7WD3: ATPase family gene 2 protein

Cryo-EM structure of Drg1 hexamer treated with ATP and benzo-diazaborine. Determined by electron microscopy at 3.8 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 33,891
Mol. weight: 500.38 kDa
Ligands: NDT, ATP
Released: 14 Dec 2022

Explore 7WD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WD3 contains 201 α-helices and 183 β-strands across 6 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: 33 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	1
β-strand	35-37	3	2
β-strand	50	1	3
α-helix	55-60	6
β-strand	69	1	4
β-strand	70-73	4	1
β-strand	82	1	4
β-strand	83	1	3
β-strand	95-97	3	2
α-helix	99-103	5
β-strand	114-117	4	1
β-strand	125	1	5
β-strand	129-131	3	6
β-strand	132-133	2	7
α-helix	145-153	9
β-strand	158	1	8
β-strand	178-179	2	7
β-strand	214	1	8
β-strand	216	1	5
β-strand	219	1	9
β-strand	222	1	9
β-strand	224-226	3	6
α-helix	234-236	3
α-helix	238-242	5
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	10
α-helix	292-301	10
β-strand	306-310	5	10
α-helix	320-336	17
β-strand	340-344	5	10
α-helix	347-350	4
β-strand	352	1	11
α-helix	364-375	12
β-strand	383-389	7	10
β-strand	395	1	11
α-helix	397-400	4
β-strand	407-410	4	10
α-helix	416-429	14
α-helix	432-434	3
α-helix	439-448	10
α-helix	455-476	22
α-helix	481-484	4
α-helix	488-497	10
α-helix	510-512	3
α-helix	515-518	4
α-helix	523-537	15
α-helix	539-545	7
β-strand	553-556	4	12
α-helix	563-573	11
β-strand	578-581	4	12
α-helix	584-587	4
α-helix	593-607	15
β-strand	612-615	4	12
α-helix	631-644	14
β-strand	654-659	6	12
α-helix	662-664	3
β-strand	671	1	13
β-strand	674	1	13
β-strand	677-679	3	12
α-helix	686-699	14
α-helix	703-705	3
α-helix	709-715	7
α-helix	721-737	17
α-helix	747-756	10
α-helix	763-775	13

Chain B: 33 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	14
β-strand	35-36	2	15
β-strand	50	1	16
α-helix	55-60	6
β-strand	69	1	17
β-strand	70-72	3	18
β-strand	82	1	17
β-strand	83	1	16
β-strand	95-96	2	15
α-helix	99-103	5
β-strand	114	1	14
β-strand	115-117	3	18
α-helix	122-124	3
β-strand	125	1	19
α-helix	126	1
β-strand	131	1	20
β-strand	132-133	2	21
α-helix	145-152	8
β-strand	178-179	2	21
β-strand	216	1	19
β-strand	219	1	22
β-strand	222	1	22
β-strand	226	1	20
α-helix	234-236	3
α-helix	238-242	5
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	23
α-helix	292-301	10
β-strand	306-309	4	23
α-helix	320-336	17
β-strand	340-345	6	23
α-helix	347-350	4
β-strand	352	1	24
α-helix	365-376	12
β-strand	383-389	7	23
β-strand	395	1	24
β-strand	407-410	4	23
α-helix	416-430	15
α-helix	439-448	10
α-helix	455-476	22
α-helix	488-497	10
α-helix	510-512	3
α-helix	515-517	3
α-helix	523-532	10
α-helix	539-545	7
β-strand	552-556	5	25
α-helix	563-573	11
β-strand	578-581	4	25
α-helix	584-587	4
α-helix	593-607	15
β-strand	612-615	4	25
α-helix	619-621	3
α-helix	631-644	14
β-strand	654-659	6	25
α-helix	662-664	3
β-strand	671	1	26
β-strand	674	1	26
β-strand	677-679	3	25
α-helix	686-696	11
α-helix	703-705	3
α-helix	709-715	7
α-helix	721-737	17
α-helix	747-756	10
α-helix	763-775	13

Chain C: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	27
β-strand	35-37	3	28
β-strand	51-52	2	28
α-helix	55-60	6
β-strand	69-73	5	27
β-strand	81-82	2	27
β-strand	95-98	4	28
α-helix	100-103	4
β-strand	114-117	4	27
β-strand	125	1	29
β-strand	130	1	30
β-strand	131	1	31
β-strand	132-133	2	30
α-helix	145-152	8
β-strand	163-164	2	30
β-strand	178-182	5	30
β-strand	216	1	29
β-strand	226	1	31
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	32
α-helix	292-302	11
β-strand	306-309	4	32
α-helix	312-314	3
α-helix	320-336	17
β-strand	340-345	6	32
α-helix	347-350	4
α-helix	364-374	11
β-strand	383-389	7	32
α-helix	397-400	4
β-strand	407-410	4	32
α-helix	416-430	15
α-helix	439-447	9
α-helix	455-476	22
α-helix	488-497	10
β-strand	508	1	33
α-helix	509-511	3
α-helix	523-537	15
α-helix	539-545	7
β-strand	553-556	4	33
α-helix	563-573	11
β-strand	577-581	5	33
α-helix	583-589	7
α-helix	594-607	14
β-strand	611-615	5	33
α-helix	619-621	3
α-helix	631-644	14
β-strand	654-659	6	33
α-helix	662-664	3
β-strand	677-679	3	33
α-helix	686-697	12
α-helix	703-705	3
α-helix	709-715	7
α-helix	721-736	16
α-helix	747-756	10
α-helix	763-775	13

Chain D: 34 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	34
β-strand	35-37	3	35
α-helix	55-60	6
β-strand	69	1	36
β-strand	70-73	4	34
β-strand	82	1	36
β-strand	95-97	3	35
α-helix	99-103	5
β-strand	114-117	4	34
α-helix	122-124	3
β-strand	125	1	37
α-helix	126	1
β-strand	131	1	38
β-strand	132-133	2	39
α-helix	145-151	7
β-strand	158	1	40
α-helix	170-172	3
β-strand	178-179	2	39
β-strand	214	1	40
β-strand	216	1	37
β-strand	219	1	41
β-strand	222	1	41
β-strand	226	1	38
α-helix	234-236	3
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	42
α-helix	292-302	11
β-strand	306-310	5	42
α-helix	320-336	17
β-strand	340-344	5	42
α-helix	347-350	4
β-strand	352	1	43
α-helix	364-374	11
β-strand	383-389	7	42
β-strand	395	1	43
α-helix	397-400	4
β-strand	407-410	4	42
α-helix	416-430	15
α-helix	439-448	10
α-helix	455-476	22
α-helix	488-497	10
β-strand	508	1	44
α-helix	510-512	3
α-helix	515-518	4
α-helix	523-537	15
α-helix	539-545	7
β-strand	553-556	4	44
α-helix	563-573	11
β-strand	578-581	4	44
α-helix	583-587	5
α-helix	593-607	15
β-strand	612-615	4	44
α-helix	619-621	3
α-helix	631-644	14
β-strand	654-659	6	44
α-helix	662-664	3
β-strand	671	1	45
β-strand	674	1	45
β-strand	677-679	3	44
α-helix	686-697	12
α-helix	703-705	3
α-helix	709-715	7
α-helix	721-737	17
α-helix	747-756	10
α-helix	764-775	12

Chain E: 37 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	35-37	3	46
β-strand	50	1	47
β-strand	52	1	46
α-helix	55-60	6
β-strand	69	1	48
β-strand	70	1	49
β-strand	73	1	50
β-strand	82	1	48
β-strand	83	1	47
β-strand	95-97	3	46
α-helix	100-103	4
α-helix	108-109	2
β-strand	114	1	50
β-strand	117	1	49
α-helix	122-124	3
β-strand	125	1	51
α-helix	126	1
β-strand	131	1	52
β-strand	132-133	2	53
α-helix	145-153	9
β-strand	178-179	2	53
β-strand	216	1	51
β-strand	219	1	54
β-strand	222	1	54
β-strand	226	1	52
α-helix	234-236	3
α-helix	241-243	3
α-helix	251-266	16
α-helix	268-274	7
α-helix	277-279	3
β-strand	281-285	5	55
α-helix	292-301	10
β-strand	306-310	5	55
α-helix	320-336	17
β-strand	340-345	6	55
α-helix	347-350	4
β-strand	352	1	56
α-helix	364-376	13
β-strand	383-389	7	55
β-strand	395	1	56
α-helix	397-400	4
β-strand	407-410	4	55
α-helix	416-430	15
α-helix	439-448	10
α-helix	455-476	22
α-helix	481-484	4
α-helix	488-497	10
β-strand	507-508	2	57
α-helix	510-512	3
α-helix	515-518	4
α-helix	523-529	7
α-helix	533-537	5
α-helix	539-545	7
β-strand	553-556	4	57
α-helix	563-573	11
β-strand	577-581	5	57
α-helix	583-587	5
α-helix	594-607	14
β-strand	611-615	5	57
α-helix	619-621	3
α-helix	631-644	14
β-strand	654-659	6	57
α-helix	662-664	3
β-strand	671	1	58
β-strand	674	1	58
β-strand	677-679	3	57
α-helix	686-697	12
α-helix	710-715	6
α-helix	721-737	17
α-helix	747-756	10
α-helix	763-775	13

Chain F: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	59
β-strand	35-37	3	60
α-helix	55-60	6
β-strand	69	1	61
β-strand	70-73	4	59
β-strand	82	1	61
β-strand	95-97	3	60
α-helix	102-105	4
β-strand	114-117	4	59
β-strand	125	1	62
β-strand	131	1	63
β-strand	132-133	2	64
α-helix	145-152	8
β-strand	178-179	2	64
β-strand	216	1	62
β-strand	226	1	63
α-helix	234-236	3
α-helix	238-242	5
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	65
α-helix	292-302	11
β-strand	306-309	4	65
α-helix	320-336	17
β-strand	339-345	7	65
α-helix	347-350	4
α-helix	360-364	5
α-helix	365-374	10
β-strand	382-389	8	65
β-strand	407-410	4	65
α-helix	416-430	15
α-helix	439-447	9
α-helix	455-476	22
α-helix	488-497	10
β-strand	508	1	66
α-helix	515-518	4
α-helix	523-529	7
α-helix	533-537	5
α-helix	539-545	7
β-strand	553-556	4	66
α-helix	563-573	11
β-strand	577-581	5	66
α-helix	584-587	4
α-helix	593-607	15
β-strand	611-615	5	66
α-helix	619-621	3
α-helix	631-644	14
β-strand	653-659	7	66
α-helix	662-664	3
β-strand	671	1	67
β-strand	674	1	67
β-strand	677-679	3	66
α-helix	686-697	12
α-helix	709-715	7
α-helix	721-736	16
α-helix	747-756	10
α-helix	763-775	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATPase family gene 2 protein	A, B, C, D, E, F	protein	748	Saccharomyces cerevisiae	P32794 (AlphaFold model)

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

>7WD3_1 ATPase family gene 2 protein (chains A, B, C, D, E, F)
KLPAEFITRPHPSKDHGKETCTAYIHPNVLSSLEINPGSFCTVGKIGENGILVIARAGDE
EVHPVNVITLSTTIRSVGNLILGDRLELKKAQVQPPYATKVTVGSLQGYNILECMEEKVI
QKLLDDSGVIMPGMIFQNLKTKAGDESIDVVITDASDDSLPDVSQLDLNMDDMYGGLDNL
FYLSPPFIFRKGSTHITFSKETQANRKYNLPEPLSYAAVGGLDKEIESLKSAIEIPLHQP
TLFSSFGVSPPRGILLHGPPGTGKTMLLRVVANTSNAHVLTINGPSIVSKYLGETEAALR
DIFNEARKYQPSIIFIDEIDSIAPNRANDDSGEVESRVVATLLTLMDGMGAAGKVVVIAA
TNRPNSVDPALRRPGRFDQEVEIGIPDVDARFDILTKQFSRMSSDRHVLDSEAIKYIASK
THGYVGADLTALCRESVMKTIQRGLGTDANIDKFSLKVTLKDVESAMVDIRPSAMREIFL
EMPKVYWSDIGGQEELKTKMKEMIQLPLEASETFARLGISAPKGVLLYGPPGCSKTLTAK
ALATESGINFLAVKGPEIFNKYVGESERAIREIFRKARSAAPSIIFFDEIDALSPDRDGS
STSAANHVLTSLLNEIDGVEELKGVVIVAATNRPDEIDAALLRPGRLDRHIYVGPPDVNA
RLEILKKCTKKFNTEESGVDLHELADRTEGYSGAEVVLLCQEAGLAAIMEDLDVAKVELR
HFEKAFKGIARGITPEMLSYYEEFALRS

Ligands and cofactors

ID	Name	Formula	Copies
NDT	2-(toluene-4-sulfonyl)-2H-BENZO[D][1,2,3]DIAZABORININ-1-ol	C14 H13 B N2 O3 S	12
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	12

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)
7WBB 3.6 Å, Cryo-EM structure of substrate engaged Drg1 hexamer
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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