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- EMDB-42295: Cryo-EM map of human clamp-clamp loader ATAD5-RFC-closed PCNA com... -

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Basic information

Entry
Database: EMDB / ID: EMD-42295
TitleCryo-EM map of human clamp-clamp loader ATAD5-RFC-closed PCNA complex in intermediate state 1
Map dataPrimary sharpen Cryo-EM map
Sample
  • Complex: ATAD5-RFC-closed PCNA
    • Protein or peptide: ATPase family AAA domain-containing protein 5
    • 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
    • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA ATPase / Clamp unloader / MOTOR PROTEIN
Function / homology
Function and homology information


DNA clamp unloader activity / positive regulation of cell cycle G2/M phase transition / positive regulation of DNA-directed DNA polymerase activity / Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / nuclear DNA replication / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication ...DNA clamp unloader activity / positive regulation of cell cycle G2/M phase transition / positive regulation of DNA-directed DNA polymerase activity / Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / nuclear DNA replication / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / positive regulation of isotype switching to IgG isotypes / purine-specific mismatch base pair DNA N-glycosylase activity / DNA clamp loader activity / nuclear lamina / Polymerase switching / isotype switching / Processive synthesis on the lagging strand / DNA replication checkpoint signaling / PCNA complex / MutLalpha complex binding / Removal of the Flap Intermediate / Telomere C-strand (Lagging Strand) Synthesis / replisome / 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 / mitotic DNA replication / response to L-glutamate / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to dexamethasone / HDR through Single Strand Annealing (SSA) / DNA strand elongation involved in DNA replication / histone acetyltransferase binding / regulation of mitotic cell cycle phase transition / DNA synthesis involved in DNA repair / leading strand elongation / DNA polymerase processivity factor activity / G1/S-Specific Transcription / Impaired BRCA2 binding to RAD51 / nuclear replication fork / SUMOylation of DNA replication proteins / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / replication fork processing / DNA repair-dependent chromatin remodeling / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / Activation of ATR in response to replication stress / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / positive regulation of B cell proliferation / signal transduction in response to DNA damage / DNA polymerase binding / translesion synthesis / epithelial cell differentiation / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / nuclear estrogen receptor binding / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / receptor tyrosine kinase binding / Recognition of DNA damage by PCNA-containing replication complex / G2/M DNA damage checkpoint / cell population proliferation / DNA-templated DNA replication / HDR through Homologous Recombination (HRR) / cellular response to hydrogen peroxide / Dual Incision in GG-NER / cellular response to UV / heart development / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / chromosome, telomeric region / DNA replication / DNA repair / centrosome / chromatin binding / chromatin / protein-containing complex binding / enzyme binding / ATP hydrolysis activity / DNA binding
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. / Proliferating cell nuclear antigen, PCNA, C-terminal ...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, C-terminal / Proliferating cell nuclear antigen, C-terminal 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, N-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
DNA sliding clamp PCNA / Replication factor C subunit 4 / Replication factor C subunit 2 / Replication factor C subunit 5 / Replication factor C subunit 3 / ATPase family AAA domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsWang F / He Q / Li H
Funding support United States, 3 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)GM115809 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader.
Authors: Feng Wang / Qing He / Nina Y Yao / Michael E O'Donnell / Huilin Li /
Abstract: Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying ...Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying structural basis of ATAD5-RFC unloading is unknown. We show here that ATAD5 has two unique locking loops that appear to tie the complex into a rigid structure, and together with a domain that plugs the DNA-binding chamber, prevent conformation changes required for DNA binding, likely explaining why ATAD5-RFC is exclusively a PCNA unloader. These features are conserved in the yeast PCNA unloader Elg1-RFC. We observe intermediates in which PCNA bound to ATAD5-RFC exists as a closed planar ring, a cracked spiral or a gapped spiral. Surprisingly, ATAD5-RFC can open a PCNA gap between PCNA protomers 2 and 3, different from the PCNA protomers 1 and 3 gap observed in all previously characterized clamp loaders.
History
DepositionOct 10, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42295.png

Downloads & links

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Map

FileDownload / File: emd_42295.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary sharpen Cryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 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: 0.19
Minimum - Maximum-1.5408309 - 2.4726567
Average (Standard dev.)0.00016050145 (±0.059475522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Primary unhsarpen cryo-EM map

Fileemd_42295_additional_1.map
AnnotationPrimary unhsarpen cryo-EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpen EM map by DeepEMhancer

Fileemd_42295_additional_2.map
AnnotationSharpen EM map by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_42295_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_42295_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATAD5-RFC-closed PCNA

EntireName: ATAD5-RFC-closed PCNA
Components
  • Complex: ATAD5-RFC-closed PCNA
    • Protein or peptide: ATPase family AAA domain-containing protein 5
    • 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
    • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ATAD5-RFC-closed PCNA

SupramoleculeName: ATAD5-RFC-closed PCNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: ATPase family AAA domain-containing protein 5

MacromoleculeName: ATPase family AAA domain-containing protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 207.902344 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MVGVLAMAAA AAPPPVKDCE IEPCKKRKKD DDTSTCKTIT KYLSPLGKTR DRVFAPPKPS NILDYFRKTS PTNEKTQLGK ECKIKSPES VPVDSNKDCT TPLEMFSNVE FKKKRKRVNL SHQLNNIKTE NEAPIEISSD DSKEDYSLNN DFVESSTSVL R YKKQVEVL ...String:
MVGVLAMAAA AAPPPVKDCE IEPCKKRKKD DDTSTCKTIT KYLSPLGKTR DRVFAPPKPS NILDYFRKTS PTNEKTQLGK ECKIKSPES VPVDSNKDCT TPLEMFSNVE FKKKRKRVNL SHQLNNIKTE NEAPIEISSD DSKEDYSLNN DFVESSTSVL R YKKQVEVL AENIQDTKSQ PNTMTSLQNS KKVNPKQGTT KNDFKKLRKR KCRDVVDLSE SLPLAEELNL LKKDGKDTKQ ME NTTSHAN SRDNVTEAAQ LNDSIITVSY EEFLKSHKEN KVEEIPDSTM SICVPSETVD EIVKSGYISE SENSEISQQV RFK TVTVLA QVHPIPPKKT GKIPRIFLKQ KQFEMENSLS DPENEQTVQK RKSNVVIQEE ELELAVLEAG SSEAVKPKCT LEER QQFMK AFRQPASDAL KNGVKKSSDK QKDLNEKCLY EVGRDDNSKK IMENSGIQMV SKNGNLQLHT DKGSFLKEKN KKLKK KNKK TLDTGAIPGK NREGNTQKKE TTFFLKEKQY QNRMSLRQRK TEFFKSSTLF NNESLVYEDI ANDDLLKVSS LCNNNK LSR KTSIPVKDIK LTQSKAESEA SLLNVSTPKS TRRSGRISST PTTETIRGID SDDVQDNSQL KASTQKAANL SEKHSLY TA ELITVPFDSE SPIRMKFTRI STPKKSKKKS NKRSEKSEAT DGGFTSQIRK ASNTSKNISK AKQLIEKAKA LHISRSKV T EEIAIPLRRS SRHQTLPERK KLSETEDSVI IIDSSPTALK HPEKNQKKLQ CLNDVLGKKL NTSTKNVPGK MKVAPLFLV RKAQKAADPV PSFDESSQDT SEKSQDCDVQ CKAKRDFLMS GLPDLLKRQI AKKAAALDVY NAVSTSFQRV VHVQQKDDGC CLWHLKPPS CPLLTKFKEL NTKVIDLSKC GIALGEFSTL NSKLKSGNSA AVFMRTRKEF TEEVRNLLLE EIRWSNPEFS L KKYFPLLL KKQIEHQVLS SECHSKQELE ADVSHKETKR KLVEAENSKS KRKKPNEYSK NLEKTNRKSE ELSKRNNSSG IK LDSSKDS GTEDMLWTEK YQPQTASELI GNELAIKKLH SWLKDWKRRA ELEERQNLKG KRDEKHEDFS GGIDFKGSSD DEE ESRLCN TVLITGPTGV GKTAAVYACA QELGFKIFEV NASSQRSGRQ ILSQLKEATQ SHQVDKQGVN SQKPCFFNSY YIGK SPKKI SSPKKVVTSP RKVPPPSPKS SGPKRALPPK TLANYFKVSP KPKNNEEIGM LLENNKGIKN SFEQKQITQT KSTNA TNSN VKDVGAEEPS RKNATSLILF EEVDVIFDED AGFLNAIKTF MATTKRPVIL TTSDPTFSLM FDGCFEEIKF STPSLL NVA SYLQMICLTE NFRTDVKDFV TLLTANTCDI RKSILYLQFW IRSGGGVLEE RPLTLYRGNS RNVQLVCSEH GLDNKIY PK NTKKKRVDLP KCDSGCAETL FGLKNIFSPS EDLFSFLKHK ITMKEEWHKF IQLLTEFQMR NVDFLYSNLE FILPLPVD T IPETKNFCGP SVTVDASAAT KSMNCLARKH SEREQPLKKS QKKKQKKTLV ILDDSDLFDT DLDFPDQSIS LSSVSSSSN AEESKTGDEE SKARDKGNNP ETKKSIPCPP KTTAGKKCSA LVSHCLNSLS EFMDNMSFLD ALLTDVREQN KYGRNDFSWT NGKVTSGLC DEFSLESNDG WTSQSSGELK AAAEALSFTK CSSAISKALE TLNSCKKLGR DPTNDLTFYV SQKRNNVYFS Q SAANLDNA WKRISVIKSV FSSRSLLYVG NRQASIIEYL PTLRNICKTE KLKEQGKSKR RFLHYFEGIH LDIPKETVNT LA ADFP

UniProtKB: ATPase family AAA domain-containing protein 5

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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: Insect cell expression vector pTIE1 (others)
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

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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: Insect cell expression vector pTIE1 (others)
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

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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: Insect cell expression vector pTIE1 (others)
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

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Macromolecule #5: Replication factor C subunit 3

MacromoleculeName: Replication factor C subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.614332 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MSLWVDKYRP CSLGRLDYHK EQAAQLRNLV QCGDFPHLLV YGPSGAGKKT RIMCILRELY GVGVEKLRIE HQTITTPSKK KIEISTIAS NYHLEVNPSD AGNSDRVVIQ EMLKTVAQSQ QLETNSQRDF KVVLLTEVDK LTKDAQHALR RTMEKYMSTC R LILCCNST ...String:
MSLWVDKYRP CSLGRLDYHK EQAAQLRNLV QCGDFPHLLV YGPSGAGKKT RIMCILRELY GVGVEKLRIE HQTITTPSKK KIEISTIAS NYHLEVNPSD AGNSDRVVIQ EMLKTVAQSQ QLETNSQRDF KVVLLTEVDK LTKDAQHALR RTMEKYMSTC R LILCCNST SKVIPPIRSR CLAVRVPAPS IEDICHVLST VCKKEGLNLP SQLAHRLAEK SCRNLRKALL MCEACRVQQY PF TADQEIP ETDWEVYLRE TANAIVSQQT PQRLLEVRGR LYELLTHCIP PEIIMKGLLS ELLHNCDGQL KGEVAQMAAY YEH RLQLGS KAIYHLEAFV AKFMALYKKF MEDGLEGMMF

UniProtKB: Replication factor C subunit 3

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Macromolecule #6: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 6 / 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: DNA sliding clamp PCNA

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 8 / Number of copies: 4 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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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

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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

Concentration1.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
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: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 232350
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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