2024-10-16 REL RCSB RCSB RCSB 2023-03-14 2024-03-27 2024-03-27 2024-10-16 Australian Research Council (ARC) DP210100365 Australia E. coli clamp loader with closed clamp 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 8giy FULLOVERLAP E. coli clamp loader with closed clamp E. coli clamp loader with closed clamp 0 1 2 3 4 5
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.
Escherichia coli K-12 0.331 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 0.047601766000000004 3 Escherichia coli BL21 LEVO MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCR EIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQ KLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAM LGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELARTI PPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFHPRMPLPEPEVPRQSFAPVAPTAVMTPTQVPPQPQSAPQQA PTVPLPETTSQVLAARQQLQRVQGATKAKKE 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 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER 0.0005232469999999999 3 AGS MAGNESIUM ION 2.4305e-05 3 MG ZINC ION 6.5409e-05 4 ZN singleParticle particle 7.5 30.0 HEPES 3.0 MgCl2 Magnesium Chloride 2.0 dithiothreitol 0.25 EDTA 2.0 glycerol 1.0 ATPgammaS
30 mM Na.HEPES pH 7.5, 3 mM MgCl2, 2 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol, 1 mM ATPgammaS.
 Quantifoil R1.2/1.3 GOLD PLASMA CLEANING AIR 0.03
Use a Zepto Low-pressure plasma systems (PLASMA CLEANER) (Diener Electronic) at 10% power for 120 seconds.
 ETHANE 100 279 FEI VITROBOT MARK IV
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.
 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 7269 6.0 50.0 1 1376000
Ab-initio model from RELION
 2 C1 BACK PROJECTION 3.7 FSC 0.143 CUT-OFF RELION 3.1 373000 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_40079.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.2 295.2 295.2 90.0 90.0 90.0 X Y Z -0.009739092 0.020211676 0.0000070083724 0.00076375547 0.82000005 0.82000005 0.82000005 0.0037 AUTHOR CLC.Beta2-Closed 3GLH PDB experimental model 1MMI PDB experimental model RIGID BODY FIT emd_40079_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.2 295.2 295.2 90.0 90.0 90.0 X Y Z -0.018877393 0.028523028 0.0000059147665 0.0015810927 0.82000005 0.82000005 0.82000005 AUTHOR CLC.Beta2-Closed half map 2 emd_40079_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 295.2 295.2 295.2 90.0 90.0 90.0 X Y Z -0.017841948 0.027902259 0.0000058836704 0.00157909 0.82000005 0.82000005 0.82000005 AUTHOR CLC.Beta2-Closed half map 1