5OPX: GroEL mutant A109C

Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2. Determined by X-ray diffraction at 3.64 Å resolution. Released 10 Jan 2018.

Method: X-ray diffraction
Resolution: 3.64 Å
Organism: Escherichia coli (strain K12)
Chains: 28
Atoms: 63,865
Mol. weight: 957.34 kDa
Ligands: BEF, MG, ADP
Released: 10 Jan 2018

Explore 5OPX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OPX contains 363 α-helices and 476 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 1, 2, O, P, S, T, U, V, W, X, Y and Z: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	103
β-strand	10-14	5	104
α-helix	26-28	3
β-strand	37-43	7	104
β-strand	46-48	3	105
α-helix	49	1
β-strand	54-56	3	105
β-strand	64-67	4	104
β-strand	74-78	5	104
β-strand	81-86	6	104
α-helix	88-90	3
β-strand	91-95	5	104

Chains A, B, C, D, E, F, G, H, J, K, L and M: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
α-helix	9-28	20
β-strand	37-40	4	2
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	175-179	5	4
β-strand	186-189	4	4
β-strand	194-195	2	5
β-strand	199	1	6
α-helix	202-204	3
β-strand	207	1	5
β-strand	212-216	5	5
β-strand	219-223	5	6
α-helix	226	1
β-strand	227	1	7
α-helix	230-232	3
α-helix	234-241	8
β-strand	247-251	5	6
β-strand	254	1	7
α-helix	256-268	13
β-strand	273-276	4	6
α-helix	277-278	2
α-helix	283-296	14
β-strand	300-301	2	6
α-helix	314-316	3
β-strand	318-319	2	6
β-strand	320-326	7	5
β-strand	330-335	6	5
α-helix	339-352	14
α-helix	359-372	14
β-strand	377-381	5	4
α-helix	386-409	24
β-strand	411-413	3	3
α-helix	417-425	9
α-helix	434-447	14
α-helix	449-456	8
α-helix	462-471	10
β-strand	476-479	4	8
β-strand	484-487	4	8
β-strand	494-496	3	3
α-helix	497-514	18
β-strand	517-523	7	1

Chain I: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	55
α-helix	9-28	20
β-strand	37-40	4	62
β-strand	48-50	3	62
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	63
α-helix	141-151	11
α-helix	156-169	14
β-strand	175-179	5	64
β-strand	186-189	4	64
β-strand	194-195	2	65
β-strand	199	1	66
α-helix	202-204	3
β-strand	207	1	65
β-strand	212-216	5	65
β-strand	219-223	5	66
α-helix	226	1
β-strand	227	1	67
α-helix	230-232	3
α-helix	234-241	8
β-strand	247-251	5	66
β-strand	254	1	67
α-helix	256-268	13
β-strand	273-276	4	66
α-helix	277-278	2
α-helix	283-296	14
β-strand	300-301	2	66
α-helix	314-316	3
β-strand	318-319	2	66
β-strand	320-326	7	65
β-strand	330-335	6	65
α-helix	339-352	14
α-helix	359-372	14
β-strand	377-381	5	64
α-helix	386-409	24
β-strand	411-413	3	63
α-helix	417-425	9
α-helix	434-447	14
α-helix	449-456	8
α-helix	462-470	9
β-strand	476-479	4	68
β-strand	484-487	4	68
β-strand	494-496	3	63
α-helix	497-514	18
β-strand	517-523	7	55

Chain N: 22 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	90
α-helix	9-28	20
β-strand	37-40	4	54
β-strand	48-50	3	54
α-helix	53-57	5
α-helix	65-84	20
α-helix	89-108	20
α-helix	113-134	22
β-strand	136	1	97
α-helix	141-151	11
α-helix	156-169	14
β-strand	175-179	5	98
β-strand	186-189	4	98
β-strand	194-195	2	99
β-strand	199	1	100
α-helix	202-204	3
β-strand	207	1	99
β-strand	212-216	5	99
β-strand	219-223	5	100
α-helix	226	1
β-strand	227	1	101
α-helix	230-232	3
α-helix	234-241	8
β-strand	247-251	5	100
β-strand	254	1	101
α-helix	256-268	13
β-strand	273-276	4	100
α-helix	283-296	14
β-strand	300-301	2	100
α-helix	314-316	3
β-strand	318-319	2	100
β-strand	320-326	7	99
β-strand	330-335	6	99
α-helix	339-352	14
α-helix	359-372	14
β-strand	377-381	5	98
α-helix	386-409	24
β-strand	411-413	3	97
α-helix	417-425	9
α-helix	434-447	14
α-helix	449-456	8
α-helix	462-471	10
β-strand	476-479	4	102
β-strand	484-487	4	102
β-strand	494-496	3	97
α-helix	497-514	18
β-strand	517-523	7	90

Chain Q: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	111
β-strand	10-13	4	113
α-helix	26-28	3
β-strand	37-43	7	113
β-strand	46-48	3	114
α-helix	49	1
β-strand	54-56	3	114
β-strand	64-67	4	113
β-strand	74-78	5	113
β-strand	81-86	6	113
α-helix	88-90	3
β-strand	91-94	4	113

Chain R: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	113
β-strand	10-14	5	115
α-helix	26-28	3
β-strand	37-43	7	115
β-strand	46-48	3	116
α-helix	49	1
β-strand	54-56	3	116
β-strand	64-67	4	115
β-strand	74-78	5	115
β-strand	81-86	6	115
α-helix	88-90	3
β-strand	91-95	5	115

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	548	Escherichia coli (strain K12)	P0A6F5 (AlphaFold model)
10 kDa chaperonin	1, 2, O, P, Q, R, S, T, U, V, W, X, Y, Z	protein	97	Escherichia coli (strain K12)	P0A6F9 (AlphaFold model)

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

>5OPX_1 60 kDa chaperonin (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N)
MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREI
ELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVACGMNPMDLKRGI
DKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDG
TGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAV
AKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTV
ISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDY
DREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALI
RVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNA
ATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGG
MGGMGGMM

Sequence of entity 2 (1, 2, O, P, Q, R, S, T, U, V, W, X, Y, Z), FASTA

>5OPX_2 10 kDa chaperonin (chains 1, 2, O, P, Q, R, S, T, U, V, W, X, Y, Z)
MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVK
VGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Ligands and cofactors

ID	Name	Formula	Copies
BEF	Beryllium trifluoride ion	Be F3	14
MG	Magnesium ion	Mg	14
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	14

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

Primary citation

GroEL Ring Separation and Exchange in the Chaperonin Reaction. Yan, X., Shi, Q., Bracher, A. et al. Cell (2018) 172:605-617.e11. DOI 10.1016/j.cell.2017.12.010 · 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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