8VAL: E. coli clamp loader

Structure of the E. coli clamp loader bound to the beta clamp in a Open-DNAp/t conformation. Determined by electron microscopy at 3.7 Å resolution. Released 27 Mar 2024.

Method

Electron microscopy

Resolution

3.7 Å

Organisms

Escherichia coli, synthetic construct

Chains

9

Atoms

20,714

Mol. weight

300.4 kDa

Ligands

BEF, MG, ADP, ZN

Released

27 Mar 2024

Explore 8VAL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VAL contains 141 α-helices and 97 β-strands across 7 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 8 β-strands

Molecules and chains

>8VAL_1 DNA polymerase III subunit delta (chains A)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

>8VAL_2 DNA polymerase III subunit tau (chains B, C, D)
GPHMSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARL
LAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPAR
GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKA
LDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAV
SAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQL
SPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRAL
AFHPRMPLPEPEVPRQ

>8VAL_3 DNA polymerase III subunit delta' (chains E)
GPHMRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHK
SCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDA
ALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLS
REVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALN
HEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIR
EQLMSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

>8VAL_4 Beta sliding clamp (chains F, G)
GPHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARV
ALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFP
NLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRL
AVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLV
DGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNP
EQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSA
AYVVMPMRL

>8VAL_5 DNA (5'-D(*AP*GP*AP*CP*AP*CP*TP*AP*CP*GP*AP*GP*TP*AP*CP*AP*TP*A)-3') (chains H)
GCAGACACTACGAGTACATA

>8VAL_6 DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*AP*TP*GP*TP*AP*CP*TP*CP*GP*TP*AP*GP*TP*GP*TP*CP*T)-3') (chains I)
TTTTTTTTTTTATGTACTCGTAGTGTCTGC

Ligands and cofactors

Primary citation

Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication. Landeck, J.T., Pajak, J., Norman, E.K. et al. J Biol Chem (2024) 300:107166-107166. DOI 10.1016/j.jbc.2024.107166 · PubMed

Related structures

Other PDB entries of the same protein (UniProt P28630 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 1JQL 2.5 Å, Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader…
• 9OYJ 2.53 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
• 9OYH 2.54 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
• 9OYI 2.54 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
• 8GJ2 2.6 Å, E. coli clamp loader with closed clamp on primed template DNA
• 9OYK 2.6 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
• 9OYM 2.6 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
• 1JR3 2.7 Å, Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA…
• 8GIZ 2.7 Å, E. coli clamp loader with open clamp
• 9OYN 2.7 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
• 9OYC 2.71 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…
• 9OYE 2.72 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…

Browse structure collections

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