7WBB: Substrate engaged Drg1 hexamer

Cryo-EM structure of substrate engaged Drg1 hexamer. Determined by electron microscopy at 3.6 Å resolution. Released 28 Dec 2022.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Saccharomyces cerevisiae, Escherichia coli
Chains: 7
Atoms: 33,634
Mol. weight: 516.65 kDa
Ligands: ATP
Released: 28 Dec 2022

Explore 7WBB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WBB contains 217 α-helices and 191 β-strands across 7 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: 39 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	1
β-strand	35	1	2
β-strand	38	1	3
β-strand	50-51	2	1
α-helix	55-60	6
β-strand	68-73	6	1
β-strand	79-83	5	1
β-strand	95	1	2
β-strand	98	1	3
α-helix	102-104	3
β-strand	114-117	4	1
β-strand	129-133	5	4
α-helix	147-153	7
β-strand	178-183	6	4
β-strand	224-226	3	4
α-helix	232-233	2
α-helix	234-236	3
α-helix	244-246	3
α-helix	251-265	15
α-helix	269-271	3
α-helix	276-278	3
β-strand	284-285	2	5
α-helix	292-302	11
α-helix	322-337	16
β-strand	341-345	5	5
α-helix	347-350	4
β-strand	352	1	6
α-helix	358-360	3
α-helix	363-374	12
β-strand	384-389	6	5
β-strand	395	1	6
α-helix	397-400	4
α-helix	403-405	3
β-strand	410	1	5
α-helix	411-414	4
α-helix	419-430	12
α-helix	439-447	9
α-helix	454-476	23
α-helix	481-483	3
α-helix	488-498	11
α-helix	510-512	3
α-helix	522-537	16
α-helix	540-545	6
β-strand	552-556	5	7
α-helix	563-570	8
α-helix	571-575	5
β-strand	579-581	3	7
α-helix	584-586	3
β-strand	590	1	8
α-helix	593-603	11
β-strand	613-615	3	7
α-helix	618-620	3
α-helix	632-644	13
β-strand	655-659	5	7
α-helix	662-664	3
β-strand	677-679	3	7
α-helix	682-684	3
α-helix	686-696	11
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-754	8
α-helix	763-776	14

Chain B: 40 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	9
β-strand	35-38	4	10
α-helix	42-43	2
β-strand	52-53	2	11
α-helix	55-60	6
β-strand	70-72	3	12
β-strand	84-85	2	11
β-strand	95-98	4	10
α-helix	100-106	7
β-strand	114	1	9
β-strand	115-117	3	12
α-helix	122-124	3
β-strand	125	1	13
β-strand	128-133	6	14
α-helix	148-151	4
β-strand	158	1	15
β-strand	164	1	14
β-strand	170	1	16
β-strand	174	1	16
β-strand	178-179	2	14
β-strand	183-184	2	14
β-strand	215	1	15
β-strand	216	1	13
β-strand	224-227	4	14
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-272	5
α-helix	277-279	3
β-strand	281-285	5	17
α-helix	292-302	11
β-strand	306-309	4	17
α-helix	313-315	3
β-strand	319	1	18
α-helix	322-337	16
β-strand	340-345	6	17
α-helix	347-350	4
β-strand	352	1	19
α-helix	362-376	15
β-strand	383-389	7	17
α-helix	392-394	3
β-strand	395	1	19
α-helix	402-405	4
β-strand	407-410	4	17
α-helix	416-429	14
α-helix	432-434	3
β-strand	435	1	20
α-helix	439-448	10
α-helix	454-475	22
α-helix	481-483	3
β-strand	486	1	20
α-helix	488-497	10
α-helix	498-500	3
α-helix	501-503	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	21
α-helix	563-572	10
β-strand	578-581	4	21
α-helix	584-586	3
β-strand	590	1	22
α-helix	593-607	15
β-strand	612-616	5	21
α-helix	618-620	3
α-helix	631-644	14
α-helix	649-650	2
β-strand	654-659	6	21
α-helix	662-664	3
α-helix	667-670	4
β-strand	677-679	3	21
α-helix	686-697	12
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-756	10
α-helix	763-776	14

Chain C: 34 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	56
β-strand	52	1	57
α-helix	55-60	6
β-strand	69-72	4	58
β-strand	78-80	3	58
β-strand	84	1	57
β-strand	95-97	3	56
α-helix	100-105	6
β-strand	113-114	2	56
β-strand	115-118	4	58
β-strand	131	1	59
α-helix	146-150	5
β-strand	158	1	60
β-strand	163	1	61
β-strand	179	1	61
β-strand	180	1	59
β-strand	215	1	60
β-strand	226	1	59
α-helix	234-236	3
α-helix	244-246	3
α-helix	251-265	15
α-helix	269-274	6
α-helix	277-279	3
β-strand	281-285	5	62
α-helix	292-302	11
β-strand	306-310	5	62
α-helix	313-315	3
β-strand	319	1	54
α-helix	322-336	15
β-strand	340-345	6	62
α-helix	347-350	4
β-strand	352	1	63
α-helix	362-374	13
β-strand	383-389	7	62
α-helix	392-394	3
β-strand	395	1	63
α-helix	402-405	4
β-strand	407-410	4	62
α-helix	416-429	14
β-strand	435	1	64
α-helix	439-448	10
α-helix	454-475	22
α-helix	481-483	3
β-strand	486	1	64
α-helix	488-497	10
α-helix	515-517	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	553-556	4	65
α-helix	563-573	11
β-strand	578-582	5	65
β-strand	590	1	55
α-helix	593-607	15
β-strand	612-616	5	65
α-helix	618-621	4
α-helix	623-624	2
α-helix	631-645	15
β-strand	646	1	66
β-strand	648	1	66
β-strand	654-659	6	65
β-strand	677-679	3	65
α-helix	686-697	12
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-756	10
α-helix	763-776	14

Chain D: 39 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	23
β-strand	50-51	2	24
α-helix	55-61	7
β-strand	68-72	5	24
β-strand	79-83	5	24
α-helix	88-90	3
β-strand	95-97	3	23
α-helix	100-103	4
β-strand	113-114	2	23
β-strand	115-117	3	24
α-helix	121-124	4
β-strand	125	1	25
α-helix	126	1
β-strand	128-133	6	26
α-helix	146-149	4
α-helix	150-154	5
β-strand	157-158	2	25
β-strand	163-164	2	26
β-strand	178-184	7	26
β-strand	215-216	2	25
β-strand	223-226	4	26
α-helix	232-233	2
α-helix	234-236	3
α-helix	238-242	5
α-helix	251-266	16
α-helix	277-279	3
β-strand	282-285	4	27
α-helix	292-302	11
β-strand	306-309	4	27
α-helix	313-315	3
β-strand	319	1	28
α-helix	320-336	17
β-strand	340-345	6	27
α-helix	347-350	4
β-strand	352	1	29
α-helix	361-374	14
β-strand	383-389	7	27
β-strand	395	1	29
β-strand	407-410	4	27
α-helix	416-434	19
α-helix	439-448	10
α-helix	454-475	22
α-helix	481-483	3
α-helix	489-497	9
α-helix	499-500	2
α-helix	502-505	4
α-helix	515-517	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	30
α-helix	563-574	12
β-strand	578-582	5	30
α-helix	583-586	4
β-strand	590	1	31
α-helix	594-607	14
β-strand	612-616	5	30
α-helix	618-620	3
α-helix	633-645	13
β-strand	649	1	32
β-strand	654-659	6	30
α-helix	667-670	4
β-strand	677-679	3	30
α-helix	686-696	11
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-756	10
α-helix	763-773	11

Chain E: 34 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	33
β-strand	51-53	3	33
α-helix	55-60	6
β-strand	68-72	5	34
β-strand	78	1	35
β-strand	79-82	4	34
β-strand	83-85	3	33
β-strand	95-98	4	33
α-helix	102-105	4
β-strand	113-114	2	33
β-strand	115-117	3	34
α-helix	122-124	3
β-strand	125	1	36
α-helix	126	1
β-strand	129-131	3	37
α-helix	146-154	9
β-strand	158	1	38
β-strand	163	1	39
β-strand	179	1	39
β-strand	180-183	4	37
β-strand	210	1	35
β-strand	215	1	38
β-strand	216	1	36
β-strand	225-226	2	37
α-helix	234-236	3
α-helix	251-266	16
α-helix	268-274	7
α-helix	277-279	3
β-strand	281-285	5	40
α-helix	292-301	10
β-strand	307-311	5	40
α-helix	312-314	3
β-strand	319	1	41
α-helix	323-336	14
β-strand	341-345	5	40
α-helix	347-350	4
β-strand	352	1	42
α-helix	362-374	13
β-strand	384-389	6	40
β-strand	395	1	42
β-strand	407-410	4	40
α-helix	416-429	14
α-helix	439-448	10
α-helix	454-472	19
α-helix	488-494	7
α-helix	509-511	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	43
α-helix	565-574	10
β-strand	578-581	4	43
α-helix	583-586	4
β-strand	590	1	44
α-helix	593-607	15
β-strand	612-615	4	43
α-helix	618-620	3
α-helix	631-644	14
β-strand	654-659	6	43
α-helix	662-664	3
α-helix	667-670	4
β-strand	678-679	2	43
α-helix	686-699	14
α-helix	702-705	4
α-helix	710-717	8
α-helix	721-738	18
α-helix	747-756	10
α-helix	763-774	12

Chain F: 31 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	45
β-strand	35-37	3	46
β-strand	50-52	3	46
α-helix	55-60	6
β-strand	68-69	2	46
β-strand	70-72	3	47
β-strand	81-84	4	46
β-strand	95-97	3	46
α-helix	100-105	6
β-strand	114	1	45
β-strand	115-117	3	47
α-helix	122-124	3
β-strand	125	1	48
α-helix	126	1
β-strand	130-133	4	49
α-helix	147-153	7
β-strand	158	1	50
β-strand	170	1	51
β-strand	175	1	51
β-strand	178-182	5	49
β-strand	215	1	50
β-strand	216	1	48
β-strand	225-228	4	49
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	52
α-helix	293-301	9
β-strand	306-310	5	52
α-helix	317	1
α-helix	323-336	14
β-strand	340-345	6	52
α-helix	347-350	4
α-helix	361-376	16
β-strand	383-388	6	52
β-strand	408-410	3	52
α-helix	412-414	3
α-helix	416-429	14
α-helix	439-448	10
α-helix	457-476	20
α-helix	481-483	3
α-helix	489-498	10
α-helix	522-537	16
α-helix	540-545	6
α-helix	547-549	3
β-strand	553-556	4	53
α-helix	563-574	12
β-strand	581	1	53
α-helix	600-608	9
β-strand	614-615	2	53
α-helix	631-650	20
β-strand	656-659	4	53
α-helix	662-664	3
α-helix	667-670	4
β-strand	677-680	4	53
α-helix	686-698	13
α-helix	711-715	5
α-helix	723-738	16
α-helix	747-756	10
α-helix	763-776	14

Chain H: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	18
β-strand	4	1	54
β-strand	6	1	28
β-strand	8	1	41
β-strand	14	1	8
β-strand	16	1	22
β-strand	18	1	55
β-strand	20	1	31
β-strand	22	1	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AFG2 isoform 1	A, B, C, D, E, F	protein	780	Saccharomyces cerevisiae	P32794 (AlphaFold model)
substrate	H	protein	23	Escherichia coli

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

>7WBB_1 AFG2 isoform 1 (chains A, B, C, D, E, F)
MAPKSSSSGSKKKSSASSNSADAKASKFKLPAEFITRPHPSKDHGKETCTAYIHPNVLSS
LEINPGSFCTVGKIGENGILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQ
VQPPYATKVTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESIDVVI
TDASDDSLPDVSQLDLNMDDMYGGLDNLFYLSPPFIFRKGSTHITFSKETQANRKYNLPE
PLSYAAVGGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGKTMLLRVVA
NTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSIIFIDQIDSIAPNRANDDSG
EVESRVVATLLTLMDGMGAAGKVVVIAATNRPNSVDPALRRPGRFDQEVEIGIPDVDARF
DILTKQFSRMSSDRHVLDSEAIKYIASKTHGYVGADLTALCRESVMKTIQRGLGTDANID
KFSLKVTLKDVESAMVDIRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASE
TFARLGISAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVGESERAIRE
IFRKARSAAPSIIFFDQIDALSPDRDGSSTSAANHVLTSLLNEIDGVEELKGVVIVAATN
RPDEIDAALLRPGRLDRHIYVGPPDVNARLEILKKCTKKFNTEESGVDLHELADRTEGYS
GAEVVLLCQEAGLAAIMEDLDVAKVELRHFEKAFKGIARGITPEMLSYYEEFALRSGSSS

Sequence of entity 2 (H), FASTA

>7WBB_2 substrate (chains H)
XXXXXXXXXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	11

Primary citation

Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition. Ma, C., Wu, D., Chen, Q. et al. Nat Commun (2022) 13:6765-6765. DOI 10.1038/s41467-022-34511-2 · PubMed

Other PDB entries of the same protein (UniProt P32794 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z11 3.2 Å, Structure of substrate bound DRG1 (AFG2)
7NKU 3.4 Å, diazaborine bound Drg1(AFG2)
7WD3 3.8 Å, Cryo-EM structure of Drg1 hexamer treated with ATP and benzo-diazaborine
7Z34 3.8 Å, Structure of pre-60S particle bound to DRG1(AFG2).
7YKZ 4.3 Å, Cryo-EM structure of Drg1 hexamer in the planar state treated with ADP/AMPPNP/Diazaborine
7YKL 5.6 Å, Cryo-EM structure of Drg1 hexamer treated with AMPPNP
7YKK 5.9 Å, Cryo-EM structure of Drg1 hexamer treated with ADP
7YKT 5.9 Å, Cryo-EM structure of Drg1 hexamer in helical state treated with…

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