[English] 日本語
Yorodumi
- EMDB-49161: CryoEM structure of U7 Sm Ring in complex with symplekin N-termin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49161
TitleCryoEM structure of U7 Sm Ring in complex with symplekin N-terminal domain
Map dataCryoEM structure of U7 Sm Ring in complex with symplekin N-terminal domain
Sample
  • Complex: U7 Sm Ring in complex with symplekin N-terminal domain
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D3
    • Protein or peptide: Small nuclear ribonucleoprotein-associated proteins B and B'
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm10
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm11
    • Protein or peptide: Small nuclear ribonucleoprotein E
    • Protein or peptide: Small nuclear ribonucleoprotein F
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • Protein or peptide: Symplekin
    • RNA: modified H2a pre-mRNA
    • RNA: U7 snRNA
KeywordsSymplekin / 3' end processing / U7 snRNP / Histone pre-mRNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


cytoplasmic U snRNP body / mRNA 3'-end processing by stem-loop binding and cleavage / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / nuclear stress granule / U7 snRNP / histone pre-mRNA 3'end processing complex ...cytoplasmic U snRNP body / mRNA 3'-end processing by stem-loop binding and cleavage / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / nuclear stress granule / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / pICln-Sm protein complex / mRNA 3'-end processing / snRNP binding / Transport of Mature mRNA Derived from an Intronless Transcript / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / P granule / telomerase holoenzyme complex / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type spliceosomal complex / U2-type catalytic step 2 spliceosome / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U4 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / U5 snRNP / positive regulation of G1/S transition of mitotic cell cycle / bicellular tight junction / spliceosomal snRNP assembly / Cajal body / U4/U6 x U5 tri-snRNP complex / negative regulation of protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / cytoskeleton / cell adhesion / nuclear body / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G ...: / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein Sm D3 / 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. / LSM domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Symplekin / U7 snRNA-associated Sm-like protein LSm10
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsDesotell A / Tong L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM029832 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: An N-terminal helix of Lsm11 stabilizes CPSF73 in U7 snRNP for histone pre-mRNA 3'-end processing.
Authors: Anthony Desotell / William F Marzluff / Zbigniew Dominski / Liang Tong /
Abstract: The U7 snRNP (small nuclear ribonucleoprotein) is responsible for the 3'-end processing of replication-dependent histone messenger RNA precursors (pre-mRNAs). A helix in the Lsm11 N-terminal ...The U7 snRNP (small nuclear ribonucleoprotein) is responsible for the 3'-end processing of replication-dependent histone messenger RNA precursors (pre-mRNAs). A helix in the Lsm11 N-terminal extension contacts the metallo-β-lactamase domain of the U7 snRNP endonuclease CPSF73. We mutated or deleted this helix and found that the mutant machineries had substantially reduced cleavage activity toward the pre-mRNA. Our cryo-electron microscopy (cryo-EM) studies indicated that the helix was important for helping to hold CPSF73 in its correct position for the cleavage reaction. We also reconstituted a wild-type U7 snRNP in complex with a methylated, noncleavable pre-mRNA. We observed that CPSF73 could achieve an open conformation independent of RNA binding to its active site. Finally, we found that a previously uninterpreted EM density for a small helix at the CPSF73-CPSF100 interface belonged to the C-terminal end of CstF77, copurified from insect cells and highly conserved among CstF77 homologs. This CstF77 binding site had a small effect on the cleavage activity of U7 snRNP. Overall, our studies have revealed the importance of the conserved helix in the Lsm11 N-terminal extension for U7 snRNP, provided structural evidence that CPSF73 can achieve an open, active conformation without RNA binding in its active site, and identified a previously unknown binding site for CstF77 in CPSF100.
History
DepositionFeb 10, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49161.png

Downloads & links

-
Map

FileDownload / File: emd_49161.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of U7 Sm Ring in complex with symplekin N-terminal domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324.9 Å		1.08 Å/pix.
x 300 pix.
= 324.9 Å		1.08 Å/pix.
x 300 pix.
= 324.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.4675004 - 2.2868793
Average (Standard dev.)0.00009692904 (±0.030072762)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.9 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map A

Fileemd_49161_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_49161_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : U7 Sm Ring in complex with symplekin N-terminal domain

EntireName: U7 Sm Ring in complex with symplekin N-terminal domain
Components
  • Complex: U7 Sm Ring in complex with symplekin N-terminal domain
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D3
    • Protein or peptide: Small nuclear ribonucleoprotein-associated proteins B and B'
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm10
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm11
    • Protein or peptide: Small nuclear ribonucleoprotein E
    • Protein or peptide: Small nuclear ribonucleoprotein F
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • Protein or peptide: Symplekin
    • RNA: modified H2a pre-mRNA
    • RNA: U7 snRNA

+
Supramolecule #1: U7 Sm Ring in complex with symplekin N-terminal domain

SupramoleculeName: U7 Sm Ring in complex with symplekin N-terminal domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.111671 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ VYIRGSKIR FLILPDMLKN APMLKSMKNK NQGSGAGRGK AAILKAQVAA RGRGRGMGRG NIFQKRR

UniProtKB: Small nuclear ribonucleoprotein Sm D3

+
Macromolecule #2: Small nuclear ribonucleoprotein-associated proteins B and B'

MacromoleculeName: Small nuclear ribonucleoprotein-associated proteins B and B'
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.911931 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTVGKSSKML QHIDYRMRCI LQDGRIFIGT FKAFDKHMNL ILCDCDEFRK IKPKNSKQAE REEKRVLGLV LLRGENLVSM TVEGPPPKD TGIARV

UniProtKB: Small nuclear ribonucleoprotein-associated proteins B and B'

+
Macromolecule #3: U7 snRNA-associated Sm-like protein LSm10

MacromoleculeName: U7 snRNA-associated Sm-like protein LSm10 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.102057 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAVSHSVKER TISENSLIIL LQGLQGRVTT VDLRDESVAH GRIDNVDAFM NIRLAKVTYT DRWGHQVKLD DLFVTGRNVR YVHIPDDVN ITSTIEQQLQ IIHRVRNFGG KGQGRWEFPP KNCK

UniProtKB: U7 snRNA-associated Sm-like protein LSm10

+
Macromolecule #4: U7 snRNA-associated Sm-like protein LSm11

MacromoleculeName: U7 snRNA-associated Sm-like protein LSm11 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.399312 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHSGG SMEERERGAR SAGAGSPARP PSPRLDVSSD SFDPLLALYA PRLPPIPYPN APCFNNVAEY ESFLRTGVRG GGRGRGRAR GAAAGSGVPA APGPSGRTRR RPDAPAPDPE EAQEAERAMV AKEEGDGAAG AGRRGPGRSR KAPRNVLTRM P LHEGSPLG ...String:
MHHHHHHSGG SMEERERGAR SAGAGSPARP PSPRLDVSSD SFDPLLALYA PRLPPIPYPN APCFNNVAEY ESFLRTGVRG GGRGRGRAR GAAAGSGVPA APGPSGRTRR RPDAPAPDPE EAQEAERAMV AKEEGDGAAG AGRRGPGRSR KAPRNVLTRM P LHEGSPLG ELHRCIREGV KVNVHIRTFK GLRGVCTGFL VAFDKFWNMA LTDVDETYRK PVLQSRKKKR KPKVDYQQVF TR HINQIFI RGENVLLVHL AQ

+
Macromolecule #5: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.817601 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAYRGQGQKV QKVMVQPINL IFRYLQNRSR IQVWLYEQVN MRIEGCIIGF DEYMNLVLDD AEEIHSKTKS RKQLGRIMLK GDNITLLQS VSN

UniProtKB: Small nuclear ribonucleoprotein E

+
Macromolecule #6: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.734171 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSLPLNPKPF LNGLTGKPVM VKLKWGMEYK GYLVSVDGYM NMQLANTEEY IDGALSGHLG EVLIRCNNVL YIRGVEEEEE DGEMRE

UniProtKB: Small nuclear ribonucleoprotein F

+
Macromolecule #7: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.579236 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSKAHPPELK KFMDKKLSLK LNGGRHVQGI LRGFDPFMNL VIDECVEMAT SGQQNNIGMV VIRGNSIIML EALERVLEHH HHHH

UniProtKB: Small nuclear ribonucleoprotein G

+
Macromolecule #8: Symplekin

MacromoleculeName: Symplekin / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120.355125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTTSERVVDL LNQAALITND SKITVLKQVQ ELIINKDPTL LDNFLDEIIA FQADKSIEVR KFVIGFIEEA CKRDIELLLK LIANLNMLL RDENVNVVKK AILTMTQLYK VALQWMVKSR VISELQEACW DMVSAMAGDI ILLLDSDNDG IRTHAIKFVE G LIVTLSPR ...String:
MTTSERVVDL LNQAALITND SKITVLKQVQ ELIINKDPTL LDNFLDEIIA FQADKSIEVR KFVIGFIEEA CKRDIELLLK LIANLNMLL RDENVNVVKK AILTMTQLYK VALQWMVKSR VISELQEACW DMVSAMAGDI ILLLDSDNDG IRTHAIKFVE G LIVTLSPR MADSEIPRRQ EHDISLDRIP RDHPYIQYNV LWEEGKAALE QLLKFMVHPA ISSINLTTAL GSLANIARQR PM FMSEVIQ AYETLHANLP PTLAKSQVSS VRKNLKLHLL SVLKHPASLE FQAQITTLLV DLGTPQAEIA RNMPSSKDTR KRP RDDSDS TLKKMKLEPN LGEDDEDKDL EPGPSGTSKA SAQISGQSDT DITAEFLQPL LTPDNVANLV LISMVYLPEA MPAS FQAIY TPVESAGTEA QIKHLARLMA TQMTAAGLGP GVEQTKQCKE EPKEEKVVKT ESVLIKRRLS AQGQAISVVG SLSSM SPLE EEAPQAKRRP EPIIPVTQPR LAGAGGRKKI FRLSDVLKPL TDAQVEAMKL GAVKRILRAE KAVACSGAAQ VRIKIL ASL VTQFNSGLKA EVLSFILEDV RARLDLAFAW LYQEYNAYLA AGASGSLDKY EDCLIRLLSG LQEKPDQKDG IFTKVVL EA PLITESALEV VRKYCEDESR TYLGMSTLRD LIFKRPSRQF QYLHVLLDLS SHEKDKVRSQ ALLFIKRMYE KEQLREYV E KFALNYLQLL VHPNPPSVLF GADKDTEVAA PWTEETVKQC LYLYLALLPQ NHKLIHELAA VYTEAIADIK RTVLRVIEQ PIRGMGMNSP ELLLLVENCP KGAETLVTRC LHSLTDKVPP SPELVKRVRD LYHKRLPDVR FLIPVLNGLE KKEVIQALPK LIKLNPIVV KEVFNRLLGT QHGEGNSALS PLNPGELLIA LHNIDSVKCD MKSIIKATNL CFAERNVYTS EVLAVVMQQL M EQSPLPML LMRTVIQSLT MYPRLGGFVM NILSRLIMKQ VWKYPKVWEG FIKCCQRTKP QSFQVILQLP PQQLGAVFDK CP ELREPLL AHVRSFTPHQ QAHIPNSIMT ILEAS

UniProtKB: Symplekin

+
Macromolecule #9: modified H2a pre-mRNA

MacromoleculeName: modified H2a pre-mRNA / type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 19.237537 KDa
SequenceString:
CCAAAGGCUC UUUUCAGAGC CACCCACUGA AUCAGAUAAA GAGCUGUAAC ACGGUAGCCA

+
Macromolecule #10: U7 snRNA

MacromoleculeName: U7 snRNA / type: rna / ID: 10 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.013709 KDa
SequenceString:
CAGUGUUACA GCUCUUUUAG AAUUUGUCUA GUAGGCUUUC UGGCUUUUUA CCGGAAAGCC CCU

GENBANK: GENBANK: U47924.1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMNaClsodium chloride
10.0 mMEDTAEthylenediaminetetraacetic Acid
5.0 mMDTTDithiothreitol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 14 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 8741039
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6v4x

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 236295
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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