[English] 日本語
Yorodumi
- EMDB-9645: Cryo-EM structure of a human post-catalytic spliceosome (P comple... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 9645
TitleCryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom
Map dataThe 3.0 angstrom map of the human P complex
SampleHuman Post_catalytic Spliceosome
  • Protein mago nashi homolog 2
  • RNA-binding protein 8A
  • Eukaryotic initiation factor 4A-III
  • Protein CASC3
  • Pre-mRNA-processing-splicing factor 8
  • (nucleic-acidNucleic acid) x 4
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • Crooked neck-like protein 1
  • Cell division cycle 5-like protein
  • (Pre-mRNA-splicing factor ...) x 6
  • Protein BUD31 homolog
  • Spliceosome-associated protein CWC15 homolog
  • SNW domain-containing protein 1
  • (Peptidyl-prolyl cis-trans ...) x 2
  • Pleiotropic regulator 1
  • Serine/arginine repetitive matrix protein 2
  • (Pre-mRNA-processing factor ...) x 2
  • PRKR-interacting protein 1
  • RNA helicase aquarius
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • Small nuclear ribonucleoprotein-associated protein
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • ATP-dependent RNA helicase DHX8
  • (ligand) x 5
Function / homologyJAB1/MPN/MOV34 metalloenzyme domain / Helicase-associated domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / S1 domain / HAT (Half-A-TPR) repeat / U2A'/phosphoprotein 32 family A, C-terminal / U box domain / MIF4G-like, type 3 / Initiation factor eIF-4 gamma, MA3 / SKI-interacting protein SKIP, SNW domain ...JAB1/MPN/MOV34 metalloenzyme domain / Helicase-associated domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / S1 domain / HAT (Half-A-TPR) repeat / U2A'/phosphoprotein 32 family A, C-terminal / U box domain / MIF4G-like, type 3 / Initiation factor eIF-4 gamma, MA3 / SKI-interacting protein SKIP, SNW domain / Mago nashi protein / Translation elongation factor EFTu-like, domain 2 / Sec63 domain / Small GTP-binding protein domain / Translation elongation factor EFG/EF2, domain IV / Pre-mRNA-splicing factor Cwf15/Cwc15 / RNA-binding motif protein 8 / G10 protein / Ribonuclease H-like superfamily / 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 / Pre-mRNA-splicing factor SPF27 / 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 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / WD40 repeat / mRNA splicing factor Cwf21 domain / Mago nashi protein / PROCT (NUC072) domain / PROCN (NUC071) domain / PRO8NT (NUC069), PrP8 N-terminal domain / Oligonucleotide/oligosaccharide-binding (OB)-fold / Protein of unknown function (DUF1168) / Breast carcinoma amplified sequence 2 (BCAS2) / Cwf15/Cwc15 cell cycle control protein / U-box domain / WD domain, G-beta repeat / Helicase associated domain (HA2) / Elongation factor G, domain IV / Elongation factor Tu domain 2 / Sec63 Brl domain / MA3 domain / SKIP/SNW domain / Helicase, C-terminal / ATP-dependent RNA helicase DEAD-box, conserved site / Leucine-rich repeat / LSM domain, eukaryotic/archaea-type / SANT/Myb domain / Transcription factor, GTP-binding domain / Ricin B, lectin domain / Elongation factor EFG, domain V-like / Zinc finger, CCCH-type / HAT (Half-A-TPR) repeat / S1 RNA binding domain / RNA recognition motif domain / Elongation factor G C-terminus / G10 protein / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / LSM domain / Zinc finger, RING/FYVE/PHD-type / mRNA splicing factor SYF2 / cwf21 domain / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Pre-mRNA-processing-splicing factor 8 / Protein CASC3 / Cyclophilin-like domain superfamily / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Intron-binding protein aquarius, N-terminal / Leucine-rich repeat domain superfamily / Pre-mRNA-processing factor 17 / RBM8, RNA recognition motif / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein D1 / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / EF-G domain III/V-like / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-processing factor 19 / DEAD/DEAH box helicase / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Elongation factor Tu GTP binding domain / Pre-mRNA-splicing factor SLU7 / Pre-mRNA-splicing factor Cwc2/Slt11 / MPN domain / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Zinc finger, CCCH-type superfamily / Mago nashi superfamily / Winged helix DNA-binding domain superfamily
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 3 Å resolution
AuthorsZhang X / Zhan X / Yan C / Shi Y
CitationJournal: Cell Res. / Year: 2019
Title: Structures of the human spliceosomes before and after release of the ligated exon.
Authors: Xiaofeng Zhang / Xiechao Zhan / Chuangye Yan / Wenyu Zhang / Dongliang Liu / Jianlin Lei / Yigong Shi
Validation ReportPDB-ID: 6icz

SummaryFull reportAbout validation report
DateDeposition: Sep 7, 2018 / Header (metadata) release: Mar 13, 2019 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

-
Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6icz
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_9645.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.34 Å/pix.
= 535.2 Å
400 pix
1.34 Å/pix.
= 535.2 Å
400 pix
1.34 Å/pix.
= 535.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.338 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.2877726 - 0.5523746
Average (Standard dev.)0.00029300732 (0.011212082)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 535.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z535.200535.200535.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2880.5520.000

-
Supplemental data

-
Sample components

+
Entire Human Post_catalytic Spliceosome

EntireName: Human Post_catalytic Spliceosome / Number of components: 47

+
Component #1: protein, Human Post_catalytic Spliceosome

ProteinName: Human Post_catalytic Spliceosome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

+
Component #2: protein, Protein mago nashi homolog 2

ProteinName: Protein mago nashi homolog 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.301799 kDa
SourceSpecies: Human (human)

+
Component #3: protein, RNA-binding protein 8A

ProteinName: RNA-binding protein 8A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.92507 kDa
SourceSpecies: Human (human)

+
Component #4: protein, Eukaryotic initiation factor 4A-III

ProteinName: Eukaryotic initiation factor 4A-III / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.930961 kDa
SourceSpecies: Human (human)

+
Component #5: protein, Protein CASC3

ProteinName: Protein CASC3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 76.381992 kDa
SourceSpecies: Human (human)

+
Component #6: protein, Pre-mRNA-processing-splicing factor 8

ProteinName: Pre-mRNA-processing-splicing factor 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 273.97425 kDa
SourceSpecies: Human (human)

+
Component #7: nucleic-acid, U5snRNA

Nucleic-acidName: U5snRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUACUCUGGU UUCUCUUCAG AUCGCAUAAA UCUUUCGCCU UUUACUAAAG AUUUCCGUGG AGAGGAACAA CUCUGAGUCU UAACCCAAUU UUUUGAGGCC UUGCUUUGGC AAGGCUA
MassTheoretical: 37.254855 kDa
SourceSpecies: Human (human)

+
Component #8: protein, 116 kDa U5 small nuclear ribonucleoprotein component

ProteinName: 116 kDa U5 small nuclear ribonucleoprotein component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 109.560625 kDa
SourceSpecies: Human (human)

+
Component #9: protein, U5 small nuclear ribonucleoprotein 40 kDa protein

ProteinName: U5 small nuclear ribonucleoprotein 40 kDa protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.359492 kDa
SourceSpecies: Human (human)

+
Component #10: nucleic-acid, U6snRNA

Nucleic-acidName: U6snRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUGCUCGCUU CGGCAGCACA UAUACUAAAA UUGGAACGAU ACAGAGAAGA UUAGCAUGGC CCCUGCGCAA GGAUGACACG CAAAUUCGUG AAGCGUUCCA UAUUUUU
MassTheoretical: 34.404438 kDa
SourceSpecies: Human (human)

+
Component #11: nucleic-acid, pre-mRNA

Nucleic-acidName: pre-mRNAPrimary transcript / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GAAUACACGG AAUUCGAGCU CGCCCACUCU UGGAUCGGAA ACCCGUCGGC CUCCGAACGN GUAAGAGCCU AGCAUGUAGA ACUGGUUACC UGCAGCCCAA GCUUGCGUAC ACCAUCAGGG UACGUACUAG UACGUACACC AUCAGGGUAC GGCUGCACGU CUAGGGCGCA GUAGUCCAGG GUUUCCUUGA UGAUGUCAUA CUUAUCCUGU CCCUUUUUUU UCCACAGCUC GCGGUUGAGG ACAAACUCUU CGCGGUCUUU CCAGUGGGGA UCC
MassTheoretical: 87.382422 kDa
SourceSpecies: Human (human)

+
Component #12: nucleic-acid, U2snRNA

Nucleic-acidName: U2snRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCGCUUCUC GGCCUUUUGG CUAAGAUCAA GUGUAGUAUC UGUUCUUAUC AGUUUAAUAU CUGAUACGUC CUCUAUCCGA GGACAAUAUA UUAAAUGGAU UUUUGGAGCA GGGAGAUGGA AUAGGAGCUU GCUCCGUCCA CUCCACGCAU CGACCUGGUA UUGCAGUACC UCCAGGAACG GUGCACCC
MassTheoretical: 60.186445 kDa
SourceSpecies: Human (human)

+
Component #13: protein, Crooked neck-like protein 1

ProteinName: Crooked neck-like protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.610008 kDa
SourceSpecies: Human (human)

+
Component #14: protein, Cell division cycle 5-like protein

ProteinName: Cell division cycle 5-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 92.406883 kDa
SourceSpecies: Human (human)

+
Component #15: protein, Pre-mRNA-splicing factor SYF2

ProteinName: Pre-mRNA-splicing factor SYF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.780518 kDa
SourceSpecies: Human (human)

+
Component #16: protein, Protein BUD31 homolog

ProteinName: Protein BUD31 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.03285 kDa
SourceSpecies: Human (human)

+
Component #17: protein, Pre-mRNA-splicing factor RBM22

ProteinName: Pre-mRNA-splicing factor RBM22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.959555 kDa
SourceSpecies: Human (human)

+
Component #18: protein, Spliceosome-associated protein CWC15 homolog

ProteinName: Spliceosome-associated protein CWC15 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.674447 kDa
SourceSpecies: Human (human)

+
Component #19: protein, SNW domain-containing protein 1

ProteinName: SNW domain-containing protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 61.770648 kDa
SourceSpecies: Human (human)

+
Component #20: protein, Peptidyl-prolyl cis-trans isomerase-like 1

ProteinName: Peptidyl-prolyl cis-trans isomerase-like 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.257805 kDa
SourceSpecies: Human (human)

+
Component #21: protein, Pleiotropic regulator 1

ProteinName: Pleiotropic regulator 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.280758 kDa
SourceSpecies: Human (human)

+
Component #22: protein, Serine/arginine repetitive matrix protein 2

ProteinName: Serine/arginine repetitive matrix protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 300.255312 kDa
SourceSpecies: Human (human)

+
Component #23: protein, Pre-mRNA-splicing factor CWC22 homolog

ProteinName: Pre-mRNA-splicing factor CWC22 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.646578 kDa
SourceSpecies: Human (human)

+
Component #24: protein, Pre-mRNA-processing factor 17

ProteinName: Pre-mRNA-processing factor 17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.61218 kDa
SourceSpecies: Human (human)

+
Component #25: protein, PRKR-interacting protein 1

ProteinName: PRKR-interacting protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.040176 kDa
SourceSpecies: Human (human)

+
Component #26: protein, Pre-mRNA-splicing factor SLU7

ProteinName: Pre-mRNA-splicing factor SLU7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.510844 kDa
SourceSpecies: Human (human)

+
Component #27: protein, Pre-mRNA-splicing factor SYF1

ProteinName: Pre-mRNA-splicing factor SYF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.148711 kDa
SourceSpecies: Human (human)

+
Component #28: protein, Peptidyl-prolyl cis-trans isomerase E

ProteinName: Peptidyl-prolyl cis-trans isomerase E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.475773 kDa
SourceSpecies: Human (human)

+
Component #29: protein, RNA helicase aquarius

ProteinName: RNA helicase aquarius / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 171.502453 kDa
SourceSpecies: Human (human)

+
Component #30: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.940308 kDa
SourceSpecies: Human (human)

+
Component #31: protein, Small nuclear ribonucleoprotein-associated protein

ProteinName: Small nuclear ribonucleoprotein-associated protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.686004 kDa
SourceSpecies: Human (human)

+
Component #32: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.310653 kDa
SourceSpecies: Human (human)

+
Component #33: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.551928 kDa
SourceSpecies: Human (human)

+
Component #34: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.734171 kDa
SourceSpecies: Human (human)

+
Component #35: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.817601 kDa
SourceSpecies: Human (human)

+
Component #36: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.508084 kDa
SourceSpecies: Human (human)

+
Component #37: protein, U2 small nuclear ribonucleoprotein A'

ProteinName: U2 small nuclear ribonucleoprotein A' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.456584 kDa
SourceSpecies: Human (human)

+
Component #38: protein, U2 small nuclear ribonucleoprotein B''

ProteinName: U2 small nuclear ribonucleoprotein B'' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.524367 kDa
SourceSpecies: Human (human)

+
Component #39: protein, ATP-dependent RNA helicase DHX8

ProteinName: ATP-dependent RNA helicase DHX8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 139.522312 kDa
SourceSpecies: Human (human)

+
Component #40: protein, Pre-mRNA-splicing factor SPF27

ProteinName: Pre-mRNA-splicing factor SPF27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.16342 kDa
SourceSpecies: Human (human)

+
Component #41: protein, Pre-mRNA-processing factor 19

ProteinName: Pre-mRNA-processing factor 19 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 55.245547 kDa
SourceSpecies: Human (human)

+
Component #42: protein, U5 small nuclear ribonucleoprotein 200 kDa helicase

ProteinName: U5 small nuclear ribonucleoprotein 200 kDa helicase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 244.823422 kDa
SourceSpecies: Human (human)

+
Component #43: ligand, INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE

LigandName: INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.660035 kDa

+
Component #44: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #45: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #46: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #47: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.9
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 143320
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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