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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | E. coli clamp loader with closed clamp | |||||||||
![]() | CLC.Beta2-Closed | |||||||||
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![]() | clamp loader / DNA clamp / AAA+ / ATPase / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity / error-prone translesion synthesis ...DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / response to radiation / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Oakley AJ / Xu Z-Q / Dixon NE | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterisation of the complete cycle of sliding clamp loading in E. coli Authors: Xu Z-Q / Oakley AJ / Dixon NE | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 140.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.4 KB 26.4 KB | Display Display | ![]() |
Images | ![]() | 56.7 KB | ||
Filedesc metadata | ![]() | 7.9 KB | ||
Others | ![]() ![]() | 140.9 MB 140.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8giyMC ![]() 8gizC ![]() 8gj0C ![]() 8gj1C ![]() 8gj2C ![]() 8gj3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | CLC.Beta2-Closed | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: CLC.Beta2-Closed half map 1
File | emd_40079_half_map_1.map | ||||||||||||
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Annotation | CLC.Beta2-Closed half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CLC.Beta2-Closed half map 2
File | emd_40079_half_map_2.map | ||||||||||||
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Annotation | CLC.Beta2-Closed half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : E. coli clamp loader with closed clamp
Entire | Name: E. coli clamp loader with closed clamp |
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Components |
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-Supramolecule #1: E. coli clamp loader with closed clamp
Supramolecule | Name: E. coli clamp loader with closed clamp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 Details: Clamp loader complex composed of DNA polymerase III delta gamma(3) delta' chi and psi subunits. Clamp composed of DNA polymerase III beta(2) subunits. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 331 KDa |
-Macromolecule #1: DNA polymerase III subunit delta
Macromolecule | Name: DNA polymerase III subunit delta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 38.745574 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH HTFSIDPNTD WNAIFSLCQA MSLFASRQTL LLLLPENGP NAAINEQLLT LTGLLHDDLL LIVRGNKLSK AQENAAWFTA LANRSVQVTC QTPEQAQLPR WVAARAKQLN L ELDDAANQ ...String: MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH HTFSIDPNTD WNAIFSLCQA MSLFASRQTL LLLLPENGP NAAINEQLLT LTGLLHDDLL LIVRGNKLSK AQENAAWFTA LANRSVQVTC QTPEQAQLPR WVAARAKQLN L ELDDAANQ VLCYCYEGNL LALAQALERL SLLWPDGKLT LPRVEQAVND AAHFTPFHWV DALLMGKSKR ALHILQQLRL EG SEPVILL RTLQRELLLL VNLKRQSAHT PLRALFDKHR VWQNRRGMMG EALNRLSQTQ LRQAVQLLTR TELTLKQDYG QSV WAELEG LSLLLCHKPL ADVFIDG UniProtKB: DNA polymerase III subunit delta |
-Macromolecule #2: DNA polymerase III subunit tau
Macromolecule | Name: DNA polymerase III subunit tau / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 47.601766 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSYQVLARKW RPQTFADVVG QEHVLTALAN GLSLGRIHHA YLFSGTRGVG KTSIARLLAK GLNCETGITA TPCGVCDNCR EIEQGRFVD LIEIDAASRT KVEDTRDLLD NVQYAPARGR FKVYLIDEVH MLSRHSFNAL LKTLEEPPEH VKFLLATTDP Q KLPVTILS ...String: MSYQVLARKW RPQTFADVVG QEHVLTALAN GLSLGRIHHA YLFSGTRGVG KTSIARLLAK GLNCETGITA TPCGVCDNCR EIEQGRFVD LIEIDAASRT KVEDTRDLLD NVQYAPARGR FKVYLIDEVH MLSRHSFNAL LKTLEEPPEH VKFLLATTDP Q KLPVTILS RCLQFHLKAL DVEQIRHQLE HILNEEHIAH EPRALQLLAR AAEGSLRDAL SLTDQAIASG DGQVSTQAVS AM LGTLDDD QALSLVEAMV EANGERVMAL INEAAARGIE WEALLVEMLG LLHRIAMVQL SPAALGNDMA AIELRMRELA RTI PPTDIQ LYYQTLLIGR KELPYAPDRR MGVEMTLLRA LAFHPRMPLP EPEVPRQSFA PVAPTAVMTP TQVPPQPQSA PQQA PTVPL PETTSQVLAA RQQLQRVQGA TKAKKE UniProtKB: DNA polymerase III subunit tau |
-Macromolecule #3: DNA polymerase III subunit delta'
Macromolecule | Name: DNA polymerase III subunit delta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.980484 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC QQPQGHKSCG HCRGCQLMQA GTHPDYYTLA PEKGKNTLG VDAVREVTEK LNEHARLGGA KVVWVTDAAL LTDAAANALL KTLEEPPAET WFFLATREPE RLLATLRSRC R LHYLAPPP ...String: MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC QQPQGHKSCG HCRGCQLMQA GTHPDYYTLA PEKGKNTLG VDAVREVTEK LNEHARLGGA KVVWVTDAAL LTDAAANALL KTLEEPPAET WFFLATREPE RLLATLRSRC R LHYLAPPP EQYAVTWLSR EVTMSQDALL AALRLSAGSP GAALALFQGD NWQARETLCQ ALAYSVPSGD WYSLLAALNH EQ APARLHW LATLLMDALK RHHGAAQVTN VDVPGLVAEL ANHLSPSRLQ AILGDVCHIR EQLMSVTGIN RELLITDLLL RIE HYLQPG VVLPVPHL UniProtKB: DNA polymerase III subunit delta' |
-Macromolecule #4: DNA polymerase III subunit psi
Macromolecule | Name: DNA polymerase III subunit psi / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.188276 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTSRRDWQLQ QLGITQWSLR RPGALQGEIA IAIPAHVRLV MVANDLPALT DPLVSDVLRA LTVSPDQVLQ LTPEKIAMLP QGSHCNSWR LGTDEPLSLE GAQVASPALT DLRANPTARA ALWQQICTYE HDFFPRND UniProtKB: DNA polymerase III subunit psi |
-Macromolecule #5: Beta sliding clamp
Macromolecule | Name: Beta sliding clamp / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 40.630508 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV QPHEPGATTV PARKFFDICR GLPEGAEIA VQLEGERMLV RSGRSRFSLS TLPAADFPNL DDWQSEVEFT LPQATMKRLI EATQFSMAHQ DVRYYLNGML F ETEGEELR ...String: MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV QPHEPGATTV PARKFFDICR GLPEGAEIA VQLEGERMLV RSGRSRFSLS TLPAADFPNL DDWQSEVEFT LPQATMKRLI EATQFSMAHQ DVRYYLNGML F ETEGEELR TVATDGHRLA VCSMPIGQSL PSHSVIVPRK GVIELMRMLD GGDNPLRVQI GSNNIRAHVG DFIFTSKLVD GR FPDYRRV LPKNPDKHLE AGCDLLKQAF ARAAILSNEK FRGVRLYVSE NQLKITANNP EQEEAEEILD VTYSGAEMEI GFN VSYVLD VLNALKCENV RMMLTDSVSS VQIEDAASQS AAYVVMPMRL UniProtKB: Beta sliding clamp |
-Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 3 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ![]() ChemComp-AGS: |
-Macromolecule #7: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
Details: 30 mM Na.HEPES pH 7.5, 3 mM MgCl2, 2 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol, 1 mM ATPgammaS. | |||||||||||||||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa Details: Use a Zepto Low-pressure plasma systems (PLASMA CLEANER) (Diener Electronic) at 10% power for 120 seconds. | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||
Details | 30 microL of 6 microM delta/gamma3/delta' mixed with chi/psi complex at a molar ratio of 1:1.2, beta2 at 1:1.3, and dialysed twice at 4 degrees C against 250 mL of 30 mM Na.HEPES pH 7.5, 3 mM MgCl2, 2 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol. 1 mM ATPgammaS was added to the dialysate. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Details: unfiltered mode |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 7269 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |