7YKL: Drg1 hexamer treated with AMPPNP

Cryo-EM structure of Drg1 hexamer treated with AMPPNP. Determined by electron microscopy at 5.6 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 5.6 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 33,917
Mol. weight: 512.15 kDa
Ligands: ATP
Released: 14 Dec 2022

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

Secondary structure: helices and β-sheets

7YKL contains 191 α-helices and 124 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: 31 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	7
β-strand	52	1	8
α-helix	55-61	7
β-strand	68-69	2	9
β-strand	82-83	2	9
β-strand	85	1	8
β-strand	95-97	3	7
α-helix	100-105	6
β-strand	113-114	2	7
α-helix	118-123	6
α-helix	147-151	5
α-helix	240-242	3
α-helix	244-246	3
α-helix	251-265	15
α-helix	268-272	5
α-helix	276-279	4
β-strand	281-285	5	10
α-helix	292-302	11
β-strand	307-308	2	10
α-helix	322-336	15
β-strand	341-345	5	10
α-helix	347-350	4
α-helix	364-375	12
β-strand	385-389	5	10
β-strand	407-410	4	10
α-helix	416-428	13
α-helix	431-434	4
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	488-497	10
α-helix	522-545	24
β-strand	554-556	3	11
α-helix	564-574	11
β-strand	578-581	4	11
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	11
α-helix	631-644	14
β-strand	654-659	6	11
α-helix	662-664	3
β-strand	680	1	11
α-helix	686-699	14
α-helix	702-705	4
α-helix	711-715	5
α-helix	725-739	15
α-helix	747-756	10
α-helix	763-774	12

Chain B: 33 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	12
β-strand	35-37	3	13
β-strand	52-53	2	14
α-helix	55-61	7
β-strand	68-69	2	15
β-strand	70-71	2	16
β-strand	82-83	2	15
β-strand	85-86	2	14
β-strand	95-97	3	13
α-helix	100-105	6
β-strand	114	1	12
β-strand	116-117	2	16
α-helix	121-123	3
α-helix	147-152	6
α-helix	238-242	5
α-helix	251-266	16
α-helix	268-274	7
β-strand	282-285	4	17
α-helix	292-302	11
β-strand	307-309	3	17
α-helix	313-315	3
α-helix	320-336	17
β-strand	341-345	5	17
α-helix	347-350	4
α-helix	364-375	12
β-strand	385-389	5	17
β-strand	407-410	4	17
α-helix	416-434	19
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	488-497	10
β-strand	508	1	18
α-helix	510-512	3
α-helix	522-532	11
α-helix	534-537	4
α-helix	539-545	7
β-strand	554-555	2	19
α-helix	558-560	3
α-helix	564-574	11
β-strand	578	1	19
β-strand	580	1	18
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	19
α-helix	631-644	14
β-strand	654-657	4	19
α-helix	667-670	4
β-strand	678-679	2	19
α-helix	682-684	3
α-helix	686-696	11
α-helix	711-715	5
α-helix	723-736	14
α-helix	747-756	10
α-helix	763-774	12

Chain C: 32 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	20
β-strand	35-36	2	21
α-helix	55-61	7
β-strand	69	1	22
β-strand	70-71	2	23
β-strand	82	1	22
β-strand	95-96	2	21
α-helix	100-105	6
β-strand	114	1	20
β-strand	116-117	2	23
α-helix	121-123	3
β-strand	131	1	24
α-helix	141-143	3
α-helix	147-152	6
β-strand	226	1	24
α-helix	238-242	5
α-helix	244-246	3
α-helix	251-262	12
α-helix	268-272	5
β-strand	281-285	5	25
α-helix	292-302	11
β-strand	306-308	3	25
α-helix	313-315	3
α-helix	320-335	16
β-strand	340-345	6	25
α-helix	347-350	4
α-helix	364-375	12
β-strand	385-389	5	25
β-strand	407-410	4	25
α-helix	416-418	3
α-helix	420-430	11
α-helix	439-448	10
α-helix	454-476	23
α-helix	481-484	4
α-helix	488-497	10
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	26
α-helix	566-574	9
β-strand	579-581	3	26
α-helix	593-607	15
β-strand	612-615	4	26
α-helix	631-645	15
β-strand	654-659	6	26
α-helix	662-664	3
β-strand	677-679	3	26
α-helix	686-697	12
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	748-756	9
α-helix	764-775	12

Chain D: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	27
β-strand	35-36	2	28
β-strand	52-53	2	29
α-helix	55-60	6
β-strand	68-69	2	30
β-strand	82-83	2	30
β-strand	85-86	2	29
β-strand	95-96	2	28
α-helix	100-105	6
β-strand	114	1	27
α-helix	118-123	6
α-helix	141-143	3
α-helix	147-152	6
β-strand	162	1	31
β-strand	178	1	31
α-helix	240-242	3
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	32
α-helix	292-302	11
β-strand	306-308	3	32
α-helix	321-335	15
β-strand	340-345	6	32
α-helix	347-350	4
β-strand	352	1	33
α-helix	364-374	11
β-strand	384-389	6	32
β-strand	395	1	33
β-strand	408-410	3	32
α-helix	416-434	19
α-helix	439-448	10
α-helix	454-475	22
α-helix	481-484	4
α-helix	488-498	11
β-strand	508	1	34
α-helix	510-512	3
α-helix	522-537	16
α-helix	539-545	7
β-strand	552-556	5	35
α-helix	565-574	10
β-strand	580	1	34
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	35
α-helix	631-645	15
β-strand	654-659	6	35
β-strand	671	1	36
β-strand	674	1	36
β-strand	677-679	3	35
α-helix	686-696	11
α-helix	702-705	4
α-helix	711-716	6
α-helix	721-739	19
α-helix	747-756	10
α-helix	763-775	13

Chain E: 34 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	37
β-strand	35-37	3	38
β-strand	52-53	2	39
α-helix	55-60	6
β-strand	68-69	2	40
β-strand	82-83	2	40
β-strand	85-86	2	39
β-strand	95-97	3	38
α-helix	100-106	7
β-strand	114	1	37
α-helix	121-123	3
β-strand	131	1	41
α-helix	141-143	3
α-helix	147-152	6
β-strand	226	1	41
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-274	7
β-strand	281-285	5	42
α-helix	292-301	10
β-strand	306-308	3	42
α-helix	312-315	4
α-helix	320-335	16
β-strand	340-345	6	42
α-helix	347-350	4
α-helix	364-375	12
β-strand	383-389	7	42
α-helix	392-394	3
β-strand	409-410	2	42
α-helix	416-434	19
α-helix	439-448	10
α-helix	454-476	23
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	43
α-helix	565-573	9
β-strand	579-581	3	43
α-helix	583-586	4
α-helix	593-608	16
β-strand	612-615	4	43
α-helix	631-645	15
β-strand	654-659	6	43
α-helix	662-664	3
β-strand	671	1	44
β-strand	674	1	44
β-strand	677-679	3	43
α-helix	686-696	11
α-helix	697-699	3
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: 31 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	1
β-strand	35	1	2
α-helix	38-39	2
α-helix	55-60	6
β-strand	68-69	2	3
β-strand	82-83	2	3
β-strand	95	1	2
α-helix	100-105	6
β-strand	114	1	1
α-helix	121-123	3
β-strand	130	1	4
α-helix	141-144	4
α-helix	147-152	6
β-strand	181-182	2	4
α-helix	244-246	3
α-helix	251-266	16
α-helix	268-274	7
β-strand	282-285	4	5
α-helix	292-301	10
β-strand	306-308	3	5
α-helix	312-315	4
α-helix	320-336	17
β-strand	340-345	6	5
α-helix	347-350	4
α-helix	364-375	12
β-strand	385-389	5	5
β-strand	409-410	2	5
α-helix	416-430	15
α-helix	439-448	10
α-helix	454-476	23
α-helix	491-497	7
α-helix	510-512	3
α-helix	515-517	3
α-helix	522-545	24
β-strand	553-556	4	6
α-helix	565-574	10
β-strand	578-581	4	6
α-helix	583-586	4
α-helix	593-607	15
β-strand	612-615	4	6
α-helix	632-645	14
β-strand	654-659	6	6
β-strand	677-679	3	6
α-helix	687-697	11
α-helix	702-705	4
α-helix	711-715	5
α-helix	721-739	19
α-helix	747-754	8
α-helix	763-774	12

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

>7YKL_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
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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