8BM1: Chaperonin GroEL

Structure of GroEL:GroES-ATP complex under continuous turnover conditions. Determined by electron microscopy at 2.7 Å resolution. Released 9 Aug 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Escherichia coli
Chains: 21
Atoms: 61,416
Mol. weight: 884.78 kDa
Ligands: MG, ATP
Released: 9 Aug 2023

Explore 8BM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BM1 contains 359 α-helices and 418 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.

Chain A: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	2
α-helix	9-28	20
β-strand	37-40	4	23
α-helix	47	1
β-strand	48-50	3	23
α-helix	53-59	7
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	24
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	25
β-strand	186-191	6	25
β-strand	199	1	26
α-helix	202-204	3
β-strand	207	1	27
β-strand	212	1	27
β-strand	213-216	4	28
β-strand	219-223	5	26
β-strand	227	1	29
α-helix	234-243	10
β-strand	247-251	5	26
β-strand	254	1	29
α-helix	256-268	13
β-strand	273-277	5	26
α-helix	278	1
α-helix	284-296	13
β-strand	300-301	2	26
β-strand	318-319	2	26
β-strand	320-325	6	28
β-strand	330-335	6	28
α-helix	339-355	17
α-helix	359-372	14
β-strand	375-381	7	25
α-helix	386-409	24
β-strand	411-413	3	24
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	30
β-strand	484-487	4	30
β-strand	494-496	3	24
α-helix	497-515	19
β-strand	517-523	7	2

Chains B, E and W: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	31
β-strand	9-14	6	10
α-helix	15-17	3
β-strand	20	1	32
β-strand	26	1	32
α-helix	29-31	3
α-helix	33-35	3
β-strand	37-43	7	10
β-strand	47-48	2	33
α-helix	49	1
β-strand	54-55	2	33
α-helix	56-57	2
β-strand	64-67	4	10
β-strand	74-78	5	10
β-strand	81-87	7	10
β-strand	91-95	5	10

Chain C: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	34
α-helix	9-28	20
β-strand	37-40	4	14
α-helix	47	1
β-strand	48-50	3	14
α-helix	53-59	7
α-helix	65-85	21
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	35
α-helix	138-141	4
α-helix	144-151	8
α-helix	156-169	14
β-strand	175-180	6	36
β-strand	186-190	5	36
β-strand	193-195	3	37
β-strand	199	1	38
α-helix	202-204	3
β-strand	213-216	4	37
β-strand	219-222	4	38
β-strand	223	1	39
α-helix	226-227	2
α-helix	230-242	13
β-strand	243	1	21
β-strand	247-251	5	38
α-helix	256-266	11
β-strand	274-277	4	38
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	39
β-strand	318-319	2	38
β-strand	322-325	4	37
β-strand	330-334	5	37
α-helix	339-355	17
α-helix	359-374	16
β-strand	376-382	7	36
α-helix	386-409	24
β-strand	411-413	3	35
α-helix	417-425	9
α-helix	434-446	13
α-helix	449-458	10
α-helix	462-471	10
β-strand	476-479	4	40
β-strand	484-487	4	40
α-helix	488-491	4
β-strand	494-496	3	35
α-helix	497-514	18
β-strand	517-523	7	34

Chain D: 21 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	23
α-helix	9-28	20
β-strand	37-40	4	41
α-helix	47	1
β-strand	48-50	3	41
α-helix	53-59	7
α-helix	65-85	21
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	42
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	43
β-strand	186-191	6	43
β-strand	194-195	2	44
β-strand	199	1	45
α-helix	202-204	3
β-strand	207	1	46
β-strand	212	1	46
β-strand	213-216	4	44
β-strand	219-223	5	45
β-strand	227	1	47
α-helix	234-243	10
β-strand	247-251	5	45
β-strand	254	1	47
α-helix	256-268	13
β-strand	273-277	5	45
α-helix	278	1
α-helix	284-296	13
β-strand	300-301	2	45
β-strand	318-319	2	45
β-strand	320-325	6	44
β-strand	330-335	6	44
α-helix	339-355	17
α-helix	359-372	14
β-strand	375-381	7	43
α-helix	386-409	24
β-strand	411-413	3	42
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	48
β-strand	484-487	4	48
β-strand	494-496	3	42
α-helix	497-514	18
β-strand	517-523	7	23

Chain F: 24 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	52
α-helix	9-28	20
β-strand	37-40	4	34
α-helix	47	1
β-strand	48-50	3	34
α-helix	53-59	7
α-helix	65-85	21
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	53
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	54
β-strand	186-190	5	54
β-strand	193-195	3	55
β-strand	199	1	56
α-helix	202-204	3
β-strand	213-216	4	55
β-strand	219-223	5	56
α-helix	226-227	2
α-helix	230-243	14
β-strand	247-251	5	56
β-strand	254	1	57
α-helix	259-266	8
β-strand	274-277	4	56
α-helix	278-279	2
α-helix	282-296	15
β-strand	300-301	2	56
β-strand	318-319	2	56
β-strand	322-325	4	55
β-strand	330-334	5	55
α-helix	339-355	17
α-helix	359-374	16
β-strand	376-381	6	54
α-helix	382	1
α-helix	386-409	24
β-strand	411-413	3	53
α-helix	417-425	9
α-helix	434-446	13
α-helix	449-458	10
α-helix	462-471	10
β-strand	476-479	4	58
β-strand	484-487	4	58
α-helix	488-491	4
β-strand	494-496	3	53
α-helix	497-514	18
β-strand	517-523	7	52

Chain G: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	14
α-helix	9-28	20
β-strand	37-40	4	15
α-helix	47	1
β-strand	48-50	3	15
α-helix	53-59	7
α-helix	65-85	21
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	16
α-helix	143-151	9
α-helix	156-169	14
β-strand	175-179	5	17
β-strand	186-190	5	17
β-strand	193-195	3	18
β-strand	199	1	19
α-helix	202-204	3
β-strand	213-216	4	18
β-strand	219-222	4	19
β-strand	223	1	20
α-helix	226-227	2
α-helix	234-243	10
β-strand	247-251	5	19
β-strand	254	1	21
α-helix	256-266	11
β-strand	273-277	5	19
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	20
β-strand	318-319	2	19
β-strand	320-325	6	18
β-strand	330-335	6	18
α-helix	339-355	17
α-helix	359-374	16
β-strand	376-381	6	17
α-helix	382	1
α-helix	386-409	24
β-strand	411-413	3	16
α-helix	417-425	9
α-helix	434-446	13
α-helix	449-458	10
α-helix	462-471	10
β-strand	476-479	4	22
β-strand	484-487	4	22
α-helix	488-491	4
β-strand	494-496	3	16
α-helix	497-514	18
β-strand	517-523	7	14

Chains H, I, O and R: 21 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	41
α-helix	9-28	20
β-strand	37-40	4	59
α-helix	47	1
β-strand	48-50	3	59
α-helix	53-59	7
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	60
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	61
β-strand	186-191	6	61
β-strand	193	1	62
β-strand	199	1	63
α-helix	202-204	3
β-strand	207	1	64
β-strand	212	1	64
β-strand	213-216	4	62
β-strand	219-223	5	63
β-strand	227	1	65
α-helix	234-243	10
β-strand	247-251	5	63
β-strand	254	1	65
α-helix	256-268	13
β-strand	273-277	5	63
α-helix	278	1
α-helix	285-296	12
β-strand	300-301	2	63
β-strand	318-319	2	63
β-strand	320-325	6	62
β-strand	330-335	6	62
α-helix	339-355	17
α-helix	359-372	14
β-strand	375-381	7	61
α-helix	386-409	24
β-strand	411-413	3	60
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	66
β-strand	484-487	4	66
β-strand	494-496	3	60
α-helix	497-515	19
β-strand	517-523	7	41

Chains J, M, P and S: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	67
β-strand	9-14	6	49
α-helix	15-17	3
β-strand	20	1	68
β-strand	26	1	68
α-helix	29-31	3
α-helix	33-35	3
β-strand	37-43	7	49
β-strand	47-48	2	69
α-helix	49	1
α-helix	53	1
β-strand	54-55	2	69
α-helix	56-57	2
β-strand	64-67	4	49
β-strand	74-78	5	49
β-strand	81-87	7	49
β-strand	91-95	5	49

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chaperonin GroEL	A, C, D, F, G, H, I, K, L, N, O, Q, R, T	protein	548	Escherichia coli	P0A6F5 (AlphaFold model)
Co-chaperonin GroES	B, E, J, M, P, S, W	protein	98	Escherichia coli	P0A6F9 (AlphaFold model)

Sequence of entity 1 (A, C, D, F, G, H, I, K, L, N, O, Q, R, T), FASTA

>8BM1_1 Chaperonin GroEL (chains A, C, D, F, G, H, I, K, L, N, O, Q, R, T)
MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREI
ELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGI
DKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDG
TGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAV
AKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTV
ISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDY
DREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALI
RVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNA
ATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGG
MGGMGGMM

Sequence of entity 2 (B, E, J, M, P, S, W), FASTA

>8BM1_2 Co-chaperonin GroES (chains B, E, J, M, P, S, W)
MANIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDV
KVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	14
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	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…
8BKZ 2.3 Å, GroEL:GroES-ATP complex under continuous turnover conditions

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