7YKK: Drg1 hexamer treated with ADP

Cryo-EM structure of Drg1 hexamer treated with ADP. Determined by electron microscopy at 5.9 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 5.9 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 33,897
Mol. weight: 512.15 kDa
Ligands: ATP
Released: 14 Dec 2022

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

Secondary structure: helices and β-sheets

7YKK contains 193 α-helices and 136 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	25
β-strand	35-36	2	26
α-helix	55-60	6
β-strand	68-69	2	27
β-strand	70-71	2	28
β-strand	82-83	2	27
β-strand	95-96	2	26
α-helix	100-106	7
β-strand	114	1	25
β-strand	116-117	2	28
α-helix	121-123	3
β-strand	131	1	29
α-helix	141-143	3
α-helix	147-151	5
β-strand	226	1	29
α-helix	251-266	16
α-helix	268-274	7
β-strand	282-285	4	30
α-helix	293-302	10
β-strand	307-308	2	30
α-helix	313-315	3
α-helix	320-336	17
β-strand	340-345	6	30
α-helix	347-350	4
α-helix	364-375	12
β-strand	383-389	7	30
α-helix	397-399	3
α-helix	402-405	4
β-strand	407-410	4	30
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	489-497	9
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	31
α-helix	565-569	5
α-helix	570-574	5
β-strand	578-581	4	31
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	31
α-helix	631-644	14
β-strand	654-659	6	31
α-helix	662-664	3
β-strand	677-679	3	31
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	763-775	13

Chain B: 32 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	32
β-strand	35-36	2	33
β-strand	52-53	2	34
α-helix	55-60	6
β-strand	68-69	2	35
β-strand	70-71	2	36
β-strand	82-83	2	35
β-strand	85-86	2	34
β-strand	95-96	2	33
α-helix	100-105	6
β-strand	114	1	32
β-strand	116-117	2	36
α-helix	121-123	3
β-strand	131	1	37
β-strand	134	1	38
α-helix	141-143	3
α-helix	147-152	6
β-strand	177	1	38
β-strand	226	1	37
α-helix	232-233	2
α-helix	251-266	16
α-helix	268-272	5
β-strand	281-285	5	39
α-helix	292-301	10
β-strand	306-309	4	39
α-helix	320-336	17
β-strand	339-345	7	39
α-helix	347-350	4
α-helix	364-375	12
β-strand	382-389	8	39
α-helix	402-405	4
β-strand	407-410	4	39
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-475	22
α-helix	481-484	4
α-helix	488-497	10
α-helix	510-512	3
α-helix	515-517	3
α-helix	522-545	24
β-strand	552-556	5	40
α-helix	565-574	10
β-strand	578-581	4	40
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	40
α-helix	631-645	15
β-strand	654-659	6	40
α-helix	662-664	3
β-strand	677-679	3	40
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	763-775	13

Chain C: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	41
β-strand	35	1	42
β-strand	52-53	2	43
α-helix	55-60	6
β-strand	68-69	2	44
β-strand	70-71	2	45
β-strand	82-83	2	44
β-strand	85-86	2	43
β-strand	95	1	42
α-helix	100-105	6
β-strand	114	1	41
β-strand	116-117	2	45
α-helix	121-123	3
β-strand	134	1	46
α-helix	147-152	6
β-strand	177	1	46
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-272	5
β-strand	282-285	4	47
α-helix	292-301	10
β-strand	306-309	4	47
α-helix	313-315	3
α-helix	320-336	17
β-strand	340-345	6	47
α-helix	347-350	4
β-strand	352	1	48
α-helix	364-374	11
β-strand	383-389	7	47
β-strand	395	1	48
α-helix	397-399	3
α-helix	402-405	4
β-strand	408-410	3	47
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	489-497	9
α-helix	515-517	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	49
α-helix	565-574	10
β-strand	578-581	4	49
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	49
α-helix	631-645	15
β-strand	646	1	50
β-strand	648-649	2	50
β-strand	654-659	6	49
β-strand	677-679	3	49
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	763-775	13

Chain D: 32 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	1
β-strand	52-53	2	2
α-helix	55-60	6
β-strand	68-69	2	3
β-strand	70-71	2	4
β-strand	82-83	2	3
β-strand	85-86	2	2
β-strand	95-97	3	1
α-helix	100-106	7
β-strand	113-114	2	1
β-strand	116-117	2	4
α-helix	121-123	3
α-helix	141-143	3
α-helix	147-152	6
β-strand	157	1	5
β-strand	197	1	5
α-helix	254-266	13
α-helix	268-274	7
β-strand	282-285	4	6
α-helix	293-301	9
β-strand	306-309	4	6
α-helix	313-315	3
α-helix	320-336	17
β-strand	340-345	6	6
α-helix	347-350	4
α-helix	364-375	12
β-strand	383-389	7	6
α-helix	400-404	5
β-strand	408-410	3	6
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	489-497	9
α-helix	510-512	3
α-helix	515-517	3
α-helix	522-545	24
β-strand	552-556	5	7
α-helix	565-574	10
β-strand	578-581	4	7
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	7
α-helix	631-645	15
β-strand	654-659	6	7
α-helix	662-664	3
β-strand	671	1	8
β-strand	674	1	8
β-strand	677-679	3	7
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	763-775	13

Chain E: 31 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	9
β-strand	35	1	10
α-helix	55-60	6
β-strand	68-69	2	11
β-strand	70-71	2	12
β-strand	82-83	2	11
β-strand	95	1	10
α-helix	100-105	6
β-strand	114	1	9
β-strand	116-117	2	12
α-helix	121-123	3
α-helix	147-152	6
α-helix	234-236	3
α-helix	251-262	12
α-helix	268-274	7
β-strand	281-285	5	13
α-helix	292-302	11
β-strand	306-308	3	13
α-helix	320-336	17
β-strand	340-344	5	13
α-helix	364-374	11
β-strand	383-389	7	13
β-strand	407-410	4	13
α-helix	416-434	19
α-helix	439-448	10
α-helix	454-475	22
α-helix	481-484	4
α-helix	489-497	9
α-helix	510-512	3
α-helix	515-517	3
α-helix	522-533	12
α-helix	539-545	7
β-strand	553-556	4	14
α-helix	564-574	11
β-strand	578-581	4	14
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	14
α-helix	618-621	4
α-helix	631-645	15
β-strand	654-659	6	14
α-helix	662-664	3
β-strand	677-679	3	14
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	763-775	13

Chain F: 33 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	15
β-strand	35	1	16
β-strand	52-53	2	17
α-helix	55-60	6
β-strand	68-69	2	18
β-strand	70	1	19
β-strand	82-83	2	18
β-strand	85-86	2	17
β-strand	95	1	16
α-helix	100-105	6
β-strand	114	1	15
β-strand	117	1	19
α-helix	121-123	3
β-strand	134	1	20
α-helix	141-143	3
α-helix	147-153	7
β-strand	177	1	20
α-helix	240-242	3
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-272	5
β-strand	282-285	4	21
α-helix	292-301	10
β-strand	306-309	4	21
α-helix	313-315	3
α-helix	320-336	17
β-strand	340-345	6	21
α-helix	347-350	4
α-helix	365-375	11
β-strand	383-389	7	21
α-helix	402-405	4
β-strand	408-410	3	21
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	489-497	9
β-strand	508	1	22
α-helix	510-512	3
α-helix	522-536	15
α-helix	539-545	7
β-strand	552-556	5	23
α-helix	565-574	10
β-strand	580	1	22
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	23
α-helix	634-645	12
β-strand	654-659	6	23
β-strand	671	1	24
β-strand	674	1	24
β-strand	677-679	3	23
α-helix	686-696	11
α-helix	702-705	4
α-helix	711-715	5
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	780	Saccharomyces cerevisiae	P32794 (AlphaFold model)

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

>7YKK_1 ATPase family gene 2 protein (chains A, B, C, D, E, F)
MAPKSSSSGSKKKSSASSNSADAKASKFKLPAEFITRPHPSKDHGKETCTAYIHPNVLSS
LEINPGSFCTVGKIGENGILVIARAGDEEVHPVNVITLSTTIRSVGNLILGDRLELKKAQ
VQPPYATKVTVGSLQGYNILECMEEKVIQKLLDDSGVIMPGMIFQNLKTKAGDESIDVVI
TDASDDSLPDVSQLDLNMDDMYGGLDNLFYLSPPFIFRKGSTHITFSKETQANRKYNLPE
PLSYAAVGGLDKEIESLKSAIEIPLHQPTLFSSFGVSPPRGILLHGPPGTGKTMLLRVVA
NTSNAHVLTINGPSIVSKYLGETEAALRDIFNEARKYQPSIIFIDEIDSIAPNRANDDSG
EVESRVVATLLTLMDGMGAAGKVVVIAATNRPNSVDPALRRPGRFDQEVEIGIPDVDARF
DILTKQFSRMSSDRHVLDSEAIKYIASKTHGYVGADLTALCRESVMKTIQRGLGTDANID
KFSLKVTLKDVESAMVDIRPSAMREIFLEMPKVYWSDIGGQEELKTKMKEMIQLPLEASE
TFARLGISAPKGVLLYGPPGCSKTLTAKALATESGINFLAVKGPEIFNKYVGESERAIRE
IFRKARSAAPSIIFFDEIDALSPDRDGSSTSAANHVLTSLLNEIDGVEELKGVVIVAATN
RPDEIDAALLRPGRLDRHIYVGPPDVNARLEILKKCTKKFNTEESGVDLHELADRTEGYS
GAEVVLLCQEAGLAAIMEDLDVAKVELRHFEKAFKGIARGITPEMLSYYEEFALRSGSSS

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	6

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
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
7YKT 5.9 Å, Cryo-EM structure of Drg1 hexamer in helical state treated with…

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