8P4O: Chaperonin GroEL

CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx. Determined by electron microscopy at 3.04 Å resolution. Released 3 Jul 2024.

Method: Electron microscopy
Resolution: 3.04 Å
Organism: Escherichia coli
Chains: 15
Atoms: 34,605
Mol. weight: 519.52 kDa
Ligands: BEF, MG, ADP
Released: 3 Jul 2024

Explore 8P4O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P4O contains 213 α-helices and 280 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.

Chain 1: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	82
α-helix	16-34	19
β-strand	39-46	8	83
β-strand	50-58	9	83
α-helix	65-76	12
β-strand	79	1	84
β-strand	86	1	84
β-strand	91-97	7	83
α-helix	112-114	3
α-helix	115-116	2
β-strand	117	1	85
β-strand	121-124	4	86
β-strand	127-128	2	87
α-helix	137-155	19
β-strand	161-174	14	82
β-strand	177-190	14	82
α-helix	196-203	8
α-helix	204-208	5
β-strand	222-225	4	82
α-helix	236-238	3
β-strand	241-242	2	83
α-helix	247-251	5
β-strand	266	1	83
α-helix	271-288	18
β-strand	294-295	2	87
β-strand	296-301	6	86
β-strand	305	1	85
β-strand	311-314	4	86
α-helix	323-333	11
α-helix	340-345	6
α-helix	352-355	4
α-helix	367-369	3
α-helix	374-381	8

Chain A: 24 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	53-59	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	156-169	14
β-strand	173-179	7	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	227	1	9
α-helix	234-243	10
β-strand	247-250	4	6
β-strand	254	1	9
α-helix	256-267	12
β-strand	275-276	2	6
α-helix	277-279	3
α-helix	283-296	14
β-strand	301	1	8
α-helix	309-311	3
α-helix	314-316	3
β-strand	318-319	2	6
β-strand	320-325	6	5
β-strand	330-335	6	5
α-helix	339-354	16
α-helix	359-372	14
β-strand	375-381	7	4
α-helix	386-408	23
β-strand	411-413	3	3
α-helix	417-425	9
α-helix	434-446	13
α-helix	449-458	10
α-helix	462-470	9
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	497-514	18
β-strand	517-523	7	1

Chain B: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	11
α-helix	10-27	18
α-helix	28-30	3
β-strand	37-40	4	1
β-strand	48-50	3	1
α-helix	53-57	5
α-helix	65-84	20
α-helix	90-109	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	219-222	4	15
β-strand	223	1	17
α-helix	226	1
β-strand	227	1	18
α-helix	231-233	3
α-helix	234-243	10
β-strand	247-251	5	15
β-strand	254	1	18
α-helix	256-268	13
β-strand	273-277	5	15
α-helix	278-279	2
α-helix	283-296	14
β-strand	301	1	17
α-helix	314-316	3
β-strand	318-319	2	15
β-strand	320-325	6	14
β-strand	330-335	6	14
α-helix	339-353	15
α-helix	360-372	13
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	449-458	10
α-helix	462-470	9
β-strand	476-479	4	19
β-strand	484-487	4	19
α-helix	488-491	4
β-strand	494-496	3	12
α-helix	497-515	19
β-strand	517-523	7	11

Chain C: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	20
α-helix	10-28	19
β-strand	37-40	4	11
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	21
α-helix	141-150	10
α-helix	156-169	14
β-strand	174-179	6	22
β-strand	186-191	6	22
β-strand	193-195	3	23
β-strand	199	1	24
α-helix	202-204	3
β-strand	213-216	4	23
β-strand	219-222	4	24
β-strand	223	1	25
β-strand	227	1	26
α-helix	231-233	3
α-helix	234-241	8
β-strand	247-251	5	24
β-strand	254	1	26
α-helix	256-268	13
β-strand	273-277	5	24
α-helix	278-279	2
α-helix	282-296	15
β-strand	301	1	25
α-helix	309-311	3
α-helix	314-316	3
β-strand	318-319	2	24
β-strand	320-325	6	23
β-strand	330-335	6	23
α-helix	339-355	17
α-helix	359-372	14
β-strand	375-381	7	22
α-helix	386-408	23
β-strand	411-413	3	21
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	27
β-strand	484-487	4	27
β-strand	494-496	3	21
α-helix	497-515	19
β-strand	517-523	7	20

Chain D: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	28
α-helix	10-28	19
β-strand	37-40	4	20
α-helix	47	1
β-strand	48-50	3	20
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-107	19
α-helix	113-134	22
β-strand	136	1	29
α-helix	141-151	11
α-helix	156-169	14
β-strand	173-179	7	30
β-strand	186-190	5	30
β-strand	193-195	3	31
β-strand	199	1	32
α-helix	202-204	3
β-strand	207	1	33
β-strand	212	1	33
β-strand	213-216	4	31
β-strand	219-222	4	32
β-strand	223	1	34
α-helix	226	1
β-strand	227	1	35
α-helix	231-233	3
α-helix	234-243	10
β-strand	247-250	4	32
β-strand	254	1	35
α-helix	256-268	13
β-strand	273-276	4	32
α-helix	277-278	2
α-helix	283-296	14
β-strand	301	1	34
α-helix	309-311	3
β-strand	318-319	2	32
β-strand	322-325	4	31
β-strand	330-333	4	31
α-helix	339-354	16
α-helix	359-372	14
β-strand	375-381	7	30
α-helix	386-409	24
β-strand	411-413	3	29
α-helix	417-424	8
α-helix	434-446	13
α-helix	449-457	9
α-helix	462-471	10
β-strand	476-479	4	36
β-strand	484-487	4	36
β-strand	494-496	3	29
α-helix	497-514	18
β-strand	517-523	7	28

Chain E: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	37
α-helix	10-27	18
α-helix	28-30	3
β-strand	37-40	4	28
β-strand	48-50	3	28
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
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
β-strand	199	1	41
α-helix	202-204	3
β-strand	207	1	42
β-strand	212	1	42
β-strand	213-216	4	40
β-strand	219-222	4	41
β-strand	223	1	43
β-strand	227	1	44
α-helix	231-233	3
α-helix	234-243	10
β-strand	247-251	5	41
β-strand	254	1	44
α-helix	256-268	13
β-strand	273-277	5	41
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	43
α-helix	303-305	3
α-helix	309-311	3
β-strand	318-319	2	41
β-strand	320-325	6	40
β-strand	330-335	6	40
α-helix	339-353	15
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	45
β-strand	484-487	4	45
β-strand	494-496	3	38
α-helix	497-515	19
β-strand	517-523	7	37

Chain F: 25 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	46
α-helix	10-27	18
α-helix	28-30	3
β-strand	37-40	4	37
β-strand	48-50	3	37
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-107	19
α-helix	113-134	22
β-strand	136	1	47
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	48
β-strand	186-191	6	48
β-strand	193-195	3	49
β-strand	199	1	50
α-helix	202-204	3
β-strand	207	1	51
β-strand	212	1	51
β-strand	213-216	4	49
β-strand	219-223	5	50
β-strand	227	1	52
α-helix	234-243	10
β-strand	247-251	5	50
β-strand	254	1	52
α-helix	256-267	12
β-strand	273-277	5	50
α-helix	278	1
α-helix	283-296	14
β-strand	300-301	2	50
α-helix	303-305	3
α-helix	309-311	3
α-helix	314-316	3
β-strand	318-319	2	50
β-strand	322-325	4	49
β-strand	330-333	4	49
α-helix	339-354	16
α-helix	359-372	14
β-strand	375-381	7	48
α-helix	386-409	24
β-strand	411-413	3	47
α-helix	417-424	8
α-helix	434-446	13
α-helix	449-458	10
α-helix	462-470	9
β-strand	476-479	4	53
β-strand	484-487	4	53
α-helix	488-491	4
β-strand	494-496	3	47
α-helix	497-515	19
β-strand	517-523	7	46

Chain G: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	2
α-helix	10-27	18
α-helix	28-30	3
β-strand	37-40	4	46
β-strand	48-50	3	46
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-107	19
α-helix	113-134	22
β-strand	136	1	54
α-helix	141-150	10
α-helix	156-169	14
β-strand	174-179	6	55
β-strand	186-191	6	55
β-strand	193-195	3	56
β-strand	199	1	57
α-helix	202-204	3
β-strand	207	1	58
β-strand	212	1	58
β-strand	213-216	4	56
β-strand	219-223	5	57
β-strand	227	1	59
α-helix	230-232	3
α-helix	234-241	8
β-strand	247-251	5	57
β-strand	254	1	59
α-helix	256-267	12
β-strand	273-277	5	57
α-helix	278	1
α-helix	283-296	14
β-strand	300-301	2	57
α-helix	309-311	3
β-strand	318-319	2	57
β-strand	320-325	6	56
β-strand	330-335	6	56
α-helix	339-354	16
α-helix	359-372	14
β-strand	375-381	7	55
α-helix	386-408	23
β-strand	411-413	3	54
α-helix	417-424	8
α-helix	434-446	13
α-helix	449-458	10
α-helix	462-471	10
β-strand	476-479	4	60
β-strand	484-487	4	60
β-strand	494-496	3	54
α-helix	497-515	19
β-strand	517-523	7	2

7 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	547	Escherichia coli	P0A6F5 (AlphaFold model)
Co-chaperonin GroES	O, P, Q, R, S, T, U	protein	97	Escherichia coli	P0A6F9 (AlphaFold model)
S-adenosylmethionine synthase	1	protein	384	Escherichia coli	P0A817 (AlphaFold model)

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

>8P4O_1 Chaperonin GroEL (chains A, B, C, D, E, F, G)
AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIE
LEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID
KAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGT
GLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA
KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVI
SEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD
REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIR
VASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA
TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGGM
GGMGGMM

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

>8P4O_2 Co-chaperonin GroES (chains O, P, Q, R, S, T, U)
MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVK
VGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Sequence of entity 3 (1), FASTA

>8P4O_3 S-adenosylmethionine synthase (chains 1)
MAKHLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTS
AWVDIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVDRADPLEQGAGDQ
GLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDGKIVG
IDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGPMGDC
GLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCEIQVS
YAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHPIYKETAAYGH
FGREHFPWEKTDKAQLLRDAAGLK

Ligands and cofactors

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