8BKZ: Chaperonin GroEL

GroEL:GroES-ATP complex under continuous turnover conditions. Determined by electron microscopy at 2.3 Å resolution. Released 9 Aug 2023.

Method: Electron microscopy
Resolution: 2.3 Å
Organism: Escherichia coli
Chains: 28
Atoms: 67,875
Mol. weight: 955.25 kDa
Ligands: ATP, MG
Released: 9 Aug 2023

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

Secondary structure: helices and β-sheets

8BKZ contains 379 α-helices and 517 β-strands across 28 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, BA, E, G, I, K, M, O, Q, S, V, X and Z: 20 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	26
α-helix	9-28	20
β-strand	37-40	4	1
β-strand	48-50	3	1
α-helix	53-59	7
α-helix	65-85	21
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	27
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	28
β-strand	186-191	6	28
β-strand	193-195	3	29
β-strand	199	1	30
α-helix	202-204	3
β-strand	207	1	31
β-strand	212	1	31
β-strand	213-216	4	29
β-strand	219-223	5	30
β-strand	227	1	32
α-helix	234-243	10
β-strand	247-251	5	30
β-strand	254	1	32
α-helix	257-268	12
β-strand	273-277	5	30
α-helix	278	1
α-helix	285-296	12
β-strand	300-301	2	30
β-strand	318-319	2	30
β-strand	320-325	6	29
β-strand	330-335	6	29
α-helix	339-355	17
α-helix	359-372	14
β-strand	375-381	7	28
α-helix	386-409	24
β-strand	411-413	3	27
α-helix	417-425	9
α-helix	434-446	13
α-helix	449-457	9
α-helix	462-471	10
β-strand	476-479	4	33
β-strand	484-487	4	33
β-strand	494-496	3	27
α-helix	497-514	18
β-strand	517-523	7	26

Chains AA, B, CA, D, F, H, J, L, N, P, R, T, W and Y: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	142
β-strand	9-14	6	152
α-helix	15-17	3
β-strand	20	1	153
α-helix	25	1
β-strand	26	1	153
α-helix	27	1
α-helix	29-31	3
α-helix	33-35	3
β-strand	37-43	7	152
β-strand	47-48	2	154
α-helix	49	1
β-strand	54-55	2	154
β-strand	64-67	4	152
β-strand	74-78	5	152
β-strand	81-87	7	152
α-helix	88-90	3
β-strand	91-95	5	152

Chain C: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	37
α-helix	9-28	20
β-strand	37-40	4	26
β-strand	48-50	3	26
α-helix	53-59	7
α-helix	65-85	21
α-helix	89-108	20
α-helix	113-122	10
α-helix	126-134	9
β-strand	136	1	38
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	39
β-strand	186-191	6	39
β-strand	193-195	3	40
α-helix	202-204	3
β-strand	207	1	41
β-strand	212	1	41
β-strand	213-216	4	40
β-strand	219-223	5	42
β-strand	227	1	43
α-helix	234-243	10
β-strand	247-251	5	42
β-strand	254	1	43
α-helix	257-268	12
β-strand	273-277	5	42
α-helix	278	1
α-helix	285-296	12
β-strand	300-301	2	42
β-strand	318-319	2	42
β-strand	320-325	6	40
β-strand	330-335	6	40
α-helix	339-355	17
α-helix	359-372	14
β-strand	375-381	7	39
α-helix	386-409	24
β-strand	411-413	3	38
α-helix	417-425	9
α-helix	434-446	13
α-helix	449-457	9
α-helix	462-471	10
β-strand	476-479	4	44
β-strand	484-487	4	44
β-strand	494-496	3	38
α-helix	497-514	18
β-strand	517-523	7	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chaperonin GroEL	A, BA, C, E, G, I, K, M, O, Q, S, V, X, Z	protein	548	Escherichia coli	P0A6F5 (AlphaFold model)
Co-chaperonin GroES	AA, B, CA, D, F, H, J, L, N, P, R, T, W, Y	protein	96	Escherichia coli	P0A6F9 (AlphaFold model)

Sequence of entity 1 (A, BA, C, E, G, I, K, M, O, Q, S, V, X, Z), FASTA

>8BKZ_1 Chaperonin GroEL (chains A, BA, C, E, G, I, K, M, O, Q, S, V, X, Z)
MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREI
ELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGI
DKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDG
TGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAV
AKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTV
ISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDY
DREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALI
RVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNA
ATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGG
MGGMGGMM

Sequence of entity 2 (AA, B, CA, D, F, H, J, L, N, P, R, T, W, Y), FASTA

>8BKZ_2 Co-chaperonin GroES (chains AA, B, CA, D, F, H, J, L, N, P, R, T, W, Y)
NIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVKV
GDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	14
MG	Magnesium ion	Mg	14

Water and common crystallization additives (K) are not listed.

Primary citation

Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting. Torino, S., Dhurandhar, M., Stroobants, A. et al. Nat Methods (2023) 20:1400-1408. DOI 10.1038/s41592-023-01967-z · 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…
8BL2 2.3 Å, Structure of GroEL-ATP complex plunge frozen 200 ms after reaction initiation

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