7PBX: GroEL-GroES complex with ADP

Cryo-EM structure of the GroEL-GroES complex with ADP bound to both rings ("tight" conformation). Determined by electron microscopy at 3.43 Å resolution. Released 24 Nov 2021.

Method: Electron microscopy
Resolution: 3.43 Å
Organism: Escherichia coli (strain K12)
Chains: 21
Atoms: 59,472
Mol. weight: 852.21 kDa
Ligands: ADP, MG
Released: 24 Nov 2021

Explore 7PBX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PBX contains 343 α-helices and 448 β-strands across 21 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 Ac, Ai, Ao, Au, Ba, Bg and Bm: 23 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
α-helix	9-29	21
α-helix	35-37	3
β-strand	38-40	3	2
α-helix	47	1
β-strand	48-50	3	2
α-helix	53-59	7
α-helix	65-84	20
α-helix	89-107	19
α-helix	113-134	22
β-strand	136	1	3
α-helix	141-151	11
α-helix	156-168	13
β-strand	174-179	6	4
β-strand	186-190	5	4
β-strand	193-195	3	5
β-strand	199	1	6
β-strand	215-216	2	5
β-strand	219-222	4	6
β-strand	227	1	7
α-helix	230-243	14
β-strand	247-251	5	6
β-strand	254	1	7
α-helix	256-267	12
β-strand	273-277	5	6
α-helix	278	1
α-helix	282-296	15
β-strand	302	1	8
β-strand	307	1	8
β-strand	318-319	2	6
β-strand	320	1	9
β-strand	322-325	4	5
β-strand	330-332	3	5
β-strand	335	1	9
α-helix	339-342	4
α-helix	344-352	9
α-helix	359-374	16
β-strand	376-381	6	4
α-helix	386-409	24
β-strand	411-413	3	3
α-helix	417-425	9
α-helix	426-428	3
α-helix	434-458	25
α-helix	462-471	10
β-strand	476-479	4	10
β-strand	484-487	4	10
α-helix	488-491	4
β-strand	494-496	3	3
α-helix	497-515	19
β-strand	519-523	5	1

Chains Ad, Aj, Ap, Av, Bb, Bh and Bn: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	11
α-helix	9-30	22
β-strand	37-40	4	12
α-helix	41-42	2
β-strand	48-50	3	12
α-helix	53-59	7
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	13
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-180	7	14
β-strand	186-191	6	14
β-strand	193-195	3	15
β-strand	199	1	16
α-helix	202-204	3
β-strand	207	1	17
β-strand	212	1	17
β-strand	213-216	4	15
β-strand	219-223	5	16
α-helix	230-243	14
β-strand	247-251	5	16
α-helix	256-266	11
β-strand	273-277	5	16
α-helix	278	1
α-helix	282-296	15
β-strand	300-301	2	16
α-helix	309-311	3
β-strand	318-319	2	16
β-strand	320-325	6	15
β-strand	330-335	6	15
α-helix	339-355	17
α-helix	359-372	14
β-strand	375-382	8	14
α-helix	386-409	24
β-strand	411-413	3	13
α-helix	417-425	9
α-helix	434-447	14
α-helix	449-458	10
α-helix	462-471	10
β-strand	476-479	4	18
β-strand	484-487	4	18
α-helix	488-491	4
β-strand	494-496	3	13
α-helix	497-515	19
β-strand	517-523	7	11

Chains Af, Al, Ar, Ax, Bd, Bj and Bp: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	19
β-strand	9-14	6	20
β-strand	17	1	21
β-strand	21-22	2	22
β-strand	26-27	2	22
β-strand	34	1	21
β-strand	37-43	7	20
β-strand	46-47	2	23
α-helix	49-51	3
β-strand	55-56	2	23
α-helix	57	1
β-strand	64-67	4	20
β-strand	74-78	5	20
β-strand	81-87	7	20
α-helix	88-90	3
β-strand	91-93	3	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
60 kDa chaperonin	Ac, Ad, Ai, Aj, Ao, Ap, Au, Av, Ba, Bb, Bg, Bh, Bm, Bn	protein	524	Escherichia coli (strain K12)	P0A6F5 (AlphaFold model)
10 kDa chaperonin	Af, Al, Ar, Ax, Bd, Bj, Bp	protein	97	Escherichia coli (strain K12)	P0A6F9 (AlphaFold model)

Sequence of entity 1 (Ac, Ad, Ai, Aj, Ao, Ap, Au, Av, Ba, Bb, Bg, Bh, Bm, Bn), FASTA

>7PBX_1 60 kDa chaperonin (chains Ac, Ad, Ai, Aj, Ao, Ap, Au, Av, Ba, Bb, Bg, Bh, Bm, Bn)
AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIE
LEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID
KAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGT
GLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA
KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVI
SEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD
REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIR
VASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA
TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP

Sequence of entity 2 (Af, Al, Ar, Ax, Bd, Bj, Bp), FASTA

>7PBX_2 10 kDa chaperonin (chains Af, Al, Ar, Ax, Bd, Bj, Bp)
MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVK
VGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	14
MG	Magnesium ion	Mg	14

Primary citation

Novel cryo-EM structure of an ADP-bound GroEL-GroES complex. Kudryavtseva, S.S., Pichkur, E.B., Yaroshevich, I.A. et al. Sci Rep (2021) 11:18241-18241. DOI 10.1038/s41598-021-97657-x · PubMed

Other PDB entries of the same protein (UniProt P0A6F5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VZ6 1.5 Å, Crystal Structure Analysis of the Mini-chaperonines, variant with Gly 184 replaced with…
1KID 1.7 Å, Groel (HSP60 class) fragment (apical domain) comprising residues 191-376, mutant with…
3VZ7 1.8 Å, Crystal Structure Analysis of the mini-chaperonin variant with Pro 187 Gly
3VZ8 1.9 Å, Crystal Structure Analysis of the Mini-chaperonin variant with Leu 185, Val 186, Pro…
1KP8 2.0 Å, Structural Basis for GroEL-assisted Protein Folding from the Crystal Structure of…
1SX3 2.0 Å, GroEL14-(ATPgammaS)14
1DK7 2.02 Å, Crystal structure of an isolated apical domain of groel
1LA1 2.06 Å, Gro-EL Fragment (Apical Domain) Comprising Residues 188-379
1DKD 2.1 Å, Crystal structure of a groel (apical domain) and a dodecameric peptide complex
1FY9 2.2 Å, Crystal structure of the hexa-substituted mutant of the molecular chaperonin groel…
1FYA 2.2 Å, Crystal structure of the hexa-substituted mutant of the molecular chaperonin groel…
8BKZ 2.3 Å, GroEL:GroES-ATP complex under continuous turnover conditions

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