[English] 日本語
Yorodumi
- PDB-6lk8: Structure of Xenopus laevis Cytoplasmic Ring subunit. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lk8
TitleStructure of Xenopus laevis Cytoplasmic Ring subunit.
Components
  • (Nuclear pore complex protein ...) x 2
  • (Nup214 complex Coiled coil region 2, helix ...) x 3
  • (Nup214 complex coiled coil region 1, helix ...) x 2
  • GATOR complex protein SEC13
  • MGC154553 protein
  • MGC83295 protein
  • MGC83926 protein
  • Nuclear pore complex protein
  • Nucleoporin SEH1-A
  • Nup214 complex Coiled-coil region 1, helix 1
  • Nup358 complex, clamps
  • bridge domain
  • outer Nup133
  • outer Nup160
KeywordsSTRUCTURAL PROTEIN / building block of vertebrate NPC.
Function / homology
Function and homology information


: / macromolecule localization / nitrogen compound transport / nephron development / GATOR2 complex / macromolecule metabolic process / Seh1-associated complex / nuclear pore inner ring / protein exit from endoplasmic reticulum / COPII-coated vesicle budding ...: / macromolecule localization / nitrogen compound transport / nephron development / GATOR2 complex / macromolecule metabolic process / Seh1-associated complex / nuclear pore inner ring / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / positive regulation of TOR signaling / mRNA transport / intracellular transport / nuclear pore / mRNA export from nucleus / cellular response to nutrient levels / positive regulation of TORC1 signaling / GTPase activator activity / cellular response to amino acid starvation / kinetochore / protein import into nucleus / protein transport / nuclear membrane / lysosomal membrane / cell division / positive regulation of DNA-templated transcription / structural molecule activity / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Nuclear pore complex protein NUP98-NUP96 / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain ...Nuclear pore complex protein NUP98-NUP96 / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Sec13/Seh1 family / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Nuclear pore complex protein Nup133 / Nuclear pore complex protein Nup98-Nup96 / Nuclear pore complex protein Nup153 / Nuclear pore complex protein / MGC154553 protein / Nucleoporin SEH1-A / MGC83295 protein / Nucleoporin Nup37 / Nuclear pore complex protein Nup85 / Protein SEC13 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsShi, Y. / Huang, G. / Yan, C. / Zhang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31430020 China
National Natural Science Foundation of China (NSFC)31621092 China
CitationJournal: Cell Res / Year: 2020
Title: Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis.
Authors: Gaoxingyu Huang / Yanqing Zhang / Xuechen Zhu / Chao Zeng / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi /
Abstract: The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle ...The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.
History
DepositionDec 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-0909
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0909
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MGC83295 protein
B: Nuclear pore complex protein Nup85
C: MGC154553 protein
D: Nucleoporin SEH1-A
E: outer Nup160
F: MGC83926 protein
G: Nuclear pore complex protein Nup96
H: GATOR complex protein SEC13
I: Nuclear pore complex protein
J: outer Nup133
S: Nup358 complex, clamps
T: Nup358 complex, clamps
U: Nup358 complex, clamps
V: Nup358 complex, clamps
K: Nup214 complex Coiled-coil region 1, helix 1
L: Nup214 complex coiled coil region 1, helix 2
M: Nup214 complex coiled coil region 1, helix 3
N: Nup214 complex Coiled coil region 2, helix 1
O: Nup214 complex Coiled coil region 2, helix 2
P: Nup214 complex Coiled coil region 2, helix 3
Q: bridge domain
R: bridge domain
a: MGC83295 protein
b: Nuclear pore complex protein Nup85
c: MGC154553 protein
d: Nucleoporin SEH1-A
e: outer Nup160
f: MGC83926 protein
g: Nuclear pore complex protein Nup96
h: GATOR complex protein SEC13
i: Nuclear pore complex protein
j: outer Nup133


Theoretical massNumber of molelcules
Total (without water)3,291,33132
Polymers3,291,33132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 11 types, 23 molecules AaCcDdEeFfHhIiJjSTUVKQR

#1: Protein MGC83295 protein


Mass: 227854.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642R6
#3: Protein MGC154553 protein / outer Nup43


Mass: 41744.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q05AW3
#4: Protein Nucleoporin SEH1-A / outer Seh1 / GATOR complex protein SEH1-A / Nup107-160 subcomplex subunit seh1-A


Mass: 36037.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q4FZW5
#5: Protein outer Nup160


Mass: 162658.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8GIX3
#6: Protein MGC83926 protein


Mass: 36588.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q66IZ6
#8: Protein GATOR complex protein SEC13 / Protein SEC13 homolog


Mass: 35315.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZYJ8
#9: Protein Nuclear pore complex protein


Mass: 105398.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A2RV69
#10: Protein outer Nup133


Mass: 127551.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8H1I9
#11: Protein
Nup358 complex, clamps


Mass: 322784.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HGL2
#12: Protein Nup214 complex Coiled-coil region 1, helix 1


Mass: 5890.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#18: Protein bridge domain


Mass: 33293.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)

-
Nuclear pore complex protein ... , 2 types, 4 molecules BbGg

#2: Protein Nuclear pore complex protein Nup85 / 85 kDa nucleoporin / Nucleoporin Nup85


Mass: 75160.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q68FJ0
#7: Protein Nuclear pore complex protein Nup96 / Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / ...Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / Nucleoporin Nup98


Mass: 105079.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HBE3

-
Nup214 complex coiled coil region 1, helix ... , 2 types, 2 molecules LM

#13: Protein Nup214 complex coiled coil region 1, helix 2


Mass: 6826.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#14: Protein Nup214 complex coiled coil region 1, helix 3


Mass: 6230.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)

-
Nup214 complex Coiled coil region 2, helix ... , 3 types, 3 molecules NOP

#15: Protein/peptide Nup214 complex Coiled coil region 2, helix 1


Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#16: Protein/peptide Nup214 complex Coiled coil region 2, helix 2


Mass: 2996.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)
#17: Protein/peptide Nup214 complex Coiled coil region 2, helix 3


Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog)

-
Details

Sequence detailsAuthors know the chains K,L,M and N,O,P come from the coiled-coil region from Nup88,Nup62 and ...Authors know the chains K,L,M and N,O,P come from the coiled-coil region from Nup88,Nup62 and Nup214 (termed Nup214 complex). However, at the current resolution, the three helices of the coiled coil cannot be distinguished a nd there are no crystal structure of the three proteins. (1) Xl_Nup214_Q9PVZ2 MEDDTDLPPERETKDFQFRQLKKVRLFDYPADLPKQRSNLLVISNKYGLLFVGGFMGLKV FHTKDILVTVKPKENANKTVVGPQGIHVPMNSPIHHLALSSDNLTLSVCMTSAEQGSSVS FYDVRTLLNESKQNKMPFASCKLLRDPSSSVTDLQWNPTLPSMVAVCLSDGSISVLQVTD TVSVFANLPATLGVTSVCWSPKGKQLAVGKQNGTVVQYLPSLQEKKVIPCPSFYDSDNPV KVLDVLWLSTYVFTVVYAAADGSLEASPQLVIVTLPKKEDKRAERFLNFTETCYSICSER QHHFFLNYIEDWEILLAASAASVDVGVIARPPDQVGWEQWLLEDSSRAEMPMTENNDDTL PMGVALDYTCQLEVFISESQILPPVPVLLLLSTDGVLCPFHVVNLNQGVKPLTTSPEQLS LDGEREMKVVGGTAVSTPPAPLTSVSAPAPPASAAPRSAAPPPYPFGLSTASSGAPTPVL NPPASLAPAATPTKTTSQPAAAATSIFQPAGPAAGSLQPPSLPAFSFSSANNAANASAPS SFPFGAAMVSSNTAKVSAPPAMSFQPAMGTRPFSLATPVTVQAATAPGFTPTPSTVKVNL KDKFNASDTPPPATISSAAALSFTPTSKPNATVPVKSQPTVIPSQASVQPNRPFAVEAPQ APSSVSIASVQKTVRVNPPATKITPQPQRSVALENQAKVTKESDSILNGIREEIAHFQKE LDDLKARTSRACFQVGSEEEKRQLRTESDGLHSFFLEIKETTESLRGEFSAMKIKNLEGF ASIEDVQQRNKLKQDPKYLQLLYKKPLDPKSETQMQEIRRLNQYVKNAVQDVNDVLDLEW DQYLEEKQKKKGIIIPERETLFNSLANHQEIINQQRPKLEQLVENLQKLRLYNQISQWNV PDSSTKSFDVELENMQKTLSQTAIDTQTKPQAKLPAKISPVKQSQLRNFLSKRKTPPVRS LAPANLSRSAFLAPSFFEDLDDVSSTSSLSDMADNDNRNPPPKEIERQETPPPESTPVRV PKHAPVARTTSVQPGLGTASLPFQSGLHPATSTPVAPSQSIRVIPQGADSTMLATKTVKH GAPNITAAQKAAVAAMRRQTASQIPAASLTESTLQTVPQVVNVKELKNNGPGPTIPTVIG PTVPQSAAQVIHQVLATVGSVSARQAAPAAPLKNPPASASSIAPQTWQGSAPNKPAAQAI PKSDPSASQAPAPSVSQVNKPVSFSPAAGGFSFSNVTSAPVTSALGSSSAGCAATARDSN QASSYMFGGTGKSLGSEGSFSFASLKPASSSSSSSVVEPTMSKPSVVTAASTTATVTSTT AASSKPGEGLFQGFSGGETLGSFSGLRVGQADEASKVEVAKTPTAAQPVKLPSNPVLFSF AGAPQPAKVGEAPSTTSSTSASLFGNVQLASAGSTASAFTQSGSKPAFTFGIPQSTSTTA GASSAIPASFQSLLVSAAPATTTPSAPINSGLDVKQPIKPLSEPADSSSSQQQTLTTQSA AEQVPTVTPAATTATALPPPVPTIPSTAEAKIEGAAAPAIPASVISSQTVPFTSTVLASQ TPLASTPAGGPTSQVPVLVTTAPPVTTESAQTVSLTGQPVAGSSAFAQSTVTAASTPVFG QALASGAAPSPFAQPTSSSVSTSANSSTGFGTSAFGATGGNGGFGQPSFGQAPLWKGPAT SQSTLPFSQPTFGTQPAFGQPAASTATSSAGSLFGCTSSASSFSFGQASNTSGTSTSGVL FGQSSAPVFGQSAAFPQAAPAFGSASVSTTTTASFGFGQPAGFASGTSGSLFNPSQSGST SVFGQQPASSSGGLFGAGSGGASTVGLFSGLGAKPSQEAANKNPFGSPGSSGFGSAGASN SSNLFGNSGAKAFGFGGTSFGDKPSATFSAGGSVASQGFSFNSPTKTGGFGAAPVFGSPP TFGGSPGFGGSPAFGTAAAFSNTLGSTGGKVFGEGTSAATTGGFGFGSNSSTAAFGSLAT QNTPTFGSISQQSPGFGGQSSGFSGFGAGPGAAAGNTGGFGFGVSNPTSPGFGCWRS (2) Xl_Nup88A_Q4KLQ6 MAAGEHWQSALSEHALFSSLKERLRDVEELREEGERRASKDKQLRNLLCVLDGDLLVWDA EECAFHTVTLRSLSVESTGSSSSGEQKLLCTNPPLFDVNEVLLSPTQHHVALVGSKGVMV LEIPKRWGKKSEFEGGEKTVNCRTIPIAERIFTSSTSLLLKQAIWYPSETQEPHLILLTS DNILRLYNLQDLFTPVKVISLSSAEEETTLPHNGRSYKASLGETAVACDFGPLAVLPKGF GQHSKEDTVAYPLYILYETGETYLMYIDLQKSNITVGKLLGPLPMYPAAEDNYGYDACAL LCLPCVPNIIVIATESGLLYHCVVLEGEEDDEQTSNKSWNSSCDLIPSLYVFECVELELA LKFATEEEESLELDFACPIKLHRDPICPSRYHCTHVAGVHSVGLTWFNKLEKFLSSGEED KDSLQELAAEQKCLVEHILCTKPLRCRLPSPIQGFWIISDLFLGTSMICITCDFECIVRP LLTTIRPPSPPLLCSQSDKSSTEILPHVLADVKGPFEEHIRGILRRNSANPLLLNSSSKD SSPPPEECLQLLSRATQVFREEYLLKQDLANEEIQRRVKLLIAQKEKQLEDLRYCREERK SLTETAERLAEKFEEAKEKQEDLINRLKRILRSFHTQLPVLSESERDMKKELQATNQQLQ QLGNSINQVNRKMSYQEKQMEKGKSPRKSSLTLSDYQKKNIKAVLKEHGEHIQEMVKQIN NIRNHVNF (3) Xl_Nup62_Q91349 MSGFNFGAASAGGFSFGNPKSTTTTAPTGFSFGAATAAPSGGFSFGTATPTPASTTGQTS GLFSFSNPAPSLAPTSGFSFGAQVTSTPAPSSGGLAFGANTSKLNSGVGNQPAGGTTQTS QPMGGFSFGAATTQTQPSATSVGGFSFAGGVGSTSTNVFAQPAASTGITLQSAVSTAAAP TATTSQPTSTFSFGTQPQAAPALNFGLLSSSSVLSTASTPAAAQPVAPTTGLSLNFGKPA DTSAAVTSTGSTTTNTPSLSSLLGTSGPSLFSSVATSTVPSVVSTVASGLSLTSTATSTG FGMKTLASSAVPTGTLATSTASLGVKAPLAGTIVQANAVGSAAATGISTATAMTYAQLEN LINKWSLELEDQEKHFLQQATQVNAWDRTLMQNGERITTLHREMEKVKLDQKRLDQELDF ILSQQKELEDLLTPLEESVKEQSGTIYLQHADEEREKTYKLAENIDAQLKRMAQDLKEVI EHLNTSAGPGDASNPLQQICKILNAHMDSLQWIDQNSALLQRKVEQVTKECESRRKEQER GFSIAFD

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cytoplasmic Ring Subunit of Xenopus laevis NPC / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 75 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 616547 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

+
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