3GLH: E. coli clamp loader

Crystal Structure of the E. coli clamp loader bound to Psi Peptide. Determined by X-ray diffraction at 3.89 Å resolution. Released 26 May 2009.

Method: X-ray diffraction
Resolution: 3.89 Å
Organism: Escherichia coli
Chains: 15
Atoms: 41,322
Mol. weight: 603.41 kDa
Released: 26 May 2009

Explore 3GLH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GLH contains 297 α-helices and 117 β-strands across 15 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.

Chains A, F and K: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	9-15	7
β-strand	20-25	6	1
α-helix	28-45	18
β-strand	49-54	6	1
α-helix	61-73	13
β-strand	78-83	6	1
α-helix	93-101	9
β-strand	105	1	1
β-strand	108-114	7	1
α-helix	116-118	3
α-helix	125-130	6
β-strand	135-139	5	1
α-helix	146-157	12
β-strand	161-162	2	2
α-helix	164-172	9
α-helix	178-191	14
β-strand	196-197	2	2
α-helix	199-209	11
α-helix	214-221	8
α-helix	226-233	8
α-helix	243-261	19
α-helix	269-276	8
α-helix	282-292	11
α-helix	295-314	20
α-helix	320-330	11

Chains B, G and L: 24 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-44	5	3
β-strand	47	1	4
β-strand	49	1	4
α-helix	51-63	13
α-helix	77-84	8
β-strand	90-94	5	3
α-helix	104-109	6
α-helix	110-112	3
α-helix	114-115	2
β-strand	121-126	6	3
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	3
α-helix	164-167	4
β-strand	171-174	4	3
α-helix	180-194	15
β-strand	198	1	5
α-helix	200-209	10
α-helix	214-228	15
β-strand	232	1	5
α-helix	234-237	4
α-helix	251-257	7
α-helix	261-273	13
α-helix	278-294	17
α-helix	299-301	3
α-helix	310-319	10
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
α-helix	364-366	3

Chains C, H and M: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-44	5	6
α-helix	51-62	12
α-helix	77-83	7
β-strand	91-94	4	6
α-helix	104-110	7
α-helix	114-115	2
β-strand	121-126	6	6
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	6
α-helix	159-161	3
α-helix	164-167	4
β-strand	171-174	4	6
α-helix	180-194	15
β-strand	198	1	7
α-helix	200-209	10
α-helix	214-227	14
β-strand	232	1	7
α-helix	234-240	7
α-helix	246-258	13
α-helix	261-273	13
α-helix	278-295	18
α-helix	305-308	4
α-helix	310-319	10
α-helix	322-338	17
α-helix	345-358	14

Chains D, I and N: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-44	5	8
α-helix	51-63	13
α-helix	77-84	8
β-strand	91-94	4	8
α-helix	104-107	4
α-helix	114-115	2
β-strand	121-126	6	8
α-helix	128-130	3
α-helix	133-143	11
β-strand	150-155	6	8
α-helix	164-167	4
β-strand	171-174	4	8
α-helix	180-193	14
β-strand	197-198	2	9
α-helix	200-209	10
α-helix	214-227	14
β-strand	231-232	2	9
α-helix	234-240	7
α-helix	248-256	9
α-helix	262-273	12
α-helix	278-297	20
α-helix	305-308	4
α-helix	310-319	10
α-helix	322-338	17
α-helix	345-358	14

Chains E, J and O: 17 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
β-strand	26-30	5	10
α-helix	37-48	12
α-helix	63-69	7
β-strand	76-79	4	10
α-helix	80-82	3
β-strand	88	1	11
α-helix	90-100	11
β-strand	110-114	5	10
α-helix	117-119	3
β-strand	120	1	11
α-helix	122-133	12
β-strand	139-145	7	10
β-strand	160-163	4	10
α-helix	169-179	11
α-helix	184-192	9
α-helix	198-205	8
α-helix	209-226	18
α-helix	229-232	4
α-helix	233-236	4
α-helix	241-259	19
α-helix	271-280	10
α-helix	283-301	19
α-helix	308-322	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III subunit delta	A, F, K	protein	343	Escherichia coli	P28630 (AlphaFold model)
DNA polymerase III subunit tau	B, C, D, G, H, I, L, M, N	protein	376	Escherichia coli	P06710 (AlphaFold model)
DNA polymerase III subunit delta'	E, J, O	protein	334	Escherichia coli	P28631 (AlphaFold model)

Sequence of entity 1 (A, F, K), FASTA

>3GLH_1 DNA polymerase III subunit delta (chains A, F, K)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

Sequence of entity 2 (B, C, D, G, H, I, L, M, N), FASTA

>3GLH_2 DNA polymerase III subunit tau (chains B, C, D, G, H, I, L, M, N)
GPHMSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARL
LAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPAR
GRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKA
LDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAV
SAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQL
SPAALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRAL
AFHPRMPLPEPEVPRQ

Sequence of entity 3 (E, J, O), FASTA

>3GLH_3 DNA polymerase III subunit delta' (chains E, J, O)
MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCG
HCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL
TDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV
TMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQ
APARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQL
MSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Primary citation

The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Simonetta, K.R., Kazmirski, S.L., Goedken, E.R. et al. Cell (2009) 137:659-671. DOI 10.1016/j.cell.2009.03.044 · PubMed

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…

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