8P4M: Chaperonin GroEL

CryoEM structure of a C7-symmetrical GroEL7-GroES7 cage in presence of ADP-BeFx. Determined by electron microscopy at 2.5 Å resolution. Released 3 Jul 2024.

Method: Electron microscopy
Resolution: 2.5 Å
Organism: Escherichia coli
Chains: 14
Atoms: 32,200
Mol. weight: 478.44 kDa
Ligands: ADP, BEF, MG
Released: 3 Jul 2024

Explore 8P4M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P4M contains 204 α-helices and 263 β-strands across 14 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: 23 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
α-helix	10-28	19
β-strand	37-40	4	2
α-helix	47	1
β-strand	48-50	3	2
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	3
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	4
β-strand	186-191	6	4
β-strand	193-195	3	5
β-strand	199	1	6
α-helix	202-204	3
β-strand	207	1	7
β-strand	212	1	7
β-strand	213-216	4	5
β-strand	219-222	4	6
β-strand	223	1	8
β-strand	226-227	2	9
α-helix	230-233	4
α-helix	234-243	10
β-strand	247-251	5	6
β-strand	253-254	2	9
α-helix	256-268	13
β-strand	273-277	5	6
α-helix	278	1
α-helix	283-296	14
β-strand	301	1	8
α-helix	309-311	3
β-strand	318-319	2	6
β-strand	322-325	4	5
β-strand	330-333	4	5
α-helix	339-353	15
α-helix	359-372	14
β-strand	375-381	7	4
α-helix	386-409	24
β-strand	411-413	3	3
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	10
β-strand	484-487	4	10
β-strand	494-496	3	3
α-helix	497-515	19
β-strand	517-523	7	1

Chains B and G: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	11
α-helix	10-28	19
β-strand	37-40	4	1
α-helix	47	1
β-strand	48-50	3	1
α-helix	53-58	6
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	12
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	13
β-strand	186-191	6	13
β-strand	193-195	3	14
β-strand	199	1	15
α-helix	202-204	3
β-strand	207	1	16
β-strand	212	1	16
β-strand	213-216	4	14
β-strand	219-223	5	15
β-strand	226-227	2	17
α-helix	230-233	4
α-helix	234-243	10
β-strand	247-251	5	15
β-strand	253-254	2	17
α-helix	256-267	12
β-strand	273-277	5	15
α-helix	278	1
α-helix	283-296	14
β-strand	300-301	2	15
α-helix	309-311	3
β-strand	318-319	2	15
β-strand	322-325	4	14
β-strand	330-333	4	14
α-helix	339-353	15
α-helix	359-372	14
β-strand	375-381	7	13
α-helix	386-409	24
β-strand	411-413	3	12
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	18
β-strand	484-487	4	18
β-strand	494-496	3	12
α-helix	497-515	19
β-strand	517-523	7	11

Chain C: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	19
α-helix	10-28	19
β-strand	37-40	4	11
α-helix	47	1
β-strand	48-50	3	11
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	20
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	21
β-strand	186-191	6	21
β-strand	193-195	3	22
β-strand	199	1	23
α-helix	202-204	3
β-strand	207	1	24
β-strand	212	1	24
β-strand	213-216	4	22
β-strand	219-223	5	23
β-strand	226-227	2	25
α-helix	230-233	4
α-helix	234-243	10
β-strand	247-251	5	23
β-strand	253-254	2	25
α-helix	256-267	12
β-strand	273-277	5	23
α-helix	278	1
α-helix	283-296	14
β-strand	300-301	2	23
β-strand	318-319	2	23
β-strand	320-325	6	22
β-strand	330-335	6	22
α-helix	339-353	15
α-helix	359-372	14
β-strand	375-381	7	21
α-helix	386-409	24
β-strand	411-413	3	20
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	26
β-strand	484-487	4	26
α-helix	488-491	4
β-strand	494-496	3	20
α-helix	497-515	19
β-strand	517-523	7	19

Chain D: 22 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	27
α-helix	10-28	19
β-strand	37-40	4	19
α-helix	47	1
β-strand	48-50	3	19
α-helix	53-58	6
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	28
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	29
β-strand	186-191	6	29
β-strand	193-195	3	30
β-strand	199	1	31
α-helix	202-204	3
β-strand	207	1	32
β-strand	212	1	32
β-strand	213-216	4	30
β-strand	219-222	4	31
β-strand	223	1	33
β-strand	226-227	2	34
α-helix	230-232	3
α-helix	234-243	10
β-strand	247-251	5	31
β-strand	253-254	2	34
α-helix	256-267	12
β-strand	273-277	5	31
α-helix	278	1
α-helix	283-296	14
β-strand	301	1	33
β-strand	318-319	2	31
β-strand	322-325	4	30
β-strand	330-333	4	30
α-helix	339-353	15
α-helix	359-372	14
β-strand	375-381	7	29
α-helix	386-409	24
β-strand	411-413	3	28
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	35
β-strand	484-487	4	35
β-strand	494-496	3	28
α-helix	497-515	19
β-strand	517-523	7	27

Chain E: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	36
α-helix	10-28	19
β-strand	37-40	4	27
α-helix	47	1
β-strand	48-50	3	27
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	37
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	38
β-strand	186-191	6	38
β-strand	193-195	3	39
β-strand	199	1	40
α-helix	202-204	3
β-strand	207	1	41
β-strand	212	1	41
β-strand	213-216	4	39
β-strand	219-222	4	40
β-strand	223	1	42
β-strand	226-227	2	43
α-helix	230-233	4
α-helix	234-243	10
β-strand	247-251	5	40
β-strand	253-254	2	43
α-helix	256-267	12
β-strand	273-277	5	40
α-helix	278	1
α-helix	283-296	14
β-strand	301	1	42
α-helix	309-311	3
β-strand	318-319	2	40
β-strand	322-325	4	39
β-strand	330-333	4	39
α-helix	339-353	15
α-helix	359-372	14
β-strand	375-381	7	38
α-helix	386-409	24
β-strand	411-413	3	37
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
α-helix	488-491	4
β-strand	494-496	3	37
α-helix	497-515	19
β-strand	517-523	7	36

Chain F: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	45
α-helix	10-28	19
β-strand	37-40	4	36
α-helix	47	1
β-strand	48-50	3	36
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	46
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	47
β-strand	186-191	6	47
β-strand	193-195	3	48
β-strand	199	1	49
α-helix	202-204	3
β-strand	207	1	50
β-strand	212	1	50
β-strand	213-216	4	48
β-strand	219-222	4	49
β-strand	223	1	51
β-strand	226-227	2	52
α-helix	230-232	3
α-helix	234-243	10
β-strand	247-251	5	49
β-strand	253-254	2	52
α-helix	256-267	12
β-strand	273-277	5	49
α-helix	278	1
α-helix	283-296	14
β-strand	301	1	51
α-helix	309-311	3
α-helix	314-316	3
β-strand	318-319	2	49
β-strand	322-325	4	48
β-strand	330-333	4	48
α-helix	339-353	15
α-helix	359-372	14
β-strand	375-381	7	47
α-helix	386-409	24
β-strand	411-413	3	46
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	53
β-strand	484-487	4	53
β-strand	494-496	3	46
α-helix	497-515	19
β-strand	517-523	7	45

Chains O, R and S: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	61
β-strand	9-14	6	62
α-helix	15-18	4
β-strand	20	1	63
α-helix	25	1
β-strand	26	1	63
α-helix	27	1
α-helix	33-35	3
β-strand	37-43	7	62
β-strand	47-48	2	64
α-helix	49	1
β-strand	54-55	2	64
α-helix	59-60	2
β-strand	64-67	4	62
β-strand	74-78	5	62
β-strand	81-87	7	62
α-helix	88-90	3
β-strand	91-95	5	62

Chain P: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	62
β-strand	9-14	6	65
α-helix	15-18	4
β-strand	20	1	66
β-strand	26	1	66
α-helix	33-35	3
β-strand	37-43	7	65
β-strand	47-48	2	67
α-helix	49	1
β-strand	54-55	2	67
α-helix	59-60	2
β-strand	64-67	4	65
β-strand	74-78	5	65
β-strand	81-87	7	65
α-helix	88-90	3
β-strand	91-95	5	65

3 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, B, C, D, E, F, G	protein	548	Escherichia coli	P0A6F5 (AlphaFold model)
Co-chaperonin GroES	O, P, Q, R, S, T, U	protein	97	Escherichia coli	P0A6F9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G), FASTA

>8P4M_1 Chaperonin GroEL (chains A, B, C, D, E, F, G)
MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREI
ELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGI
DKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDG
TGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAV
AKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTV
ISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDY
DREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALI
RVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNA
ATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGG
MGGMGGMM

Sequence of entity 2 (O, P, Q, R, S, T, U), FASTA

>8P4M_2 Co-chaperonin GroES (chains O, P, Q, R, S, T, U)
MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVK
VGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	7
BEF	Beryllium trifluoride ion	Be F3	7
MG	Magnesium ion	Mg	7

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

Primary citation

Visualizing chaperonin function in situ by cryo-electron tomography. Wagner, J., Carvajal, A.I., Bracher, A. et al. Nature (2024) 633:459-464. DOI 10.1038/s41586-024-07843-w · 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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