[English] 日本語
Yorodumi
- EMDB-52115: Cryo-EM structure of the human snRNA export complex comprising CB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52115
TitleCryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA
Map dataPrimary map
Sample
  • Complex: Human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA
    • Protein or peptide: Exportin-1
    • Protein or peptide: GTP-binding nuclear protein Ran
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
    • Protein or peptide: Phosphorylated adapter RNA export protein
    • RNA: RNA (5'-D(*(ADM))-R(P*A)-3')
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
  • Ligand: water
KeywordssnRNA export / Exportin / Cap-binding / Co-transcriptional regulation / RNA BINDING PROTEIN
Function / homology
Function and homology information


mRNA cap binding complex binding / snRNA export from nucleus / nuclear cap binding complex / RNA cap binding complex / histone mRNA metabolic process / cellular response to triglyceride / cellular response to salt / positive regulation of RNA export from nucleus / mRNA metabolic process / HuR (ELAVL1) binds and stabilizes mRNA ...mRNA cap binding complex binding / snRNA export from nucleus / nuclear cap binding complex / RNA cap binding complex / histone mRNA metabolic process / cellular response to triglyceride / cellular response to salt / positive regulation of RNA export from nucleus / mRNA metabolic process / HuR (ELAVL1) binds and stabilizes mRNA / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation / annulate lamellae / RNA stabilization / Processing of Intronless Pre-mRNAs / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / RNA nuclear export complex / snRNA binding / pre-miRNA export from nucleus / snRNA import into nucleus / miRNA-mediated post-transcriptional gene silencing / nuclear export signal receptor activity / Nuclear RNA decay / cellular response to mineralocorticoid stimulus / primary miRNA processing / manchette / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of centrosome duplication / Regulation of cholesterol biosynthesis by SREBP (SREBF) / regulatory ncRNA-mediated post-transcriptional gene silencing / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / alternative mRNA splicing, via spliceosome / importin-alpha family protein binding / RNA 7-methylguanosine cap binding / positive regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein localization to nucleolus / mRNA cis splicing, via spliceosome / NEP/NS2 Interacts with the Cellular Export Machinery / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / RNA catabolic process / regulation of translational initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase II Transcription Termination / FGFR2 alternative splicing / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein-containing complex localization / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / Signaling by FGFR2 IIIa TM / DNA metabolic process / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / dynein intermediate chain binding / spliceosomal complex assembly / Maturation of hRSV A proteins / Processing of Capped Intron-Containing Pre-mRNA / mitotic sister chromatid segregation / RNA polymerase II transcribes snRNA genes / viral process / spermatid development / 7-methylguanosine mRNA capping / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ribosomal large subunit export from nucleus / nuclear pore / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / toxic substance binding / sperm flagellum / Cajal body / Formation of HIV-1 elongation complex containing HIV-1 Tat / ribosomal subunit export from nucleus / mRNA export from nucleus / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin A/B1/B2 associated events during G2/M transition / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of RNA Pol II elongation complex / NPAS4 regulates expression of target genes / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / protein export from nucleus / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation
Similarity search - Function
Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein, RNA-binding domain / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 ...Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein, RNA-binding domain / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Ran GTPase / Small GTPase Ran-type domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / RNA recognition motif / Ras subfamily of RAS small GTPases / RNA recognition motif / Small GTPase / Ras family / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exportin-1 / Nuclear cap-binding protein subunit 2 / GTP-binding nuclear protein Ran / Nuclear cap-binding protein subunit 1 / Phosphorylated adapter RNA export protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsDubiez E / Cusack S / Kadlec J
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for the synergistic assembly of the snRNA export complex.
Authors: Etienne Dubiez / William Garland / Maja Finderup Brask / Elisabetta Boeri Erba / Torben Heick Jensen / Jan Kadlec / Stephen Cusack /
Abstract: The nuclear cap-binding complex (CBC) and its partner Arsenite-Resistance Protein 2 (ARS2) regulate the fate of RNA polymerase II transcripts via mutually exclusive interactions with RNA effectors. ...The nuclear cap-binding complex (CBC) and its partner Arsenite-Resistance Protein 2 (ARS2) regulate the fate of RNA polymerase II transcripts via mutually exclusive interactions with RNA effectors. One such effector is PHAX, which mediates the nuclear export of U-rich small nuclear RNAs (snRNAs). Here we present the cryo-electron microscopy structure of the human snRNA export complex comprising phosphorylated PHAX, CBC, CRM1-RanGTP and capped RNA. The central region of PHAX bridges CBC to the export factor CRM1-RanGTP, while also reinforcing cap dinucleotide binding. Additionally, PHAX interacts with a distant region of CRM1, facilitating contacts of the essential phosphorylated region of PHAX with the prominent basic surface of RanGTP. CBC engagement within the snRNA export complex is incompatible with its binding to other RNA effectors such as ALYREF or NCBP3. We demonstrate that snRNA export complex formation requires synergistic binding of all its components, which in turn displaces ARS2 from CBC and commits the complex for export.
History
DepositionNov 18, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52115.png

Downloads & links

-
Map

FileDownload / File: emd_52115.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.11259664 - 0.21189667
Average (Standard dev.)0.000039268776 (±0.0044500814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Sharpened map

Fileemd_52115_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local Refinement around CBC

Fileemd_52115_additional_2.map
AnnotationLocal Refinement around CBC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local Refinement around CRM1

Fileemd_52115_additional_3.map
AnnotationLocal Refinement around CRM1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1

Fileemd_52115_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 2

Fileemd_52115_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and ca...

EntireName: Human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA
Components
  • Complex: Human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA
    • Protein or peptide: Exportin-1
    • Protein or peptide: GTP-binding nuclear protein Ran
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
    • Protein or peptide: Phosphorylated adapter RNA export protein
    • RNA: RNA (5'-D(*(ADM))-R(P*A)-3')
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
  • Ligand: water

+
Supramolecule #1: Human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and ca...

SupramoleculeName: Human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Exportin-1

MacromoleculeName: Exportin-1 / type: protein_or_peptide / ID: 1 / Details: Human Exportin 1 CRM1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123.518359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPAIMTMLAD HAARQLLDFS QKLDINLLDN VVNCLYHGEG AQQRMAQEVL THLKEHPDAW TRVDTILEFS QNMNTKYYGL QILENVIKT RWKILPRNQC EGIKKYVVGL IIKTSSDPTC VEKEKVYIGK LNMILVQILK QEWPKHWPTF ISDIVGASRT S ESLCQNNM ...String:
MPAIMTMLAD HAARQLLDFS QKLDINLLDN VVNCLYHGEG AQQRMAQEVL THLKEHPDAW TRVDTILEFS QNMNTKYYGL QILENVIKT RWKILPRNQC EGIKKYVVGL IIKTSSDPTC VEKEKVYIGK LNMILVQILK QEWPKHWPTF ISDIVGASRT S ESLCQNNM VILKLLSEEV FDFSSGQITQ VKSKHLKDSM CNEFSQIFQL CQFVMENSQN APLVHATLET LLRFLNWIPL GY IFETKLI STLIYKFLNV PMFRNVSLKC LTEIAGVSVS QYEEQFVTLF TLTMMQLKQM LPLNTNIRLA YSNGKDDEQN FIQ NLSLFL CTFLKEHDQL IEKRLNLRET LMEALHYMLL VSEVEETEIF KICLEYWNHL AAELYRESPF STSASPLLSG SQHF DVPPR RQLYLPMLFK VRLLMVSRMA KPEEVLVVEN DQGEVVREFM KDTDSINLYK NMRETLVYLT HLDYVDTERI MTEKL HNQV NGTEWSWKNL NTLCWAIGSI SGAMHEEDEK RFLVTVIKDL LGLCEQKRGK DNKAIIASNI MYIVGQYPRF LRAHWK FLK TVVNKLFEFM HETHDGVQDM ACDTFIKIAQ KCRRHFVQVQ VGEVMPFIDE ILNNINTIIC DLQPQQVHTF YEAVGYM IG AQTDQTVQEH LIEKYMLLPN QVWDSIIQQA TKNVDILKDP ETVKQLGSIL KTNVRACKAV GHPFVIQLGR IYLDMLNV Y KCLSENISAA IQANGEMVTK QPLIRSMRTV KRETLKLISG WVSRSNDPQM VAENFVPPLL DAVLIDYQRN VPAAREPEV LSTMAIIVNK LGGHITAEIP QIFDAVFECT LNMINKDFEE YPEHRTNFFL LLQAVNSHCF PAFLAIPPTQ FKLVLDSIIW AFKHTMRNV ADTGLQILFT LLQNVAQEEA AAQSFYQTYF CDILQHIFSV VTDTSHTAGL TMHASILAYM FNLVEEGKIS T SLNPGNPV NNQIFLQEYV ANLLKSAFPH LQDAQVKLFV TGLFSLNQDI PAFKEHLRDF LVQIKEFAGE DTSDLFLEER EI ALRQADE EKHKRQMSVP GIFNPHEIPE EMCD

UniProtKB: Exportin-1

+
Macromolecule #2: GTP-binding nuclear protein Ran

MacromoleculeName: GTP-binding nuclear protein Ran / type: protein_or_peptide / ID: 2 / Details: RanGTP Q69L catalytic mutant / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.441135 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAQGEPQVQ FKLVLVGDGG TGKTTFVKRH LTGEFEKKYV ATLGVEVHPL VFHTNRGPIK FNVWDTAGLE KFGGLRDGYY IQAQCAIIM FDVTSRVTYK NVPNWHRDLV RVCENIPIVL CGNKVDIKDR KVKAKSIVFH RKKNLQYYDI SAKSNYNFEK P FLWLARKL ...String:
MAAQGEPQVQ FKLVLVGDGG TGKTTFVKRH LTGEFEKKYV ATLGVEVHPL VFHTNRGPIK FNVWDTAGLE KFGGLRDGYY IQAQCAIIM FDVTSRVTYK NVPNWHRDLV RVCENIPIVL CGNKVDIKDR KVKAKSIVFH RKKNLQYYDI SAKSNYNFEK P FLWLARKL IGDPNLEFVA MPALAPPEVV MDPALAAQYE HDLEVAQTTA LPDEDDDL

UniProtKB: GTP-binding nuclear protein Ran

+
Macromolecule #3: Nuclear cap-binding protein subunit 1

MacromoleculeName: Nuclear cap-binding protein subunit 1 / type: protein_or_peptide / ID: 3 / Details: Human NCBP1 CBP80 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.960297 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MSRRRHSDEN DGGQPHKRRK TSDANETEDH LESLICKVGE KSACSLESNL EGLAGVLEAD LPNYKSKILR LLCTVARLLP EKLTIYTTL VGLLNARNYN FGGEFVEAMI RQLKESLKAN NYNEAVYLVR FLSDLVNCHV IAAPSMVAMF ENFVSVTQEE D VPQVRRDW ...String:
MSRRRHSDEN DGGQPHKRRK TSDANETEDH LESLICKVGE KSACSLESNL EGLAGVLEAD LPNYKSKILR LLCTVARLLP EKLTIYTTL VGLLNARNYN FGGEFVEAMI RQLKESLKAN NYNEAVYLVR FLSDLVNCHV IAAPSMVAMF ENFVSVTQEE D VPQVRRDW YVYAFLSSLP WVGKELYEKK DAEMDRIFAN TESYLKRRQK THVPMLQVWT ADKPHPQEEY LDCLWAQIQK LK KDRWQER HILRPYLAFD SILCEALQHN LPPFTPPPHT EDSVYPMPRV IFRMFDYTDD PEGPVMPGSH SVERFVIEEN LHC IIKSHW KERKTCAAQL VSYPGKNKIP LNYHIVEVIF AELFQLPAPP HIDVMYTTLL IELCKLQPGS LPQVLAQATE MLYM RLDTM NTTCVDRFIN WFSHHLSNFQ FRWSWEDWSD CLSQDPESPK PKFVREVLEK CMRLSYHQRI LDIVPPTFSA LCPAN PTCI YKYGDESSNS LPGHSVALCL AVAFKSKATN DEIFSILKDV PNPNQDDDDD EGFSFNPLKI EVFVQTLLHL AAKSFS HSF SALAKFHEVF KTLAESDEGK LHVLRVMFEV WRNHPQMIAV LVDKMIRTQI VDCAAVANWI FSSELSRDFT RLFVWEI LH STIRKMNKHV LKIQKELEEA KEKLARQHKR RSDDDDRSSD RKDGVLEEQI ERLQEKVESA QSEQKNLFLV IFQRFIMI L TEHLVRCETD GTSVLTPWYK NCIERLQQIF LQHHQIIQQY MVTLENLLFT AELDPHILAV FQQFCALQA

UniProtKB: Nuclear cap-binding protein subunit 1

+
Macromolecule #4: Nuclear cap-binding protein subunit 2

MacromoleculeName: Nuclear cap-binding protein subunit 2 / type: protein_or_peptide / ID: 4 / Details: Human NCBP2 CBP20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.028131 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGGLLKALR SDSYVELSQY RDQHFRGDNE EQEKLLKKSC TLYVGNLSFY TTEEQIYELF SKSGDIKKII MGLDKMKKTA CGFCFVEYY SRADAENAMR YINGTRLDDR IIRTDWDAGF KEGRQYGRGR SGGQVRDEYR QDYDAGRGGY GKLAQNQ

UniProtKB: Nuclear cap-binding protein subunit 2

+
Macromolecule #5: Phosphorylated adapter RNA export protein

MacromoleculeName: Phosphorylated adapter RNA export protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.468574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALEVGDMED GQLSDSDSDM TVAPSDRPLQ LPKVLGGDSA MRAFQNTATA CAPVSHYRAV ESVDSSEESF SDSDDDSCLW KRKRQKCFN PPPKPEPFQF GQSSQKPPVA GGKKINNIWG AVLQEQNQDA VATELGILGM EGTIDRSRQS ETYNYLLAKK L RKESQEHT ...String:
MALEVGDMED GQLSDSDSDM TVAPSDRPLQ LPKVLGGDSA MRAFQNTATA CAPVSHYRAV ESVDSSEESF SDSDDDSCLW KRKRQKCFN PPPKPEPFQF GQSSQKPPVA GGKKINNIWG AVLQEQNQDA VATELGILGM EGTIDRSRQS ETYNYLLAKK L RKESQEHT KDLDKELDEY MHGGKKMGSK EEENGQGHLK RKRPVKDRLG NRPEMNYKGR YEITAEDSQE KVADEISFRL QE PKKDLIA RVVRIIGNKK AIELLMETAE VEQNGGLFIM NGSRRRTPGG VFLNLLKNTP SISEEQIKDI FYIENQKEYE NKK AARKRR TQVLGKKMKQ AIKSLNFQED DDTSRETFAS DTNEALASLD ESQEGHAEAK LEAEEAIEVD HSHDLDIF

UniProtKB: Phosphorylated adapter RNA export protein

+
Macromolecule #6: RNA (5'-D(*(ADM))-R(P*A)-3')

MacromoleculeName: RNA (5'-D(*(ADM))-R(P*A)-3') / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.439715 KDa
SequenceString:
AAUCUAUAAU AGCA

+
Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

+
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #9: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE

MacromoleculeName: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: GTA
Molecular weightTheoretical: 787.441 Da
Chemical component information

ChemComp-GTA:
P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE

+
Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 32 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8pnt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 202738
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

+
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