[English] 日本語
Yorodumi
- EMDB-60598: Structure of CTF18-PCNA with ATP and Mg2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60598
TitleStructure of CTF18-PCNA with ATP and Mg2+
Map dataSharpened map.
Sample
  • Complex: CTF18-PCNA
    • Complex: CTF18
      • Protein or peptide: Chromosome transmission fidelity protein 18 homolog
      • Protein or peptide: Replication factor C subunit 2
      • Protein or peptide: Replication factor C subunit 5
      • Protein or peptide: Replication factor C subunit 4
      • Protein or peptide: Replication factor C subunit 3
    • Complex: PCNA
      • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCTF18-RFC / human clamp loader / PCNA / sliding clamp / complex / ATP / DNA BINDING PROTEIN
Function / homology
Function and homology information


Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / DNA clamp loader activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina ...Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / DNA clamp loader activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / Transcription of E2F targets under negative control by DREAM complex / replisome / response to L-glutamate / HDR through Single Strand Annealing (SSA) / DNA strand elongation involved in DNA replication / Impaired BRCA2 binding to RAD51 / response to dexamethasone / DNA synthesis involved in DNA repair / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / replication fork processing / nuclear replication fork / Presynaptic phase of homologous DNA pairing and strand exchange / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / ATP-dependent activity, acting on DNA / translesion synthesis / mismatch repair / estrous cycle / response to cadmium ion / Activation of ATR in response to replication stress / cyclin-dependent protein kinase holoenzyme complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / DNA polymerase binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / epithelial cell differentiation / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / male germ cell nucleus / positive regulation of DNA replication / Termination of translesion DNA synthesis / replication fork / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / liver regeneration / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / G2/M DNA damage checkpoint / receptor tyrosine kinase binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-templated DNA replication / cellular response to hydrogen peroxide / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / Processing of DNA double-strand break ends / chromatin organization / heart development / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / chromosome, telomeric region / DNA replication / nuclear body / DNA repair / centrosome / chromatin binding / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
: / Replication factor C subunit 3, C-terminal domain / RCF1/5-like, AAA+ ATPase lid domain / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / DNA polymerase III, delta subunit / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Proliferating cell nuclear antigen signature 2. ...: / Replication factor C subunit 3, C-terminal domain / RCF1/5-like, AAA+ ATPase lid domain / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / DNA polymerase III, delta subunit / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / 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 / : / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Replication factor C subunit 4 / Replication factor C subunit 2 / Replication factor C subunit 5 / Replication factor C subunit 3 / Chromosome transmission fidelity protein 18 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBriola GR / Tehseen M / Al-Amodi A / Nguyen PQ / Savva CG / Hamdan SM / De Biasio A
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structure of the human CTF18 clamp loader bound to PCNA
Authors: Briola G / Tehseen M / Al-Amodi A / Nguyen PQ / Savva CG / Hamdan SM / De Biasio A
History
DepositionJun 20, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60598.png

Downloads & links

-
Map

FileDownload / File: emd_60598.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 220 pix.
= 204.6 Å		0.93 Å/pix.
x 220 pix.
= 204.6 Å		0.93 Å/pix.
x 220 pix.
= 204.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.009021559 - 0.021062361
Average (Standard dev.)0.00008388867 (±0.0010626644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 204.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_60598_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2.

Fileemd_60598_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1.

Fileemd_60598_half_map_2.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : CTF18-PCNA

EntireName: CTF18-PCNA
Components
  • Complex: CTF18-PCNA
    • Complex: CTF18
      • Protein or peptide: Chromosome transmission fidelity protein 18 homolog
      • Protein or peptide: Replication factor C subunit 2
      • Protein or peptide: Replication factor C subunit 5
      • Protein or peptide: Replication factor C subunit 4
      • Protein or peptide: Replication factor C subunit 3
    • Complex: PCNA
      • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: CTF18-PCNA

SupramoleculeName: CTF18-PCNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: CTF18 in complex with PCNA, in presence of ATP and Mg2+
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 323 KDa

+
Supramolecule #2: CTF18

SupramoleculeName: CTF18 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5

+
Supramolecule #3: PCNA

SupramoleculeName: PCNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6

+
Macromolecule #1: Chromosome transmission fidelity protein 18 homolog

MacromoleculeName: Chromosome transmission fidelity protein 18 homolog / type: protein_or_peptide / ID: 1
Details: -35: initiating methionine -34 to 0: expression tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.40707 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KENLYFQGED YEQELCGVED DFHNQFAAEL EVLAELEGAS TPSPSGVPLF TAGRPPRTF EEALARGDAA SSPAPAASVG SSQGGARKRQ VDADLQPAGS LPHAPRIKRP RLQVVKRLNF RSEEMEEPPP P DSSPTDIT ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KENLYFQGED YEQELCGVED DFHNQFAAEL EVLAELEGAS TPSPSGVPLF TAGRPPRTF EEALARGDAA SSPAPAASVG SSQGGARKRQ VDADLQPAGS LPHAPRIKRP RLQVVKRLNF RSEEMEEPPP P DSSPTDIT PPPSPEDLAE LWGHGVSEAA ADVGLTRASP AARNPVLRRP PILEDYVHVT STEGVRAYLV LRADPMAPGV QG SLLHVPW RGGGQLDLLG VSLASLKKQV DGERRERLLQ EAQKLSDTLH SLRSGEEEAA QPLGAPEEEP TDGQDASSHC LWV DEFAPR HYTELLSDDF TNRCLLKWLK LWDLVVFGHE RPSRKPRPSV EPARVSKEAT APGKWKSHEQ VLEEMLEAGL DPSQ RPKQK VALLCGPPGL GKTTLAHVIA RHAGYSVVEM NASDDRSPEV FRTRIEAATQ MESVLGAGGK PNCLVIDEID GAPVA AINV LLSILNRKGP QEVGPQGPAV PSGGGRRRRA EGGLLMRPII CICNDQFAPS LRQLKQQAFL LHFPPTLPSR LVQRLQ EVS LRQGMRADPG VLAALCEKTD NDIRACINTL QFLYSRGQRE LSVRDVQATR VGLKDQRRGL FSVWQEVFQL PRAQRRR VG QDPALPADTL LLGDGDAGSL TSASQRFYRV LHAAASAGEH EKVVQGLFDN FLRLRLRDSS LGAVCVALDW LAFDDLLA G AAHHSQSFQL LRYPPFLPVA FHVLFASSHT PRITFPSSQQ EAQNRMSQMR NLIQTLVSGI APATRSRATP QALLLDALC LLLDILAPKL RPVSTQLYST REKQQLASLV GTMLAYSLTY RQERTPDGQY IYRLEPNVEE LCRFPELPAR KPLTYQTKQL IAREIEVEK MRRAEASARV ENSPQVDGSP PGLEGLLGGI GEKGVHRPAP RNHEQRLEHI MRRAAREEQP EKDFFGRVVV R STAVPSAG DTAPEQDSVE RRMGTAVGRS EVWFRFNEGV SNAVRRSLYI RDLL

UniProtKB: Chromosome transmission fidelity protein 18 homolog

+
Macromolecule #2: Replication factor C subunit 2

MacromoleculeName: Replication factor C subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.203207 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEVEAVCGGA GEVEAQDSDP APAFSKAPGS AGHYELPWVE KYRPVKLNEI VGNEDTVSRL EVFAREGNVP NIIIAGPPGT GKTTSILCL ARALLGPALK DAMLELNASN DRGIDVVRNK IKMFAQQKVT LPKGRHKIII LDEADSMTDG AQQALRRTME I YSKTTRFA ...String:
MEVEAVCGGA GEVEAQDSDP APAFSKAPGS AGHYELPWVE KYRPVKLNEI VGNEDTVSRL EVFAREGNVP NIIIAGPPGT GKTTSILCL ARALLGPALK DAMLELNASN DRGIDVVRNK IKMFAQQKVT LPKGRHKIII LDEADSMTDG AQQALRRTME I YSKTTRFA LACNASDKII EPIQSRCAVL RYTKLTDAQI LTRLMNVIEK ERVPYTDDGL EAIIFTAQGD MRQALNNLQS TF SGFGFIN SENVFKVCDE PHPLLVKEMI QHCVNANIDE AYKILAHLWH LGYSPEDIIG NIFRVCKTFQ MAEYLKLEFI KEI GYTHMK IAEGVNSLLQ MAGLLARLCQ KTMAPVAS

UniProtKB: Replication factor C subunit 2

+
Macromolecule #3: Replication factor C subunit 5

MacromoleculeName: Replication factor C subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.545512 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: METSALKQQE QPAATKIRNL PWVEKYRPQT LNDLISHQDI LSTIQKFINE DRLPHLLLYG PPGTGKTSTI LACAKQLYKD KEFGSMVLE LNASDDRGID IIRGPILSFA STRTIFKKGF KLVILDEADA MTQDAQNALR RVIEKFTENT RFCLICNYLS K IIPALQSR ...String:
METSALKQQE QPAATKIRNL PWVEKYRPQT LNDLISHQDI LSTIQKFINE DRLPHLLLYG PPGTGKTSTI LACAKQLYKD KEFGSMVLE LNASDDRGID IIRGPILSFA STRTIFKKGF KLVILDEADA MTQDAQNALR RVIEKFTENT RFCLICNYLS K IIPALQSR CTRFRFGPLT PELMVPRLEH VVEEEKVDIS EDGMKALVTL SSGDMRRALN ILQSTNMAFG KVTEETVYTC TG HPLKSDI ANILDWMLNQ DFTTAYRNIT ELKTLKGLAL HDILTEIHLF VHRVDFPSSV RIHLLTKMAD IEYRLSVGTN EKI QLSSLI AAFQVTRDLI VAEA

UniProtKB: Replication factor C subunit 5

+
Macromolecule #4: Replication factor C subunit 4

MacromoleculeName: Replication factor C subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.735711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQAFLKGTSI STKPPLTKDR GVAASAGSSG ENKKAKPVPW VEKYRPKCVD EVAFQEEVVA VLKKSLEGAD LPNLLFYGPP GTGKTSTIL AAARELFGPE LFRLRVLELN ASDERGIQVV REKVKNFAQL TVSGSRSDGK PCPPFKIVIL DEADSMTSAA Q AALRRTME ...String:
MQAFLKGTSI STKPPLTKDR GVAASAGSSG ENKKAKPVPW VEKYRPKCVD EVAFQEEVVA VLKKSLEGAD LPNLLFYGPP GTGKTSTIL AAARELFGPE LFRLRVLELN ASDERGIQVV REKVKNFAQL TVSGSRSDGK PCPPFKIVIL DEADSMTSAA Q AALRRTME KESKTTRFCL ICNYVSRIIE PLTSRCSKFR FKPLSDKIQQ QRLLDIAKKE NVKISDEGIA YLVKVSEGDL RK AITFLQS ATRLTGGKEI TEKVITDIAG VIPAEKIDGV FAACQSGSFD KLEAVVKDLI DEGHAATQLV NQLHDVVVEN NLS DKQKSI ITEKLAEVDK CLADGADEHL QLISLCATVM QQLSQNC

UniProtKB: Replication factor C subunit 4

+
Macromolecule #5: Replication factor C subunit 3

MacromoleculeName: Replication factor C subunit 3 / type: protein_or_peptide / ID: 5 / Details: -5: INITIATING METHIONINE -4 TO 0: EXPRESSION TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.436258 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHMSLW VDKYRPCSLG RLDYHKEQAA QLRNLVQCGD FPHLLVYGPS GAGKKTRIMC ILRELYGVGV EKLRIEHQTI TTPSKKKIE ISTIASNYHL EVNPSDAGNS DRVVIQEMLK TVAQSQQLET NSQRDFKVVL LTEVDKLTKD AQHALRRTME K YMSTCRLI ...String:
MHHHHHMSLW VDKYRPCSLG RLDYHKEQAA QLRNLVQCGD FPHLLVYGPS GAGKKTRIMC ILRELYGVGV EKLRIEHQTI TTPSKKKIE ISTIASNYHL EVNPSDAGNS DRVVIQEMLK TVAQSQQLET NSQRDFKVVL LTEVDKLTKD AQHALRRTME K YMSTCRLI LCCNSTSKVI PPIRSRCLAV RVPAPSIEDI CHVLSTVCKK EGLNLPSQLA HRLAEKSCRN LRKALLMCEA CR VQQYPFT ADQEIPETDW EVYLRETANA IVSQQTPQRL LEVRGRLYEL LTHCIPPEII MKGLLSELLH NCDGQLKGEV AQM AAYYEH RLQLGSKAIY HLEAFVAKFM ALYKKFMEDG LEGMMF

UniProtKB: Replication factor C subunit 3

+
Macromolecule #6: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 6 / Details: -5: INITIATING METHIONINE -4 TO 0: EXPRESSION TAG / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.617672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHMFEA RLVQGSILKK VLEALKDLIN EACWDISSSG VNLQSMDSSH VSLVQLTLRS EGFDTYRCDR NLAMGVNLTS MSKILKCAG NEDIITLRAE DNADTLALVF EAPNQEKVSD YEMKLMDLDV EQLGIPEQEY SCVVKMPSGE FARICRDLSH I GDAVVISC ...String:
MHHHHHMFEA RLVQGSILKK VLEALKDLIN EACWDISSSG VNLQSMDSSH VSLVQLTLRS EGFDTYRCDR NLAMGVNLTS MSKILKCAG NEDIITLRAE DNADTLALVF EAPNQEKVSD YEMKLMDLDV EQLGIPEQEY SCVVKMPSGE FARICRDLSH I GDAVVISC AKDGVKFSAS GELGNGNIKL SQTSNVDKEE EAVTIEMNEP VQLTFALRYL NFFTKATPLS STVTLSMSAD VP LVVEYKI ADMGHLKYYL APKIEDEEGS

UniProtKB: Proliferating cell nuclear antigen

+
Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

+
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 50 mM Tris-HCl, 200 mM NaCl, 1 mM DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 83.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 6181 / Average exposure time: 5.0 sec. / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
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: 3216167
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 602591
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6vvo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9iin:
Structure of CTF18-PCNA with ATP and Mg2+

+
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