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- PDB-6zym: Human C Complex Spliceosome - High-resolution CORE -

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Basic information

Entry
Database: PDB / ID: 6zym
TitleHuman C Complex Spliceosome - High-resolution CORE
Components
  • (Pre-mRNA-splicing factor ...) x 5
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Cell division cycle 5-like protein
  • Corepressor interacting with RBPJ 1
  • Crooked neck-like protein 1
  • Peptidyl-prolyl cis-trans isomerase-like 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing factor 17
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • Protein FRG1
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • Spliceosome-associated protein CWC15 homolog
  • Splicing factor YJU2
  • U2 snRNAU2 spliceosomal RNA
  • U5 small nuclear ribonucleoprotein 40 kDa protein
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • WD repeat-containing protein 70
  • pre-mRNAPrimary transcript
KeywordsSPLICING / human C complex / spliceosome / hC / human step 1 spliceosome
Function / homology
Function and homology information


striated muscle dense body / regulation of histone H2B conserved C-terminal lysine ubiquitination / regulation of DNA double-strand break processing / positive regulation of vitamin D receptor signaling pathway / post-spliceosomal complex / cellular response to interleukin-2 / cellular response to wortmannin / cellular response to prolactin / leucine zipper domain binding / signal transduction involved in DNA damage checkpoint ...striated muscle dense body / regulation of histone H2B conserved C-terminal lysine ubiquitination / regulation of DNA double-strand break processing / positive regulation of vitamin D receptor signaling pathway / post-spliceosomal complex / cellular response to interleukin-2 / cellular response to wortmannin / cellular response to prolactin / leucine zipper domain binding / signal transduction involved in DNA damage checkpoint / transcription corepressor binding / regulation of vitamin D receptor signaling pathway / post-mRNA release spliceosomal complex / RNA splicing, via transesterification reactions / positive regulation of androgen receptor activity / U2-type spliceosomal complex / positive regulation of neurogenesis / protein phosphatase 1 binding / U2-type catalytic step 1 spliceosome / WD40-repeat domain binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / regulation of retinoic acid receptor signaling pathway / C2H2 zinc finger domain binding / retinoic acid receptor binding / pre-mRNA binding / positive regulation by host of viral transcription / regulation of mRNA splicing, via spliceosome / Prp19 complex / vitamin D receptor binding / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / Notch binding / K63-linked polyubiquitin modification-dependent protein binding / Cul4-RING E3 ubiquitin ligase complex / mRNA 3'-end processing / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / cellular response to fibroblast growth factor stimulus / muscle organ development / small nucleolar ribonucleoprotein complex / positive regulation of transcription of Notch receptor target / mRNA 3'-splice site recognition / RNA export from nucleus / cyclosporin A binding / spliceosomal tri-snRNP complex assembly / retinoic acid receptor signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / U5 snRNP / U5 snRNA binding / U2 snRNA binding / positive regulation of histone H3-K4 methylation / RNA processing / positive regulation of Notch signaling pathway / U6 snRNA binding / protein localization to nucleus / pre-mRNA intronic binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / SMAD binding / positive regulation of G1/S transition of mitotic cell cycle / catalytic step 2 spliceosome / response to cocaine / Cajal body / cellular response to nerve growth factor stimulus / mRNA export from nucleus / protein peptidyl-prolyl isomerization / spliceosomal complex / positive regulation of RNA splicing / RNA splicing / androgen receptor binding / cellular response to retinoic acid / microtubule organizing center / nuclear hormone receptor binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / fibrillar center / positive regulation of protein export from nucleus / protein-DNA complex / Notch signaling pathway / nuclear receptor transcription coactivator activity / rRNA processing / mRNA splicing, via spliceosome / calcium-dependent protein binding / site of double-strand break / nuclear matrix / transcription corepressor activity / positive regulation of protein import into nucleus / transcription-coupled nucleotide-excision repair / cellular response to drug / mRNA processing / Z disc / histone deacetylase binding / actin filament binding / cellular response to tumor necrosis factor / RNA polymerase II transcription regulatory region sequence-specific DNA binding / ribonucleoprotein complex / mitotic cell cycle
MIF4G-like domain superfamily / MIF4G-like, type 3 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / PRP8 domain IV core / Pre-mRNA splicing factor / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / HAT (Half-A-TPR) repeat / SKI-interacting protein SKIP, SNW domain ...MIF4G-like domain superfamily / MIF4G-like, type 3 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / PRP8 domain IV core / Pre-mRNA splicing factor / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / HAT (Half-A-TPR) repeat / SKI-interacting protein SKIP, SNW domain / Ribosomal protein S5 domain 2-type fold / Translation elongation factor EFTu-like, domain 2 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Small GTP-binding protein domain / Translation elongation factor EFG/EF2, domain IV / Pre-mRNA-splicing factor Cwf15/Cwc15 / Helicase-associated domain / Spt5 C-terminal domain / G10 protein / G-protein beta WD-40 repeat / P-loop containing nucleoside triphosphate hydrolase / SKI-interacting protein, SKIP / Myb domain / WD40-repeat-containing domain / BUD31/G10-related, conserved site / CBF1-interacting co-repressor CIR, N-terminal domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Armadillo-type fold / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif domain / WD40 repeat / RNA recognition motif, spliceosomal PrP8 / WD40 repeat, conserved site / JAB1/MPN/MOV34 metalloenzyme domain / Zinc finger, CCCH-type / Elongation factor EFG, domain V-like / Translational (tr)-type GTP-binding domain / SANT/Myb domain / Helicase, C-terminal / Saf4/Yju2 protein / Initiation factor eIF-4 gamma, MA3 / Actin-crosslinking / Pre-mRNA-processing-splicing factor 8 / Tetratricopeptide-like helical domain superfamily / Corepressor interacting with RBPJ 1 / Elongation Factor G, domain II / Ribonuclease H-like superfamily / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT domain / Nucleotide-binding alpha-beta plait domain superfamily / MPN domain / PROCT domain / Tetratricopeptide repeat-containing domain / mRNA splicing factor Cwf21 domain / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein S5 domain 2-type fold, subgroup / WD40/YVTN repeat-like-containing domain superfamily / Prp8 RNase domain IV, fingers region / Pre-mRNA-splicing factor Cwc2/Slt11 / PROCN domain / Pre-mRNA-splicing factor Isy1 superfamily / Protein FRG1 / Pre-mRNA-processing factor 17 / Homeobox-like domain superfamily / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Helix hairpin bin domain superfamily / Pre-mRNA-splicing factor Isy1 / Domain of unknown function DUF1605 / Translation protein, beta-barrel domain superfamily / Cyclophilin-like domain superfamily / EF-G domain III/V-like / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / RNA-binding domain superfamily / WD40-repeat-containing domain superfamily / DEAD/DEAH box helicase domain / Zinc finger, CCCH-type superfamily
Crooked neck-like protein 1 / gb:36516: / Peptidyl-prolyl cis-trans isomerase-like 1 / Serine/arginine repetitive matrix protein 2 / Pre-mRNA-splicing factor ISY1 homolog / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor CWC25 homolog / WD repeat-containing protein 70 / Pre-mRNA-splicing factor RBM22 / Pre-mRNA-splicing factor CWC22 homolog ...Crooked neck-like protein 1 / gb:36516: / Peptidyl-prolyl cis-trans isomerase-like 1 / Serine/arginine repetitive matrix protein 2 / Pre-mRNA-splicing factor ISY1 homolog / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor CWC25 homolog / WD repeat-containing protein 70 / Pre-mRNA-splicing factor RBM22 / Pre-mRNA-splicing factor CWC22 homolog / SNW domain-containing protein 1 / Splicing factor YJU2 / Cell division cycle 5-like protein / U5 small nuclear ribonucleoprotein 40 kDa protein / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / Corepressor interacting with RBPJ 1 / Pre-mRNA-processing-splicing factor 8 / 116 kDa U5 small nuclear ribonucleoprotein component / Protein FRG1 / Protein BUD31 homolog / Pre-mRNA-processing factor 17 / Pleiotropic regulator 1 / gb:36515:
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBertram, K. / Kastner, B.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SFB 860 Germany
CitationJournal: Mol Cell / Year: 2020
Title: Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome.
Authors: Karl Bertram / Leyla El Ayoubi / Olexandr Dybkov / Dmitry E Agafonov / Cindy L Will / Klaus Hartmuth / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core ...Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core resolution and 4.5-5.7 Å at its periphery, and aided by protein crosslinking we determine its molecular architecture. Our structure provides additional insights into the spliceosome's architecture between the catalytic steps of splicing, and how proteins aid formation of the spliceosome's catalytically active RNP (ribonucleoprotein) conformation. It reveals the spatial organization of the metazoan-specific proteins PPWD1, WDR70, FRG1, and CIR1 in human C complexes, indicating they stabilize functionally important protein domains and RNA structures rearranged/repositioned during the B to C transition. Structural comparisons with human B, C, and P complexes reveal an intricate cascade of RNP rearrangements during splicing catalysis, with intermediate RNP conformations not found in yeast, and additionally elucidate the structural basis for the sequential recruitment of metazoan-specific spliceosomal proteins.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
2: U2 snRNA
5: U5 snRNA
6: U6 snRNA
9: Corepressor interacting with RBPJ 1
A: Pre-mRNA-processing-splicing factor 8
B: 116 kDa U5 small nuclear ribonucleoprotein component
C: SNW domain-containing protein 1
D: Pleiotropic regulator 1
E: Pre-mRNA-processing factor 17
F: U5 small nuclear ribonucleoprotein 40 kDa protein
L: Cell division cycle 5-like protein
O: Crooked neck-like protein 1
P: Pre-mRNA-splicing factor RBM22
Q: Protein BUD31 homolog
R: Spliceosome-associated protein CWC15 homolog
S: Serine/arginine repetitive matrix protein 2
T: Pre-mRNA-splicing factor CWC22 homolog
V: Peptidyl-prolyl cis-trans isomerase-like 1
Y: pre-mRNA
Z: pre-mRNA
p: WD repeat-containing protein 70
r: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
s: Pre-mRNA-splicing factor ISY1 homolog
t: Pre-mRNA-splicing factor CWC25 homolog
u: Splicing factor YJU2
x: Protein FRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,956,92940
Polymers1,955,16626
Non-polymers1,76314
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 5 molecules 256YZ

#1: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36516
#2: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36515
#3: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 25480.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela S3
#19: RNA chain pre-mRNA / Primary transcript


Mass: 103979.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela S3

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Protein , 16 types, 16 molecules 9ABCDEFLOQRSVpux

#4: Protein Corepressor interacting with RBPJ 1 / CBF1-interacting corepressor / Recepin


Mass: 52441.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86X95
#5: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 207470.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#6: Protein 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP- ...Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 107225.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#7: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61610.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#8: Protein Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#9: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#10: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7
#11: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#12: Protein Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#14: Protein Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#15: Protein Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#16: Protein Serine/arginine repetitive matrix protein 2 / 300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix ...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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#18: Protein Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#20: Protein WD repeat-containing protein 70


Mass: 73306.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW82
#24: Protein Splicing factor YJU2 / Coiled-coil domain-containing protein 94


Mass: 21452.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW85
#25: Protein Protein FRG1 / FSHD region gene 1 protein


Mass: 29227.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14331

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Pre-mRNA-splicing factor ... , 5 types, 5 molecules PTrst

#13: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 25223.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#17: Protein Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8
#21: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / ATP-dependent RNA helicase DHX38 / DEAH box protein 38


Mass: 140720.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92620, RNA helicase
#22: Protein Pre-mRNA-splicing factor ISY1 homolog


Mass: 33046.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULR0
#23: Protein Pre-mRNA-splicing factor CWC25 homolog / Coiled-coil domain-containing protein 49 / Spliceosome-associated protein homolog CWC25


Mass: 49769.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NXE8

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Non-polymers , 4 types, 14 molecules

#26: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#27: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#28: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#29: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human C complex Spliceosome - High resolution core / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa S3
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES-KOH, pH 7.9HEPES-KOH1
21.5 mMMagnesium ChlorideMgCl21
3150 mMSodium chlorideNaClSodium chloride1
SpecimenConc.: 0.1 mg/ml / Details: Monodisperse particle distribution / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 132000 X / Nominal defocus max: -3 nm / Nominal defocus min: -1 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 120 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 28279
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1751359
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 411539 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01149836
ELECTRON MICROSCOPYf_angle_d1.268647
ELECTRON MICROSCOPYf_dihedral_angle_d22.1388767
ELECTRON MICROSCOPYf_chiral_restr0.0837701
ELECTRON MICROSCOPYf_plane_restr0.0087966

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