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- EMDB-39354: Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D -

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Entry
Database: EMDB / ID: EMD-39354
TitleStructure of the human endogenous PCNA-FEN1-RNase H2 complex - State D
Map data
Sample
  • Complex: endogenous state D PCNA-DNA-FEN1-RNase H2 complex
    • Protein or peptide: Proliferating cell nuclear antigen
    • Protein or peptide: Flap endonuclease 1
    • Protein or peptide: Ribonuclease H2 subunit A
    • Protein or peptide: Ribonuclease H2 subunit B
    • Protein or peptide: Ribonuclease H2 subunit C
    • DNA: upstream DNA
    • DNA: parent strand DNA
    • DNA: downstream DNA
KeywordsFlap endonuclease 1 / RNase H2 / endogenous DNA / PCNA / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


ribonucleotide metabolic process / ribonuclease H2 complex / flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication ...ribonucleotide metabolic process / ribonuclease H2 complex / flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / 5'-flap endonuclease activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / UV protection / 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 / regulation of DNA damage checkpoint / PCNA complex / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / 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 / RNA catabolic process / replisome / 5'-3' exonuclease activity / exonuclease activity / ribonuclease H / response to L-glutamate / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / Early Phase of HIV Life Cycle / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / RNA nuclease activity / translesion synthesis / mismatch repair / estrous cycle / response to cadmium ion / cyclin-dependent protein kinase holoenzyme complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / regulation of G2/M transition of mitotic cell cycle / 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 / double-strand break repair via homologous recombination / liver regeneration / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / memory / cellular response to hydrogen peroxide / positive regulation of fibroblast proliferation / RNA-DNA hybrid ribonuclease activity / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / double-strand break repair / response to estradiol / manganese ion binding / chromatin organization / heart development / double-stranded DNA binding / fibroblast proliferation / endonuclease activity / damaged DNA binding / in utero embryonic development / gene expression / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA replication / nuclear body / negative regulation of gene expression
Similarity search - Function
Ribonuclease H2, subunit C / : / Ribonuclease H2 non-catalytic subunit (Ylr154p-like) / Ribonuclease H2 subunit B, wHTH domain / Ribonuclease H2 subunit B / Rnh202, triple barrel domain / Ydr279p protein family (RNase H2 complex component) wHTH domain / Ydr279p protein triple barrel domain / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease H2, subunit A ...Ribonuclease H2, subunit C / : / Ribonuclease H2 non-catalytic subunit (Ylr154p-like) / Ribonuclease H2 subunit B, wHTH domain / Ribonuclease H2 subunit B / Rnh202, triple barrel domain / Ydr279p protein family (RNase H2 complex component) wHTH domain / Ydr279p protein triple barrel domain / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease H2, subunit A / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Ribonuclease (RNase) H type-2 domain profile. / Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Proliferating cell nuclear antigen signature 2. / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 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 / PIN-like domain superfamily / : / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Ribonuclease H2 subunit A / Proliferating cell nuclear antigen / Flap endonuclease 1 / Ribonuclease H2 subunit B / Ribonuclease H2 subunit C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.15 Å
AuthorsTian Y / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: EMBO J / Year: 2025
Title: Structural insight into Okazaki fragment maturation mediated by PCNA-bound FEN1 and RNaseH2.
Authors: Yuhui Tian / Ningning Li / Qing Li / Ning Gao /
Abstract: PCNA is a master coordinator of many DNA-metabolic events. During DNA replication, the maturation of Okazaki fragments involves at least four DNA enzymes, all of which contain PCNA-interacting motifs. ...PCNA is a master coordinator of many DNA-metabolic events. During DNA replication, the maturation of Okazaki fragments involves at least four DNA enzymes, all of which contain PCNA-interacting motifs. However, the temporal relationships and functional modulations between these PCNA-binding proteins are unclear. Here, we developed a strategy to purify endogenous PCNA-containing complexes from native chromatin, and characterized their structures using cryo-EM. Two structurally resolved classes (PCNA-FEN1 and PCNA-FEN1-RNaseH2 complexes) have captured a series of 3D snapshots for the primer-removal steps of Okazaki fragment maturation. These structures show that product release from FEN1 is a rate-liming step. Furthermore, both FEN1 and RNaseH2 undergo continuous conformational changes on PCNA that result in constant fluctuations in the bending angle of substrate DNA at the nick site, implying that these enzymes could regulate each other through conformational modulation of the bound DNA. The structures of the PCNA-FEN1-RNaseH2 complex confirm the toolbelt function of PCNA and suggests a potential unrecognized role of RNaseH2, as a dsDNA binding protein, in promoting the 5'-flap cleaving activity of FEN1.
History
DepositionMar 3, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39354.png

Downloads & links

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Map

FileDownload / File: emd_39354.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00493
Minimum - Maximum-0.008181233 - 0.018870475
Average (Standard dev.)0.00005748354 (±0.00058041094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39354_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_39354_half_map_2.map
Projections & Slices
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Sample components

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Entire : endogenous state D PCNA-DNA-FEN1-RNase H2 complex

EntireName: endogenous state D PCNA-DNA-FEN1-RNase H2 complex
Components
  • Complex: endogenous state D PCNA-DNA-FEN1-RNase H2 complex
    • Protein or peptide: Proliferating cell nuclear antigen
    • Protein or peptide: Flap endonuclease 1
    • Protein or peptide: Ribonuclease H2 subunit A
    • Protein or peptide: Ribonuclease H2 subunit B
    • Protein or peptide: Ribonuclease H2 subunit C
    • DNA: upstream DNA
    • DNA: parent strand DNA
    • DNA: downstream DNA

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Supramolecule #1: endogenous state D PCNA-DNA-FEN1-RNase H2 complex

SupramoleculeName: endogenous state D PCNA-DNA-FEN1-RNase H2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.795752 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

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Macromolecule #2: Flap endonuclease 1

MacromoleculeName: Flap endonuclease 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.661051 KDa
SequenceString: MGIQGLAKLI ADVAPSAIRE NDIKSYFGRK VAIDASMSIY QFLIAVRQGG DVLQNEEGET TSHLMGMFYR TIRMMENGIK PVYVFDGKP PQLKSGELAK RSERRAEAEK QLQQAQAAGA EQEVEKFTKR LVKVTKQHND ECKHLLSLMG IPYLDAPSEA E ASCAALVK ...String:
MGIQGLAKLI ADVAPSAIRE NDIKSYFGRK VAIDASMSIY QFLIAVRQGG DVLQNEEGET TSHLMGMFYR TIRMMENGIK PVYVFDGKP PQLKSGELAK RSERRAEAEK QLQQAQAAGA EQEVEKFTKR LVKVTKQHND ECKHLLSLMG IPYLDAPSEA E ASCAALVK AGKVYAAATE DMDCLTFGSP VLMRHLTASE AKKLPIQEFH LSRILQELGL NQEQFVDLCI LLGSDYCESI RG IGPKRAV DLIQKHKSIE EIVRRLDPNK YPVPENWLHK EAHQLFLEPE VLDPESVELK WSEPNEEELI KFMCGEKQFS EER IRSGVK RLSKSRQGST QGRLDDFFKV TGSLSSAKRK EPEPKGSTKK KAKTGAAGKF KRGK

UniProtKB: Flap endonuclease 1

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Macromolecule #3: Ribonuclease H2 subunit A

MacromoleculeName: Ribonuclease H2 subunit A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease H
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.431844 KDa
SequenceString: MDLSELERDN TGRCRLSSPV PAVCRKEPCV LGVDEAGRGP VLGPMVYAIC YCPLPRLADL EALKVADSKT LLESERERLF AKMEDTDFV GWALDVLSPN LISTSMLGRV KYNLNSLSHD TATGLIQYAL DQGVNVTQVF VDTVGMPETY QARLQQSFPG I EVTVKAKA ...String:
MDLSELERDN TGRCRLSSPV PAVCRKEPCV LGVDEAGRGP VLGPMVYAIC YCPLPRLADL EALKVADSKT LLESERERLF AKMEDTDFV GWALDVLSPN LISTSMLGRV KYNLNSLSHD TATGLIQYAL DQGVNVTQVF VDTVGMPETY QARLQQSFPG I EVTVKAKA DALYPVVSAA SICAKVARDQ AVKKWQFVEK LQDLDTDYGS GYPNDPKTKA WLKEHVEPVF GFPQFVRFSW RT AQTILEK EAEDVIWEDS ASENQEGLRK ITSYFLNEGS QARPRSSHRY FLERGLESAT SL

UniProtKB: Ribonuclease H2 subunit A

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Macromolecule #4: Ribonuclease H2 subunit B

MacromoleculeName: Ribonuclease H2 subunit B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.195727 KDa
SequenceString: MAAGVDCGDG VGARQHVFLV SEYLKDASKK MKNGLMFVKL VNPCSGEGAI YLFNMCLQQL FEVKVFKEKH HSWFINQSVQ SGGLLHFAT PVDPLFLLLH YLIKADKEGK FQPLDQVVVD NVFPNCILLL KLPGLEKLLH HVTEEKGNPE IDNKKYYKYS K EKTLKWLE ...String:
MAAGVDCGDG VGARQHVFLV SEYLKDASKK MKNGLMFVKL VNPCSGEGAI YLFNMCLQQL FEVKVFKEKH HSWFINQSVQ SGGLLHFAT PVDPLFLLLH YLIKADKEGK FQPLDQVVVD NVFPNCILLL KLPGLEKLLH HVTEEKGNPE IDNKKYYKYS K EKTLKWLE KKVNQTVAAL KTNNVNVSSR VQSTAFFSGD QASTDKEEDY IRYAHGLISD YIPKELSDDL SKYLKLPEPS AS LPNPPSK KIKLSDEPVE AKEDYTKFNT KDLKTEKKNS KMTAAQKALA KVDKSGMKSI DTFFGVKNKK KIGKV

UniProtKB: Ribonuclease H2 subunit B

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Macromolecule #5: Ribonuclease H2 subunit C

MacromoleculeName: Ribonuclease H2 subunit C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.862137 KDa
SequenceString:
MESGDEAAIE RHRVHLRSAT LRDAVPATLH LLPCEVAVDG PAPVGRFFTP AIRQGPEGLE VSFRGRCLRG EEVAVPPGLV GYVMVTEEK KVSMGKPDPL RDSGTDDQEE EPLERDFDRF IGATANFSRF TLWGLETIPG PDAKVRGALT WPSLAAAIHA Q VPED

UniProtKB: Ribonuclease H2 subunit C

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Macromolecule #6: upstream DNA

MacromoleculeName: upstream DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.101997 KDa
SequenceString:
(DA)(DT)(DT)(DT)(DT)(DT)(DA)(DA)(DT)(DT) (DT)(DA)(DT)(DA)(DA)(DT)(DT)(DA)(DT)(DT)

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Macromolecule #7: parent strand DNA

MacromoleculeName: parent strand DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.565299 KDa
SequenceString:
(DA)(DT)(DT)(DT)(DT)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DT)(DA)(DA)(DT)(DT)(DA)(DT) (DA)(DA)(DA)(DT)(DT)(DA)(DA)(DA)(DA) (DA)(DT)

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Macromolecule #8: downstream DNA

MacromoleculeName: downstream DNA / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.249797 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DA) (DA)(DA)(DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13906
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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