[English] 日本語
Yorodumi
- EMDB-24618: Archaeal DNA ligase and heterotrimeric PCNA in complex with non-l... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24618
TitleArchaeal DNA ligase and heterotrimeric PCNA in complex with non-ligatable DNA
Map dataSharpened map
Sample
  • Complex: Ternary complex of DNA Ligase with PCNA1-2-3 and non-ligatable DNA
    • Protein or peptide: DNA polymerase sliding clamp 1
    • Protein or peptide: DNA polymerase sliding clamp 2
    • Protein or peptide: DNA polymerase sliding clamp 3
    • DNA: Upstream strand DNA
    • DNA: Downstream strand DNA
    • DNA: Template strand DNA
    • Protein or peptide: DNA ligase
  • Ligand: MANGANESE (II) ION
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsDNA ligase / PCNA / cryo-EM / LIGASE-DNA complex
Function / homology
Function and homology information


DNA ligase (ATP) / DNA ligase (ATP) activity / : / lagging strand elongation / DNA biosynthetic process / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA recombination / cell division ...DNA ligase (ATP) / DNA ligase (ATP) activity / : / lagging strand elongation / DNA biosynthetic process / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA recombination / cell division / DNA repair / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA ligase, ATP-dependent, bacterial/archaeal / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region ...DNA ligase, ATP-dependent, bacterial/archaeal / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / 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 / : / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA polymerase sliding clamp 3 / DNA polymerase sliding clamp 1 / DNA polymerase sliding clamp 2 / DNA ligase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsSverzhinsky A / Pascal JM
Funding support United States, 2 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-05776 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA92584 United States
CitationJournal: Structure / Year: 2022
Title: Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase.
Authors: Aleksandr Sverzhinsky / Alan E Tomkinson / John M Pascal /
Abstract: DNA ligases act in the final step of many DNA repair pathways and are commonly regulated by the DNA sliding clamp proliferating cell nuclear antigen (PCNA), but there are limited insights into the ...DNA ligases act in the final step of many DNA repair pathways and are commonly regulated by the DNA sliding clamp proliferating cell nuclear antigen (PCNA), but there are limited insights into the physical basis for this regulation. Here, we use single-particle cryoelectron microscopy (cryo-EM) to analyze an archaeal DNA ligase and heterotrimeric PCNA in complex with a single-strand DNA break. The cryo-EM structures highlight a continuous DNA-binding surface formed between DNA ligase and PCNA that supports the distorted conformation of the DNA break undergoing repair and contributes to PCNA stimulation of DNA ligation. DNA ligase is conformationally flexible within the complex, with its domains fully ordered only when encircling the repaired DNA to form a stacked ring structure with PCNA. The structures highlight DNA ligase structural transitions while docked on PCNA, changes in DNA conformation during ligation, and the potential for DNA ligase domains to regulate PCNA accessibility to other repair factors.
History
DepositionAug 3, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7rpo
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24618.png

Downloads & links

-
Map

FileDownload / File: emd_24618.map.gz / Format: CCP4 / Size: 24.5 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.)
1.5 Å/pix.
x 186 pix.
= 279. Å		1.5 Å/pix.
x 186 pix.
= 279. Å		1.5 Å/pix.
x 186 pix.
= 279. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.021911763 - 1.8304584
Average (Standard dev.)0.0014294933 (±0.026357125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions186186186
Spacing186186186
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z186186186
origin x/y/z0.0000.0000.000
length x/y/z279.000279.000279.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS186186186
D min/max/mean-0.0221.8300.001

-
Supplemental data

-
Additional map: #1

Fileemd_24618_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Ternary complex of DNA Ligase with PCNA1-2-3 and non-ligatable DNA

EntireName: Ternary complex of DNA Ligase with PCNA1-2-3 and non-ligatable DNA
Components
  • Complex: Ternary complex of DNA Ligase with PCNA1-2-3 and non-ligatable DNA
    • Protein or peptide: DNA polymerase sliding clamp 1
    • Protein or peptide: DNA polymerase sliding clamp 2
    • Protein or peptide: DNA polymerase sliding clamp 3
    • DNA: Upstream strand DNA
    • DNA: Downstream strand DNA
    • DNA: Template strand DNA
    • Protein or peptide: DNA ligase
  • Ligand: MANGANESE (II) ION
  • Ligand: ADENOSINE MONOPHOSPHATE

+
Supramolecule #1: Ternary complex of DNA Ligase with PCNA1-2-3 and non-ligatable DNA

SupramoleculeName: Ternary complex of DNA Ligase with PCNA1-2-3 and non-ligatable DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 175 KDa

+
Macromolecule #1: DNA polymerase sliding clamp 1

MacromoleculeName: DNA polymerase sliding clamp 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 28.711961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAFKIVYPNA KDFFSFINSI TNVTDSIILN FTEDGIFSRH LTEDKVLMAI MRIPKDVLSE YSIDSPTSVK LDVSSVKKIL SKASSKKAT IELTETDSGL KIIIRDEKSG AKSTIYIKAE KGQVEQLTEP KVNLAVNFTT DESVLNVIAA DVTLVGEEMR I STEEDKIK ...String:
MAFKIVYPNA KDFFSFINSI TNVTDSIILN FTEDGIFSRH LTEDKVLMAI MRIPKDVLSE YSIDSPTSVK LDVSSVKKIL SKASSKKAT IELTETDSGL KIIIRDEKSG AKSTIYIKAE KGQVEQLTEP KVNLAVNFTT DESVLNVIAA DVTLVGEEMR I STEEDKIK IEAGEEGKRY VAFLMKDKPL KELSIDTSAS SSYSAEMFKD AVKGLRGFSA PTMVSFGENL PMKIDVEAVS GG HMIFWIA PRLLEHHHHH H

UniProtKB: DNA polymerase sliding clamp 1

+
Macromolecule #2: DNA polymerase sliding clamp 2

MacromoleculeName: DNA polymerase sliding clamp 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 27.461084 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKAKVIDAVS FSYILRTVGD FLSEANFIVT KEGIRVSGID PSRVVFLDIF LPSSYFEGFE VSQEKEIIGF KLEDVNDILK RVLKDDTLI LSSNESKLTL TFDGEFTRSF ELPLIQVEST QPPSVNLEFP FKAQLLTITF ADIIDELSDL GEVLNIHSKE N KLYFEVIG ...String:
MKAKVIDAVS FSYILRTVGD FLSEANFIVT KEGIRVSGID PSRVVFLDIF LPSSYFEGFE VSQEKEIIGF KLEDVNDILK RVLKDDTLI LSSNESKLTL TFDGEFTRSF ELPLIQVEST QPPSVNLEFP FKAQLLTITF ADIIDELSDL GEVLNIHSKE N KLYFEVIG DLSTAKVELS TDNGTLLEAS GADVSSSYGM EYVANTTKMR RASDSMELYF GSQIPLKLRF KLPQEGYGDF YI APRAD

UniProtKB: DNA polymerase sliding clamp 2

+
Macromolecule #3: DNA polymerase sliding clamp 3

MacromoleculeName: DNA polymerase sliding clamp 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 28.560268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKVVYDDVRV LKDIIQALAR LVDEAVLKFK QDSVELVALD RAHISLISVN LPREMFKEYD VNDEFKFGFN TQYLMKILKV AKRKEAIEI ASESPDSVII NIIGSTNREF NVRNLEVSEQ EIPEINLQFD ISATISSDGF KSAISEVSTV TDNVVVEGHE D RILIKAEG ...String:
MKVVYDDVRV LKDIIQALAR LVDEAVLKFK QDSVELVALD RAHISLISVN LPREMFKEYD VNDEFKFGFN TQYLMKILKV AKRKEAIEI ASESPDSVII NIIGSTNREF NVRNLEVSEQ EIPEINLQFD ISATISSDGF KSAISEVSTV TDNVVVEGHE D RILIKAEG ESEVEVEFSK DTGGLQDLEF SKESKNSYSA EYLDDVLSLT KLSDYVKISF GNQKPLQLFF NMEGGGKVTY LL APKVLEH HHHHH

UniProtKB: DNA polymerase sliding clamp 3

+
Macromolecule #7: DNA ligase

MacromoleculeName: DNA ligase / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA ligase (ATP)
Source (natural)Organism: Saccharolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 69.998375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MEFKVIAEYF DKLEKISSRL QLTALLADLL SKSDKTIIDK VVYIIQGKLW PDFLGYPELG IGEKFLIKA ISIATNTDEN SVENLYKTIG DLGEVARRLK SKQQSTGILG FLGTTSKESL TVDEVYSTLS KVALTTGEGS R DLKIRLLA ...String:
MGSSHHHHHH SSGLVPRGSH MEFKVIAEYF DKLEKISSRL QLTALLADLL SKSDKTIIDK VVYIIQGKLW PDFLGYPELG IGEKFLIKA ISIATNTDEN SVENLYKTIG DLGEVARRLK SKQQSTGILG FLGTTSKESL TVDEVYSTLS KVALTTGEGS R DLKIRLLA GLLKKADPLE AKFLVRFVEG RLRVGIGDAT VLDAMAIAFG GGQSASEIIE RAYNLRADLG NIAKIIVEKG IE ALKTLKP QVGIPIRPML AERLSNPEEI LKKMGGNAIV DYKYDGERAQ IHKKEDKIFI FSRRLENITS QYPDVVDYVS KYI EGKEFI IEGEIVAIDP ESGEMRPFQE LMHRKRKSDI YEAIKEYPVN VFLFDLMYYE DVDYTTKPLE ARRKLLESIV KPND YVKIA HHIQANNVED LKSFFYRAIS EGGEGVMVKA IGKDAIYQAG ARGWLWIKLK RDYQSEMADT VDLVVVGGFY GKGKR GGKI SSLLMAAYNP KTDSFESVCK VASGFSDEQL DELQKKLMEI KRDVKHPRVN SKMEPDIWVE PVYVAEIIGS EITISP LHT CCQDVVEKDA GLSIRFPRFI RWRDDKSPED ATTTDEILEM YNKQPKKKIE SPAVDESV

UniProtKB: DNA ligase

+
Macromolecule #4: Upstream strand DNA

MacromoleculeName: Upstream strand DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.376751 KDa
SequenceString:
(DG)(DT)(DA)(DT)(DC)(DC)(DT)(DC)(DG)(DT) (DA)(DG)(DT)(DG)(DC)(DA)(DG)(DA)(DT)(DG) (DC)(DG)(DT)(DC)

+
Macromolecule #5: Downstream strand DNA

MacromoleculeName: Downstream strand DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.127594 KDa
SequenceString:
(DG)(DT)(DC)(DG)(DG)(DA)(DC)(DT)(DG)(DA) (DT)(DT)(DC)(DG)(DG)(DT)(DA)(DG)(DA)(DT) (DC)(DT)(DG)

+
Macromolecule #6: Template strand DNA

MacromoleculeName: Template strand DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.403264 KDa
SequenceString:
(DC)(DA)(DG)(DA)(DT)(DC)(DT)(DA)(DC)(DC) (DG)(DA)(DA)(DT)(DC)(DA)(DG)(DT)(DC)(DC) (DG)(DA)(DC)(DG)(DA)(DC)(DG)(DC)(DA) (DT)(DC)(DT)(DG)(DC)(DA)(DC)(DT)(DA)(DC) (DG) (DA)(DG)(DG)(DA)(DT)(DA)(DC)

+
Macromolecule #8: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

+
Macromolecule #9: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.175 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: wait time 0, blot force 1, blot time 1, drain time 0.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3014 / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 306503
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

2hix

source_name: PDB, initial_model_type: experimental model

2hii

source_name: PDB, initial_model_type: experimental model

1x9n

chain_id: B, source_name: PDB, initial_model_type: experimental model

1x9n

chain_id: C, source_name: PDB, initial_model_type: experimental model

1x9n

chain_id: D, source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7rpo:
Archaeal DNA ligase and heterotrimeric PCNA in complex with non-ligatable DNA

+
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