[English] 日本語
Yorodumi
- EMDB-44358: Human polymerase epsilon bound to PCNA and DNA in the nucleotide ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44358
TitleHuman polymerase epsilon bound to PCNA and DNA in the nucleotide bound state
Map dataFinal sharpen cryo-em by cryosparc
Sample
  • Complex: The DNA bound Pol epsilon and PCNA complex
    • Protein or peptide: DNA polymerase epsilon catalytic subunit
    • Protein or peptide: Proliferating cell nuclear antigen
    • DNA: Primer DNA
    • DNA: Template DNA
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTER
KeywordsDNA polymerase / DNA / DNA Binding Protein-DNA complex
Function / homology
Function and homology information


epsilon DNA polymerase complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Processive synthesis on the lagging strand ...epsilon DNA polymerase complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Processive synthesis on the lagging strand / MutLalpha complex binding / PCNA complex / Removal of the Flap Intermediate / Telomere C-strand (Lagging Strand) Synthesis / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Polymerase switching on the C-strand of the telomere / replisome / response to L-glutamate / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / response to dexamethasone / DNA synthesis involved in DNA repair / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / translesion synthesis / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA repair / positive regulation of DNA replication / Translesion synthesis by REV1 / nuclear estrogen receptor binding / replication fork / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / male germ cell nucleus / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / DNA-templated DNA replication / cellular response to xenobiotic stimulus / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / 4 iron, 4 sulfur cluster binding / chromatin organization / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / chromosome, telomeric region / nuclear body / nucleotide binding / chromatin binding / centrosome / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Zinc finger domain of DNA polymerase-epsilon / : / : / DNA polymerase epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / Proliferating cell nuclear antigen signature 2. ...Zinc finger domain of DNA polymerase-epsilon / : / : / DNA polymerase epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / DNA polymerase family B, thumb domain / : / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Proliferating cell nuclear antigen / DNA polymerase epsilon catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWang F / He Q / Li H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM148159 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structures of the human leading strand Polε-PCNA holoenzyme.
Authors: Qing He / Feng Wang / Nina Y Yao / Michael E O'Donnell / Huilin Li /
Abstract: In eukaryotes, the leading strand DNA is synthesized by Polε and the lagging strand by Polδ. These replicative polymerases have higher processivity when paired with the DNA clamp PCNA. While the ...In eukaryotes, the leading strand DNA is synthesized by Polε and the lagging strand by Polδ. These replicative polymerases have higher processivity when paired with the DNA clamp PCNA. While the structure of the yeast Polε catalytic domain has been determined, how Polε interacts with PCNA is unknown in any eukaryote, human or yeast. Here we report two cryo-EM structures of human Polε-PCNA-DNA complex, one in an incoming nucleotide bound state and the other in a nucleotide exchange state. The structures reveal an unexpected three-point interface between the Polε catalytic domain and PCNA, with the conserved PIP (PCNA interacting peptide)-motif, the unique P-domain, and the thumb domain each interacting with a different protomer of the PCNA trimer. We propose that the multi-point interface prevents other PIP-containing factors from recruiting to PCNA while PCNA functions with Polε. Comparison of the two states reveals that the finger domain pivots around the [4Fe-4S] cluster-containing tip of the P-domain to regulate nucleotide exchange and incoming nucleotide binding.
History
DepositionMar 31, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44358.png

Downloads & links

-
Map

FileDownload / File: emd_44358.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal sharpen cryo-em by cryosparc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-1.0436051 - 1.6188902
Average (Standard dev.)0.00037401498 (±0.026403593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Final unsharpened EM map

Fileemd_44358_additional_1.map
AnnotationFinal unsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_44358_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_44358_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The DNA bound Pol epsilon and PCNA complex

EntireName: The DNA bound Pol epsilon and PCNA complex
Components
  • Complex: The DNA bound Pol epsilon and PCNA complex
    • Protein or peptide: DNA polymerase epsilon catalytic subunit
    • Protein or peptide: Proliferating cell nuclear antigen
    • DNA: Primer DNA
    • DNA: Template DNA
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTER

-
Supramolecule #1: The DNA bound Pol epsilon and PCNA complex

SupramoleculeName: The DNA bound Pol epsilon and PCNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 450 KDa

-
Macromolecule #1: DNA polymerase epsilon catalytic subunit

MacromoleculeName: DNA polymerase epsilon catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 261.782266 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MSLRSGGRRR ADPGADGEAS RDDGATSSVS ALKRLERSQW TDKMDLRFGF ERLKEPGEKT GWLINMHPTE ILDEDKRLGS AVDYYFIQD DGSRFKVALP YKPYFYIATR KGCEREVSSF LSKKFQGKIA KVETVPKEDL DLPNHLVGLK RNYIRLSFHT V EDLVKVRK ...String:
MSLRSGGRRR ADPGADGEAS RDDGATSSVS ALKRLERSQW TDKMDLRFGF ERLKEPGEKT GWLINMHPTE ILDEDKRLGS AVDYYFIQD DGSRFKVALP YKPYFYIATR KGCEREVSSF LSKKFQGKIA KVETVPKEDL DLPNHLVGLK RNYIRLSFHT V EDLVKVRK EISPAVKKNR EQDHASDAYT ALLSSVLQRG GVITDEEETS KKIADQLDNI VDMREYDVPY HIRLSIDLKI HV AHWYNVR YRGNAFPVEI TRRDDLVERP DPVVLAFAIA TTKLPLKFPD AETDQIMMIS YMIDGQGYLI TNREIVSEDI EDF EFTPKP EYEGPFCVFN EPDEAHLIQR WFEHVQETKP TIMVTYNGDF FDWPFVEARA AVHGLSMQQE IGFQKDSQGE YKAP QCIHM DCLRWVKRDS YLPVGSHNLK AAAKAKLGYD PVELDPEDMC RMATEQPQTL ATYSVSDAVA TYYLYMKYVH PFIFA LCTI IPMEPDEVLR KGSGTLCEAL LMVQAFHANI IFPNKQEQEF NKLTDDGHVL DSETYVGGHV EALESGVFRS DIPCRF RMN PAAFDFLLQR VEKTLRHALE EEEKVPVEQV TNFEEVCDEI KSKLASLKDV PSRIECPLIY HLDVGAMYPN IILTNRL QP SAMVDEATCA ACDFNKPGAN CQRKMAWQWR GEFMPASRSE YHRIQHQLES EKFPPLFPEG PARAFHELSR EEQAKYEK R RLADYCRKAY KKIHITKVEE RLTTICQREN SFYVDTVRAF RDRRYEFKGL HKVWKKKLSA AVEVGDAAEV KRCKNMEVL YDSLQLAHKC ILNSFYGYVM RKGARWYSME MAGIVCFTGA NIITQARELI EQIGRPLELD TDGIWCVLPN SFPENFVFKT TNVKKPKVT ISYPGAMLNI MVKEGFTNDQ YQELAEPSSL TYVTRSENSI FFEVDGPYLA MILPASKEEG KKLKKRYAVF N EDGSLAEL KGFEVKRRGE LQLIKIFQSS VFEAFLKGST LEEVYGSVAK VADYWLDVLY SKAANMPDSE LFELISENRS MS RKLEDYG EQKSTSISTA KRLAEFLGDQ MVKDAGLSCR YIISRKPEGS PVTERAIPLA IFQAEPTVRK HFLRKWLKSS SLQ DFDIRA ILDWDYYIER LGSAIQKIIT IPAALQQVKN PVPRVKHPDW LHKKLLEKND VYKQKKISEL FTLEGRRQVT MAEA SEDSP RPSAPDMEDF GLVKLPHPAA PVTVKRKRVL WESQEESQDL TPTVPWQEIL GQPPALGTSQ EEWLVWLRFH KKKWQ LQAR QRLARRKRQR LESAEGVLRP GAIRDGPATG LGSFLRRTAR SILDLPWQIV QISETSQAGL FRLWALVGSD LHCIRL SIP RVFYVNQRVA KAEEGASYRK VNRVLPRSNM VYNLYEYSVP EDMYQEHINE INAELSAPDI EGVYETQVPL LFRALVH LG CVCVVNKQLV RHLSGWEAET FALEHLEMRS LAQFSYLEPG SIRHIYLYHH AQAHKALFGI FIPSQRRASV FVLDTVRT D QMPSLGALYS AEHGLLLEKV GPELLPPPKH TFEVRAETDL KTICRAIQRF LLAYKEERRG PTLIAVQSSW ELKRLASEI PVLEEFPLVP ICVADKINYG VLDWQRHGAR RMIRHYLNLD TCLSQAFEMS RYFHIPIGNL PEDISTFGSD LFFARHLQRH NHLLWLSPT ARPDLGGKEA DDNCLVMEFD DQATVEINSS GCYSTVCVEL DLQNLAVNTI LQSHHVNDME GADSMGISFD V IQQASLED MITGGQAASA PASYDETALC SNTFRILKSM VVGWVKEITQ YHNIYADNQV MHFYRWLRSP SSLLHDPALH RT LHNMMKK LFLQLIAEFK RLGSSVIYAN FNRIILCTKK RRVEDAIAYV EYITSSIHSK ETFHSLTISF SRCWEFLLWM DPS NYGGIK GKVSSRIHCG LQDSQKAGGA EDEQENEDDE EERDGEEEEE AEESNVEDLL ENNWNILQFL PQAASCQNYF LMIV SAYIV AVYHCMKDGL RRSAPGSTPV RRRGASQLSQ EAEGAVGALP GMITFSQDYV ANELTQSFFT ITQKIQKKVT GSRNS TELS EMFPVLPGSH LLLNNPALEF IKYVCKVLSL DTNITNQVNK LNRDLLRLVD VGEFSEEAQF RDPCRSYVLP EVICRS CNF CRDLDLCKDS SFSEDGAVLP QWLCSNCQAP YDSSAIEMTL VEVLQKKLMA FTLQDLVCLK CRGVKETSMP VYCTCAG DF ALTIHTQVFM EQIGIFRNIA QHYGMSYLLE TLEWLLQKNP QLGH

UniProtKB: DNA polymerase epsilon catalytic subunit

-
Macromolecule #2: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.795752 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MFEARLVQGS ILKKVLEALK DLINEACWDI SSSGVNLQSM DSSHVSLVQL TLRSEGFDTY RCDRNLAMGV NLTSMSKILK CAGNEDIIT LRAEDNADTL ALVFEAPNQE KVSDYEMKLM DLDVEQLGIP EQEYSCVVKM PSGEFARICR DLSHIGDAVV I SCAKDGVK ...String:
MFEARLVQGS ILKKVLEALK DLINEACWDI SSSGVNLQSM DSSHVSLVQL TLRSEGFDTY RCDRNLAMGV NLTSMSKILK CAGNEDIIT LRAEDNADTL ALVFEAPNQE KVSDYEMKLM DLDVEQLGIP EQEYSCVVKM PSGEFARICR DLSHIGDAVV I SCAKDGVK FSASGELGNG NIKLSQTSNV DKEEEAVTIE MNEPVQLTFA LRYLNFFTKA TPLSSTVTLS MSADVPLVVE YK IADMGHL KYYLAPKIED EEGS

UniProtKB: Proliferating cell nuclear antigen

-
Macromolecule #3: Primer DNA

MacromoleculeName: Primer DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 10.823965 KDa
SequenceString:
(DT)(DG)(DA)(DG)(DG)(DT)(DT)(DC)(DA)(DG) (DC)(DA)(DA)(DG)(DG)(DT)(DG)(DA)(DT)(DG) (DC)(DT)(DT)(DT)(DA)(DG)(DA)(DT)(DT) (DT)(DT)(DT)(DC)(DA)(DC)

-
Macromolecule #4: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 18.13668 KDa
SequenceString: (DG)(DC)(DC)(DA)(DC)(DG)(DC)(DT)(DG)(DA) (DG)(DA)(DG)(DC)(DC)(DA)(DG)(DC)(DA)(DG) (DC)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DA) (DA)(DA)(DA)(DT)(DC)(DT)(DA)(DA)(DA)(DG) (DC) (DA)(DT)(DC)(DA)(DC)(DC) ...String:
(DG)(DC)(DC)(DA)(DC)(DG)(DC)(DT)(DG)(DA) (DG)(DA)(DG)(DC)(DC)(DA)(DG)(DC)(DA)(DG) (DC)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DA) (DA)(DA)(DA)(DT)(DC)(DT)(DA)(DA)(DA)(DG) (DC) (DA)(DT)(DC)(DA)(DC)(DC)(DT)(DT) (DG)(DC)(DT)(DG)(DA)(DA)(DC)(DC)(DT)(DC) (DA)

-
Macromolecule #5: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMNaClSodium chloride
1.0 mMDTTDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 320111
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9b8t:
Human polymerase epsilon bound to PCNA and DNA in the nucleotide bound state

+
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