
R: SNW domain-containing protein 1
S: Peptidyl-prolyl cis-trans isomerase-like 1
T: Pleiotropic regulator 1
U: Serine/arginine repetitive matrix protein 2
V: Pre-mRNA-splicing factor CWC22 homolog
W: Pre-mRNA-processing factor 17
X: PRKR-interacting protein 1
Y: ATP-dependent RNA helicase DHX8
Z: Pre-mRNA-splicing factor SLU7
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated proteins B and B'
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D2
f: Small nuclear ribonucleoprotein F
e: Small nuclear ribonucleoprotein E
g: Small nuclear ribonucleoprotein G
h: Small nuclear ribonucleoprotein Sm D3
i: Small nuclear ribonucleoprotein-associated proteins B and B'
j: Small nuclear ribonucleoprotein Sm D1
k: Small nuclear ribonucleoprotein Sm D2
m: Small nuclear ribonucleoprotein F
l: Small nuclear ribonucleoprotein E
n: Small nuclear ribonucleoprotein G
o: U2 small nuclear ribonucleoprotein A'
p: U2 small nuclear ribonucleoprotein B''
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
u: Eukaryotic initiation factor 4A-III
v: Protein mago nashi homolog 2
w: RNA-binding protein 8A
x: Protein CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,962,08074
Polyers2,958,30350
Non-polymers3,77724
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein/peptide , 18 types, 19 molecules ACJLNPQRSTUXYbiuvwx

#1: Protein/peptide Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#3: Protein/peptide 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#10: Protein/peptide Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#12: Protein/peptide Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#14: Protein/peptide Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#16: Protein/peptide Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#17: Protein/peptide Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 171502.453 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O60306
#18: Protein/peptide SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61770.648 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#19: Protein/peptide Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#20: Protein/peptide Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#21: Protein/peptide Serine/arginine repetitive matrix protein 2 / 300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related nuclear matrix protein of 300 kDa / Splicing coactivator subunit SRm300 / Tax-responsive enhancer element-binding protein 803 / TaxREB803


Mass: 300255.312 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#24: Protein/peptide PRKR-interacting protein 1


Mass: 21040.176 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H875
#25: Protein/peptide ATP-dependent RNA helicase DHX8 / DEAH box protein 8 / RNA helicase HRH1


Mass: 139508.328 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q14562, RNA helicase
#28: Protein/peptide Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 23686.004 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#37: Protein/peptide Eukaryotic initiation factor 4A-III / eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Eukaryotic translation initiation factor 4A isoform 3 / Nuclear matrix protein 265 / hNMP 265


Mass: 46930.961 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P38919, RNA helicase
#38: Protein/peptide Protein mago nashi homolog 2


Mass: 17301.799 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A72
#39: Protein/peptide RNA-binding protein 8A / Binder of OVCA1-1 / BOV-1 / RNA-binding motif protein 8A / RNA-binding protein Y14 / Ribonucleoprotein RBM8A


Mass: 19925.070 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5S9
#40: Protein/peptide Protein CASC3 / Cancer susceptibility candidate gene 3 protein / Metastatic lymph node gene 51 protein / MLN 51 / Protein barentsz / Btz


Mass: 76381.992 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O15234

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RNA chain , 4 types, 4 molecules BFGH

#2: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#6: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 34404.438 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#7: RNA chain pre-mRNA / Precursor mRNA


Mass: 87977.836 Da / Num. of mol.: 1 / Source: (synth.) Human adenovirus 2
#8: RNA chain Homo sapiens small nuclear RNA (U2) gene


Mass: 60186.445 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 609501

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U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules DE

#4: Protein/peptide U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 244823.422 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#5: Protein/peptide U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57


Mass: 39359.492 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

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Pre-mRNA-splicing factor ... , 6 types, 6 molecules IKMOVZ

#9: Protein/peptide Pre-mRNA-splicing factor SYF1 / Protein HCNP / XPA-binding protein 2


Mass: 100148.711 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#11: Protein/peptide Pre-mRNA-splicing factor SPF27 / Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome-associated protein SPF 27


Mass: 26163.420 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75934
#13: Protein/peptide Pre-mRNA-splicing factor SYF2 / CCNDBP1-interactor / p29


Mass: 28780.518 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O95926
#15: Protein/peptide Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#22: Protein/peptide Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 105646.578 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8
#26: Protein/peptide Pre-mRNA-splicing factor SLU7 / hSlu7


Mass: 68510.844 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O95391

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Pre-mRNA-processing factor ... , 2 types, 5 molecules Wqrst

#23: Protein/peptide Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#36: Protein/peptide
Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 / Senescence evasion factor


Mass: 55245.547 Da / Num. of mol.: 4 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UMS4, EC: 2.3.2.27

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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkfmelgn

#27: Protein/peptide Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#29: Protein/peptide Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#30: Protein/peptide Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#31: Protein/peptide Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#32: Protein/peptide Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#33: Protein/peptide Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op

#34: Protein/peptide U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 28456.584 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#35: Protein/peptide U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 25524.367 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P08579

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Non-polymers , 6 types, 24 molecules

#41: Chemical ChemComp-I6P / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Formula: C6H18O24P6 / Phytic acid
#42: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#43: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Formula: Mg / Magnesium
#44: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#45: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn / Zinc
#46: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

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Details

Sequence detailsThe UNK reisue between G-1 and G1 is added intentionally as per authors request to fill in the ...The UNK reisue between G-1 and G1 is added intentionally as per authors request to fill in the cleavage by RNA splicing.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human C* spliceosome / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43
Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 5 / Number of real images: 7308
EM imaging opticsEnergyfilter name: Gatan Quantum 967 LS / Energyfilter upper: 10 eV / Energyfilter lower: 0 eV / Chr aberration corrector: -10
Image scansMovie frames/image: 32 / Used frames/image: 2-32

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Processing

EM software
IDNameVersionCategory
10RELION2.0initial Euler assignment
11RELION2.0final Euler assignment
13RELION2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 100085 / Symmetry type: POINT
Least-squares processHighest resolution: 3.6 Å

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