8BA9: GroEL-GroES-ADP.AlF3-Rubisco

CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco. Determined by electron microscopy at 3.7 Å resolution. Released 27 Dec 2023.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Escherichia coli K-12
Chains: 21
Atoms: 59,451
Mol. weight: 853.07 kDa
Ligands: MG, ADP, AF3
Released: 27 Dec 2023

Explore 8BA9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BA9 contains 360 α-helices and 438 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: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
α-helix	10-28	19
β-strand	38-40	3	2
β-strand	48-50	3	2
α-helix	53-59	7
α-helix	65-85	21
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
α-helix	202-204	3
β-strand	207	1	6
β-strand	212	1	6
β-strand	213-216	4	5
β-strand	219-222	4	7
β-strand	223	1	8
β-strand	226-227	2	9
α-helix	230-243	14
β-strand	247-251	5	7
β-strand	253-254	2	9
α-helix	256-267	12
β-strand	273-277	5	7
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	8
α-helix	303-305	3
α-helix	309-311	3
β-strand	318-319	2	7
β-strand	322-325	4	5
β-strand	330-332	3	5
α-helix	339-355	17
α-helix	359-373	15
β-strand	375-381	7	4
α-helix	386-409	24
β-strand	411-413	3	3
α-helix	417-425	9
α-helix	426-428	3
α-helix	434-446	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: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	2
α-helix	10-28	19
β-strand	37-40	4	11
β-strand	48-50	3	11
α-helix	53-59	7
α-helix	65-85	21
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	186-190	5	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	227	1	17
α-helix	230-243	14
β-strand	247-251	5	15
β-strand	254	1	17
α-helix	256-267	12
β-strand	273-277	5	15
α-helix	278	1
α-helix	283-296	14
β-strand	301	1	15
α-helix	309-311	3
β-strand	318-319	2	15
β-strand	320-325	6	14
β-strand	330-335	6	14
α-helix	339-355	17
α-helix	359-373	15
β-strand	376-381	6	13
α-helix	382	1
α-helix	386-409	24
β-strand	411-413	3	12
α-helix	417-425	9
α-helix	426-428	3
α-helix	434-446	13
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	12
α-helix	497-514	18
β-strand	519-523	5	2

Chain C: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4-8	5	11
α-helix	10-28	19
β-strand	37-40	4	19
β-strand	48-50	3	19
α-helix	53-59	7
α-helix	65-85	21
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	186-190	5	21
β-strand	193-195	3	22
β-strand	199	1	23
α-helix	202-204	3
β-strand	207	1	22
β-strand	212-216	5	22
β-strand	219-222	4	23
β-strand	223	1	24
β-strand	226-227	2	25
α-helix	230-243	14
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	282-296	15
β-strand	301	1	24
α-helix	309-311	3
β-strand	318-319	2	23
β-strand	320-326	7	22
β-strand	330-335	6	22
α-helix	339-355	17
α-helix	359-372	14
β-strand	376-381	6	21
α-helix	386-409	24
β-strand	411-413	3	20
α-helix	417-425	9
α-helix	426-428	3
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	497-514	18
β-strand	517-523	7	11

Chain D: 25 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	19
α-helix	9-28	20
β-strand	38-40	3	27
β-strand	48-50	3	27
α-helix	53-59	7
α-helix	65-85	21
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	186-190	5	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	219-223	5	31
β-strand	226-227	2	33
α-helix	230-232	3
α-helix	234-243	10
β-strand	247-251	5	31
β-strand	253-254	2	33
α-helix	256-267	12
β-strand	273-277	5	31
α-helix	278	1
α-helix	283-296	14
β-strand	300-301	2	31
α-helix	303-305	3
α-helix	309-311	3
β-strand	318-319	2	31
β-strand	320-325	6	30
β-strand	330-335	6	30
α-helix	339-355	17
α-helix	359-373	15
β-strand	376-381	6	29
α-helix	386-409	24
β-strand	411-413	3	28
α-helix	417-425	9
α-helix	426-428	3
α-helix	434-446	13
α-helix	449-457	9
α-helix	462-471	10
β-strand	476-479	4	34
β-strand	484-487	4	34
α-helix	488-491	4
β-strand	494-496	3	28
α-helix	497-514	18
β-strand	517-523	7	19

Chain E: 25 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	27
α-helix	10-28	19
β-strand	38-40	3	35
α-helix	41	1
β-strand	48-50	3	35
α-helix	53-59	7
α-helix	65-85	21
α-helix	89-107	19
α-helix	113-134	22
β-strand	136	1	36
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	37
β-strand	186-190	5	37
β-strand	193-195	3	38
β-strand	199	1	39
α-helix	202-204	3
β-strand	207	1	40
β-strand	212	1	40
β-strand	213-216	4	38
β-strand	219-222	4	39
β-strand	223	1	41
β-strand	226-227	2	42
α-helix	230-232	3
α-helix	234-243	10
β-strand	247-251	5	39
β-strand	253-254	2	42
α-helix	256-267	12
β-strand	273-277	5	39
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	41
α-helix	309-311	3
β-strand	318-319	2	39
β-strand	320	1	43
β-strand	322-325	4	38
β-strand	330-332	3	38
β-strand	335	1	43
α-helix	339-355	17
α-helix	359-373	15
β-strand	376-381	6	37
α-helix	386-409	24
β-strand	411-413	3	36
α-helix	417-425	9
α-helix	426-428	3
α-helix	434-446	13
α-helix	449-458	10
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	36
α-helix	497-514	18
β-strand	519-523	5	27

Chain F: 26 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	35
α-helix	10-28	19
β-strand	37-40	4	45
α-helix	41	1
β-strand	48-50	3	45
α-helix	53-59	7
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	186-190	5	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	219-227	9	49
α-helix	230-232	3
α-helix	234-243	10
β-strand	247-254	8	49
α-helix	256-267	12
β-strand	273-277	5	49
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	49
α-helix	309-311	3
β-strand	318-319	2	49
β-strand	320-325	6	48
β-strand	330-335	6	48
α-helix	339-353	15
α-helix	359-373	15
β-strand	376-381	6	47
α-helix	382	1
α-helix	386-409	24
β-strand	411-413	3	46
α-helix	417-425	9
α-helix	426-428	3
α-helix	434-446	13
α-helix	449-458	10
α-helix	462-471	10
β-strand	476-479	4	51
β-strand	484-487	4	51
α-helix	488-491	4
β-strand	494-496	3	46
α-helix	497-514	18
β-strand	519-523	5	35

Chain G: 22 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	45
α-helix	10-28	19
β-strand	37-40	4	1
β-strand	48-50	3	1
α-helix	53-59	7
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	52
α-helix	141-151	11
α-helix	156-169	14
β-strand	174-179	6	53
β-strand	186-191	6	53
β-strand	193-195	3	54
α-helix	202-204	3
β-strand	207	1	55
β-strand	212	1	55
β-strand	213-216	4	54
β-strand	219-227	9	56
α-helix	230-243	14
β-strand	247-254	8	56
α-helix	256-267	12
β-strand	273-277	5	56
α-helix	278	1
α-helix	283-296	14
β-strand	301	1	56
β-strand	318-319	2	56
β-strand	320-325	6	54
β-strand	330-335	6	54
α-helix	339-355	17
α-helix	359-373	15
β-strand	375-381	7	53
α-helix	386-409	24
β-strand	411-413	3	52
α-helix	417-425	9
α-helix	426-428	3
α-helix	434-446	13
α-helix	449-457	9
α-helix	462-471	10
β-strand	476-479	4	57
β-strand	484-487	4	57
α-helix	488-491	4
β-strand	494-496	3	52
α-helix	497-514	18
β-strand	517-523	7	45

Chain H: 25 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	58
α-helix	10-27	18
α-helix	28-30	3
α-helix	35-36	2
β-strand	37-40	4	59
β-strand	48-50	3	59
α-helix	53-59	7
α-helix	65-85	21
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	60
α-helix	141-150	10
α-helix	156-169	14
β-strand	175-179	5	61
β-strand	186-190	5	61
β-strand	193-195	3	62
β-strand	199	1	63
β-strand	215-216	2	62
β-strand	219-223	5	63
α-helix	230-233	4
α-helix	234-243	10
β-strand	247-251	5	63
α-helix	259-266	8
β-strand	273-277	5	63
α-helix	278	1
α-helix	282-296	15
β-strand	300-301	2	63
β-strand	318-319	2	63
β-strand	320	1	64
β-strand	322-325	4	62
β-strand	330-332	3	62
β-strand	335	1	64
α-helix	339-352	14
α-helix	353-355	3
α-helix	360-373	14
α-helix	375	1
β-strand	376-381	6	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	65
β-strand	484-487	4	65
α-helix	488-491	4
β-strand	494-496	3	60
α-helix	497-515	19
β-strand	517-521	5	58

13 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
60 kDa chaperonin	A, B, C, D, E, F, G, H, I, J, K, L, M, N	protein	524	Escherichia coli K-12	P0A6F5 (AlphaFold model)
Co-chaperonin GroES	O, P, Q, R, S, T, U	protein	97	Escherichia coli K-12	P0A6F9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N), FASTA

>8BA9_1 60 kDa chaperonin (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N)
AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIE
LEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID
KAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGT
GLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA
KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVI
SEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD
REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIR
VASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA
TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP

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

>8BA9_2 Co-chaperonin GroES (chains O, P, Q, R, S, T, U)
MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVK
VGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	14
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	14
AF3	Aluminum fluoride	Al F3	7

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

Primary citation

Structural basis of substrate progression through the bacterial chaperonin cycle. Gardner, S., Darrow, M.C., Lukoyanova, N. et al. Proc Natl Acad Sci U S A (2023) 120:e2308933120-e2308933120. DOI 10.1073/pnas.2308933120 · 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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