2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation DERIVED_CALCULATIONS em_admin pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_validate_close_contact struct_conn _em_admin.last_update RCSB RCSB 2023-03-14 2024-03-27 2024-03-27 2026-08-12 Australian Research Council (ARC) DP210100365 Australia E. coli clamp loader with open clamp on primed template DNA (form 2) Oakley AJ Xu Z-Q Dixon NE clamp loader, DNA clamp, AAA+, ATPase, DNA BINDING PROTEIN-DNA complex Xu ZQ Jergic S Lo ATY Pradhan AC Brown SHJ Bouwer JC Ghodke H Lewis PJ Tolun G Oakley AJ Dixon NE Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli. Nat Commun UK 15 8372 8372 2024 39333521 doi:10.1038/s41467-024-52623-9 2041-1723 8gj1 FULLOVERLAP EMDB EMD-40082 associated EM volume
E. coli clamp loader with open clamp on primed template DNA (form 2)
 E. coli clamp loader with open clamp on primed template DNA E. coli clamp loader with open clamp on primed template DNA 0 1 2 3 4 5 6 7
Clamp loader complex composed of DNA polymerase III delta tau(3) delta' chi and psi subunits. Clamp composed of DNA polymerase III beta(2) subunits.
Escherichia coli K-12 0.419 DNA polymerase III subunit delta Escherichia coli K-12 0.038745574 1 Escherichia coli BL21 LEVO MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTL LLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNL ELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSV WAELEGLSLLLCHKPLADVFIDG P28630 2.7.7.7 DNA polymerase III subunit tau Escherichia coli K-12 0.07122864799999999 3 Escherichia coli BL21 LEVO MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCR EIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQ KLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAM LGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTI PPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHPRMPLPEPEVPRQSFAPVAPTAVMTPTQVPPQPQSAPQQA PTVPLPETTSQVLAARQQLQRVQGATKAKKSEPAAATRARPVNNAALERLASVTDRVQARPVPSALEKAPAKKEAYRWKA TTPVMQQKEVVATPKALKKALEHEKTPELAAKLAAEAIERDPWAAQVSQLSLPKLVEQVALNAWKEESDNAVCLHLRSSQ RHLNNRGAQQKLAEALSMLKGSTVELTIVEDDNPAVRTPLEWRQAIYEEKLAQARESIIADNNIQTLRRFFDAELDEESI RPI P06710 2.7.7.7 DNA polymerase III subunit delta' Escherichia coli K-12 0.036980483999999994 1 Escherichia coli BL21 LEVO MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLA PEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCR LHYLAPPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQ APARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDLLLRIE HYLQPGVVLPVPHL P28631 2.7.7.7 DNA polymerase III subunit psi Escherichia coli K-12 0.015188275999999999 1 Escherichia coli BL21 LEVO MTSRRDWQLQQLGITQWSLRRPGALQGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRALTVSPDQVLQLTPEKIAMLP QGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAALWQQICTYEHDFFPRND P28632 2.7.7.7 Beta sliding clamp Escherichia coli K-12 0.040630508 2 Escherichia coli BL21 LEVO MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICR GLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLF ETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFN VSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL P0A988 Primer Escherichia coli 0.007097623999999999 1 (DG)(DA)(DG)(DA)(DT)(DA)(DG)(DT)(DT)(DA)(DC)(DA)(DA)(DC)(DA)(DT)(DA)(DC)(DG)(DA) (DT)(DC)(DG) DNA Template Escherichia coli 0.020710217 1 (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DC)(DG)(DA)(DT)(DC)(DG)(DT)(DA)(DT)(DG)(DT)(DT)(DG)(DT)(DA) (DA)(DC)(DT)(DA)(DT)(DC)(DT)(DC) DNA ADENOSINE-5'-DIPHOSPHATE 0.000427201 3 ADP MAGNESIUM ION 2.4305e-05 3 MG TETRAFLUOROALUMINATE ION 0.000102975 3 ALF ZINC ION 6.5409e-05 4 ZN singleParticle particle 7.6 30.0 tris-HCl 3.0 MgCl2 Magnesium Chloride 2.0 dithiothreitol 0.25 EDTA 2.0 glycerol 2.0 Adenosine disphosphate 0.5 AlCl3 Aluminium Chloride 5.0 NaF Sodium Fluoride
30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol.
 UltrAuFoil R1.2/1.3 GOLD 300 GOLD PLASMA CLEANING AIR 0.03
Used a Zepto Low-pressure plasma systems (PLASMA CLEANER) (Diener Electronic) at 10% power for 120 seconds.
 ETHANE 100 279 FEI VITROBOT MARK IV
3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane..
30 microL of 6.0 microM delta/tau3/delta' complex was mixed with chi/psi complex, beta, and p/t DNA (annealed DNA oligonucleotides) at a molar ratio of 1:1.3 and dialysed at 4 degrees C against 250 mL of 30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.4 1.3 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum
unfiltered mode
 GATAN K2 SUMMIT (4k x 4k) COUNTING 4096 4096 1-60 1 4226 6.0 50.0 1 1433000 RELION 3.1
CTF refinement per-particle was performed in RELION before final 3D reconstruction.
PHASE FLIPPING AND AMPLITUDE CORRECTION
Ab-initio model from RELION
 2 C1 BACK PROJECTION 3.0 FSC 0.143 CUT-OFF RELION 3.1 80000 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 4 120000.0 RELION 3.1
Most particles were classified to two classes that were used for final 3D reconstruction.
 emd_40082.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 302.4 302.4 302.4 90.0 90.0 90.0 X Y Z -0.017161408 0.048814088 -0.000004806814 0.0013836676 0.84 0.84 0.84 0.00312 AUTHOR CLC.DNA.Beta2 Open2 3GLH PDB experimental model 1MMI PDB experimental model RIGID BODY FIT emd_40082_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 302.4 302.4 302.4 90.0 90.0 90.0 X Y Z -0.020929553 0.064245164 0.000005073392 0.0021622507 0.84 0.84 0.84 AUTHOR CLC.DNA.Beta2 Open2 half map 2 emd_40082_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 302.4 302.4 302.4 90.0 90.0 90.0 X Y Z -0.020963589 0.06569244 0.000004092456 0.0020765495 0.84 0.84 0.84 AUTHOR CLC.DNA.Beta2 Open2 half map 1