[English] 日本語
Yorodumi
- EMDB-8011: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8011
TitleFoot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Map data
Sample
  • Complex: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
    • RNA: x 2 types
    • Protein or peptide: x 10 types
  • Ligand: x 1 types
Function / homology
Function and homology information


generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / pICln-Sm protein complex / U4 snRNP / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / commitment complex / U2-type catalytic step 2 spliceosome ...generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / pICln-Sm protein complex / U4 snRNP / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / commitment complex / U2-type catalytic step 2 spliceosome / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / spliceosomal snRNP assembly / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / translation elongation factor activity / catalytic step 2 spliceosome / mRNA splicing, via spliceosome / metallopeptidase activity / GTPase activity / mRNA binding / GTP binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Snu114, GTP-binding domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG ...Snu114, GTP-binding domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / LSM domain superfamily / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribonuclease H-like superfamily / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / Resolution: 3.7 Å
AuthorsNguyen THD / Galej WP / Bai XC / Oubridge C / Scheres SHW / Newman AJ / Nagai K
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Nature / Year: 2015
Title: The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-chen Bai / Christos G Savva / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai /
Abstract: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key ...U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome.
History
DepositionDec 15, 2015-
Header (metadata) releaseFeb 3, 2016-
Map releaseFeb 3, 2016-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5gam
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_8011.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.43 Å
Density
Contour LevelBy ANNOTATOR: 0.012 / Movie #1: 0.03
Minimum - Maximum-0.07631316 - 0.19373968
Average (Standard dev.)-0.0002308518 (±0.0031405948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 543.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z543.400543.400543.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0760.194-0.000

-
Supplemental data

-
Sample components

+
Entire : Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP

EntireName: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Components
  • Complex: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
    • RNA: U5 snRNAU5 spliceosomal RNA
    • Protein or peptide: Pre-mRNA-splicing factor 8
    • Protein or peptide: Pre-mRNA-splicing factor SNU114
    • RNA: U6 snRNA, 5' endU6 spliceosomal RNA
    • Protein or peptide: Small nuclear ribonucleoprotein-associated protein B
    • Protein or peptide: Small nuclear ribonucleoprotein E
    • Protein or peptide: Small nuclear ribonucleoprotein F
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • Protein or peptide: Unknown polypeptide
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D3
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D1
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate

+
Supramolecule #1: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP

SupramoleculeName: Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 350 KDa

+
Macromolecule #1: U5 snRNA

MacromoleculeName: U5 snRNA / type: rna / ID: 1 / Details: Short form of U5 snRNA (179 nt) / Number of copies: 1
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 57.138711 KDa
SequenceString:
AAGCAGCUUU ACAGAUCAAU GGCGGAGGGA GGUCAACAUC AAGAACUGUG GGCCUUUUAU UGCCUAUAGA ACUUAUAACG AACAUGGUU CUUGCCUUUU ACCAGAACCA UCCGGGUGUU GUCUCCAUAG AAACAGGUAA AGCUGUCCGU UACUGUGGGC U UGCCAUAU UUUUUGGAAC

+
Macromolecule #4: U6 snRNA, 5' end

MacromoleculeName: U6 snRNA, 5' end / type: rna / ID: 4 / Details: The 5' end 31 nucleotides of U6 snRNA / Number of copies: 1
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 9.928893 KDa
SequenceString:
GUUCGCGAAG UAACCCUUCG UGGACAUUUG G

+
Macromolecule #2: Pre-mRNA-splicing factor 8

MacromoleculeName: Pre-mRNA-splicing factor 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 85.826102 KDa
SequenceString: MSGLPPPPPG FEEDSDLALP PPPPPPPGYE IEELDNPMVP SSVNEDTFLP PPPPPPSNFE INAEEIVDFT LPPPPPPPGL DELETKAEK KVELHGKRKL DIGKDTFVTR KSRKRAKKMT KKAKRSNLYT PKAEMPPEHL RKIINTHSDM ASKMYNTDKK A FLGALKYL ...String:
MSGLPPPPPG FEEDSDLALP PPPPPPPGYE IEELDNPMVP SSVNEDTFLP PPPPPPSNFE INAEEIVDFT LPPPPPPPGL DELETKAEK KVELHGKRKL DIGKDTFVTR KSRKRAKKMT KKAKRSNLYT PKAEMPPEHL RKIINTHSDM ASKMYNTDKK A FLGALKYL PHAILKLLEN MPHPWEQAKE VKVLYHTSGA ITFVNETPRV IEPVYTAQWS ATWIAMRREK RDRTHFKRMR FP PFDDDEP PLSYEQHIEN IEPLDPINLP LDSQDDEYVK DWLYDSRPLE EDSKKVNGTS YKKWSFDLPE MSNLYRLSTP LRD EVTDKN YYYLFDKKSF FNGKALNNAI PGGPKFEPLY PREEEEDYNE FNSIDRVIFR VPIRSEYKVA FPHLYNSRPR SVRI PWYNN PVSCIIQNDE EYDTPALFFD PSLNPIPHFI DNNSSLNVSN TKENGDFTLP EDFAPLLAEE EELILPNTKD AMSLY HSPF PFNRTKGKMV RAQDVALAKK WFLQHPDEEY PVKVKVSYQK LLKNYVLNEL HPTLPTNHNK TKLLKSLKNT KYFQQT TID WVEAGLQLCR QGHNMLNLLI HRKGLTYLHL DYNFNLKPTK TLTTKERKKS RLGNSFHLMR ELLKMMKLIV DTHVQFR LG NVDAFQLADG IHYILNHIGQ LTGIYRYKYK VMHQIRACKD LKHIIYYKFN KNLGKGPGCG FWQPAWRVWL NFLRGTIP L LERYIGNLIT RQFE

+
Macromolecule #3: Pre-mRNA-splicing factor SNU114

MacromoleculeName: Pre-mRNA-splicing factor SNU114 / type: protein_or_peptide / ID: 3 / Details: Full length Snu114 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 114.132086 KDa
SequenceString: MEGDDLFDEF GNLIGVDPFD SDEEESVLDE QEQYQTNTFE GSGNNNEIES RQLTSLGSKK ELGISLEHPY GKEVEVLMET KNTQSPQTP LVEPVTERTK LQEHTIFTQL KKNIPKTRYN RDYMLSMANI PERIINVGVI GPLHSGKTSL MDLLVIDSHK R IPDMSKNV ...String:
MEGDDLFDEF GNLIGVDPFD SDEEESVLDE QEQYQTNTFE GSGNNNEIES RQLTSLGSKK ELGISLEHPY GKEVEVLMET KNTQSPQTP LVEPVTERTK LQEHTIFTQL KKNIPKTRYN RDYMLSMANI PERIINVGVI GPLHSGKTSL MDLLVIDSHK R IPDMSKNV ELGWKPLRYL DNLKQEIDRG LSIKLNGSTL LCTDLESKSR MINFLDAPGH VNFMDETAVA LAASDLVLIV ID VVEGVTF VVEQLIKQSI KNNVAMCFVI NKLDRLILDL KLPPMDAYLK LNHIIANINS FTKGNVFSPI DNNIIFASTK LGF TFTIKE FVSYYYAHSI PSSKIDDFTT RLWGSVYYHK GNFRTKPFEN VEKYPTFVEF ILIPLYKIFS YALSMEKDKL KNLL RSNFR VNLSQEALQY DPQPFLKHVL QLIFRQQTGL VDAITRCYQP FELFDNKTAH LSIPGKSTPE GTLWAHVLKT VDYGG AEWS LVRIYSGLLK RGDTVRILDT SQSESRQKRQ LHDISKTETS NEDEDSKTET PSCEVEEIGL LGGRYVYPVH EAHKGQ IVL IKGISSAYIK SATLYSVKSK EDMKQLKFFK PLDYITEAVF KIVLQPLLPR ELPKLLDALN KISKYYPGVI IKVEESG EH VILGNGELYM DCLLYDLRAS YAKIEIKISD PLTVFSESCS NESFASIPVS NSISRLGEEN LPGLSISVAA EPMDSKMI Q DLSRNTLGKG QNCLDIDGIM DNPRKLSKIL RTEYGWDSLA SRNVWSFYNG NVLINDTLPD EISPELLSKY KEQIIQGFY WAVKEGPLAE EPIYGVQYKL LSISVPSDVN IDVMKSQIIP LMKKACYVGL LTAIPILLEP IYEVDITVHA PLLPIVEELM KKRRGSRIY KTIKVAGTPL LEVRGQVPVI ESAGFETDLR LSTNGLGMCQ LYFWHKIWRK VPGDVLDKDA FIPKLKPAPI N SLSRDFVM KTRRRKGIST GGFMSNDGPT LEKYISAELY AQLRENGLVP

+
Macromolecule #5: Small nuclear ribonucleoprotein-associated protein B

MacromoleculeName: Small nuclear ribonucleoprotein-associated protein B / type: protein_or_peptide / ID: 5 / Details: The SmB protein from the U5 snRNP Sm protein ring. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 22.42699 KDa
SequenceString: MSKIQVAHSS RLANLIDYKL RVLTQDGRVY IGQLMAFDKH MNLVLNECIE ERVPKTQLDK LRPRKDSKDG TTLNIKVEKR VLGLTILRG EQILSTVVED KPLLSKKERL VRDKKEKKQA QKQTKLRKEK EKKPGKIAKP NTANAKHTSS NSREIAQPSS S RYNGGNDN ...String:
MSKIQVAHSS RLANLIDYKL RVLTQDGRVY IGQLMAFDKH MNLVLNECIE ERVPKTQLDK LRPRKDSKDG TTLNIKVEKR VLGLTILRG EQILSTVVED KPLLSKKERL VRDKKEKKQA QKQTKLRKEK EKKPGKIAKP NTANAKHTSS NSREIAQPSS S RYNGGNDN IGANRSRFNN EAPPQTRKFQ PPPGFKRK

+
Macromolecule #6: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 6 / Details: The SmE protein from the U5 snRNP Sm protein ring. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 10.385098 KDa
SequenceString:
MSNKVKTKAM VPPINCIFNF LQQQTPVTIW LFEQIGIRIK GKIVGFDEFM NVVIDEAVEI PVNSADGKED VEKGTPLGKI LLKGDNITL ITSAD

+
Macromolecule #7: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 7 / Details: The SmF protein from the U5 snRNP Sm protein ring. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 9.669945 KDa
SequenceString:
MSESSDISAM QPVNPKPFLK GLVNHRVGVK LKFNSTEYRG TLVSTDNYFN LQLNEAEEFV AGVSHGTLGE IFIRCNNVLY IRELPN

+
Macromolecule #8: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 8 / Details: The SmG protein from the U5 snRNP Sm protein ring. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 8.490809 KDa
SequenceString:
MVSTPELKKY MDKKILLNIN GSRKVAGILR GYDIFLNVVL DDAMEINGED PANNHQLGLQ TVIRGNSIIS LEALDAI

+
Macromolecule #9: Unknown polypeptide

MacromoleculeName: Unknown polypeptide / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 1.549902 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #10: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 10
Details: The SmD3 protein from the U5 snRNP Sm protein ring.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 11.240139 KDa
SequenceString:
MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT EPQGAVTHMD QIFVRGSQIK FIVVPDLLKN APLFKKNSS RPMPPIRGPK RR

+
Macromolecule #11: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 11
Details: The SmD1 protein from the U5 snRNP Sm protein ring.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 16.296798 KDa
SequenceString:
MKLVNFLKKL RNEQVTIELK NGTTVWGTLQ SVSPQMNAIL TDVKLTLPQP RLNKLNSNGI AMASLYLTGG QQPTASDNIA SLQYINIRG NTIRQIILPD SLNLDSLLVD QKQLNSLRRS GQIANDPSKK RRRDFGAPAN KRPRRGL

+
Macromolecule #12: Small nuclear ribonucleoprotein Sm D2

MacromoleculeName: Small nuclear ribonucleoprotein Sm D2 / type: protein_or_peptide / ID: 12
Details: The SmD2 protein from the U5 snRNP Sm protein ring.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BCY123
Molecular weightTheoretical: 12.876066 KDa
SequenceString:
MSSQIIDRPK HELSRAELEE LEEFEFKHGP MSLINDAMVT RTPVIISLRN NHKIIARVKA FDRHCNMVLE NVKELWTEKK GKNVINRER FISKLFLRGD SVIVVLKTPV E

+
Macromolecule #13: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

-
Experimental details

-
Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mMHepes.KOH
150.0 mMpotassium chlorideKCl
1.0 mMmagnesium acetateMg(CH3COO)2
1.0 mMDTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 6.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
Details: Grids are made of holey carbon, carbon-coated and glow discharged in N-amylamine.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Quantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Number real images: 2477 / Average exposure time: 16.0 sec. / Average electron dose: 38.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 473827
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

Details: Startup model was 60 Angstrom low-pass filtered.
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 140155
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: RECIPROCAL
Output model

PDB-5gam:
Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more