9EMA: RUVBL1/2

RUVBL1/2 in complex with ATP and CB-6644 inhibitor. Determined by electron microscopy at 2.4 Å resolution. Released 15 May 2024.

Method: Electron microscopy
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 6
Atoms: 15,562
Mol. weight: 315.74 kDa
Ligands: MG, A1H5V, ATP
Released: 15 May 2024

Explore 9EMA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EMA contains 115 α-helices and 132 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: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
β-strand	26	1	2
α-helix	31	1
β-strand	32	1	2
α-helix	33	1
β-strand	35-36	2	3
β-strand	39-40	2	3
α-helix	43-58	16
β-strand	61	1	4
β-strand	65-69	5	5
α-helix	76-87	12
β-strand	93-97	5	5
α-helix	98-101	4
α-helix	108-118	11
β-strand	120-124	5	6
β-strand	236-239	4	6
α-helix	240-248	9
α-helix	273-288	16
β-strand	292-296	5	6
β-strand	298-302	5	5
α-helix	304-306	3
β-strand	308	1	7
α-helix	309-319	11
β-strand	326-331	6	5
β-strand	336-337	2	8
α-helix	338	1
β-strand	339	1	7
β-strand	345-346	2	8
α-helix	352-357	6
β-strand	358-362	5	5
α-helix	364-367	4
α-helix	368-381	14
β-strand	386	1	9
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	425	1	9
α-helix	427-436	10
β-strand	438	1	10
α-helix	440-449	10
β-strand	455	1	11

Chain B: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	12
β-strand	26	1	13
α-helix	31	1
β-strand	32	1	13
α-helix	33	1
β-strand	35-36	2	14
β-strand	39-40	2	14
α-helix	43-58	16
β-strand	61	1	15
β-strand	65-69	5	16
α-helix	76-87	12
β-strand	93-97	5	16
α-helix	98-101	4
α-helix	108-118	11
β-strand	120-124	5	17
β-strand	236-239	4	17
α-helix	240-248	9
α-helix	273-288	16
β-strand	292-296	5	17
β-strand	298-302	5	16
α-helix	304-306	3
β-strand	308	1	18
α-helix	309-319	11
β-strand	326-331	6	16
β-strand	336-337	2	19
α-helix	338	1
β-strand	339	1	18
β-strand	345-346	2	19
α-helix	352-356	5
β-strand	358-362	5	16
α-helix	364-367	4
α-helix	368-381	14
β-strand	386	1	20
α-helix	388-399	12
α-helix	403-408	6
α-helix	410-419	10
β-strand	425	1	20
α-helix	427-436	10
β-strand	438	1	21
α-helix	440-449	10
β-strand	455	1	22

Chain C: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	23
β-strand	26	1	24
α-helix	31	1
β-strand	32	1	24
α-helix	33	1
β-strand	35-36	2	25
β-strand	39-40	2	25
α-helix	43-57	15
β-strand	61	1	26
β-strand	65-69	5	27
α-helix	76-87	12
β-strand	93-97	5	27
α-helix	98-101	4
α-helix	108-118	11
β-strand	120-124	5	28
β-strand	236-239	4	28
α-helix	240-248	9
α-helix	273-288	16
β-strand	292-296	5	28
β-strand	298-302	5	27
α-helix	304-306	3
β-strand	308	1	29
α-helix	309-319	11
β-strand	326-331	6	27
β-strand	336-337	2	30
α-helix	338	1
β-strand	339	1	29
β-strand	345-346	2	30
α-helix	352-356	5
β-strand	358-362	5	27
α-helix	365-367	3
α-helix	368-381	14
β-strand	386	1	31
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	425	1	31
α-helix	427-436	10
β-strand	438	1	32
α-helix	440-449	10
β-strand	455	1	33

Chain D: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	4
β-strand	33	1	34
α-helix	38	1
β-strand	39	1	34
α-helix	40	1
β-strand	42-43	2	35
β-strand	46-47	2	35
α-helix	50-65	16
β-strand	68	1	12
β-strand	72-77	6	21
α-helix	83-94	12
β-strand	100-104	5	21
α-helix	105-108	4
α-helix	115-125	11
β-strand	127-132	6	36
β-strand	239-243	5	36
α-helix	244-251	8
α-helix	257-262	6
α-helix	270-286	17
β-strand	289-293	5	36
β-strand	295-299	5	21
α-helix	301-303	3
β-strand	305	1	37
α-helix	306-315	10
β-strand	323-328	6	21
β-strand	330	1	22
β-strand	332-334	3	38
α-helix	335	1
β-strand	336	1	37
β-strand	341-343	3	38
α-helix	348-352	5
β-strand	354-359	6	21
α-helix	360-362	3
α-helix	364-377	14
β-strand	382	1	39
α-helix	384-396	13
α-helix	399-415	17
β-strand	421	1	39
α-helix	423-432	10
β-strand	434	1	5
α-helix	436-444	9

Chain E: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	15
β-strand	33	1	40
α-helix	38	1
β-strand	39	1	40
α-helix	40	1
β-strand	42-43	2	41
β-strand	46-47	2	41
α-helix	50-65	16
β-strand	68	1	23
β-strand	72-77	6	32
α-helix	83-94	12
β-strand	100-104	5	32
α-helix	105-108	4
α-helix	115-125	11
β-strand	127-132	6	42
β-strand	239-243	5	42
α-helix	244-252	9
α-helix	258-262	5
α-helix	270-286	17
β-strand	289-293	5	42
β-strand	295-299	5	32
α-helix	301-303	3
β-strand	305	1	43
α-helix	306-315	10
β-strand	323-328	6	32
β-strand	330	1	33
β-strand	333-334	2	44
α-helix	335	1
β-strand	336	1	43
β-strand	341-342	2	44
α-helix	348-352	5
β-strand	354-359	6	32
α-helix	360-362	3
α-helix	364-378	15
β-strand	382	1	45
α-helix	384-396	13
α-helix	399-415	17
β-strand	421	1	45
α-helix	423-432	10
β-strand	434	1	16
α-helix	436-444	9

Chain F: 20 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	26
β-strand	33	1	46
α-helix	38	1
β-strand	39	1	46
α-helix	40	1
β-strand	42-43	2	47
β-strand	46-47	2	47
α-helix	50-65	16
β-strand	68	1	1
β-strand	72-77	6	10
α-helix	83-94	12
β-strand	100-104	5	10
α-helix	105-108	4
α-helix	115-125	11
β-strand	127-132	6	48
β-strand	239-243	5	48
α-helix	244-252	9
α-helix	256-258	3
α-helix	259-262	4
α-helix	270-286	17
β-strand	289-293	5	48
β-strand	295-299	5	10
α-helix	301-303	3
β-strand	305	1	49
α-helix	306-315	10
β-strand	323-328	6	10
β-strand	330	1	11
β-strand	332-334	3	50
α-helix	335	1
β-strand	336	1	49
β-strand	341-343	3	50
α-helix	348-351	4
β-strand	354-359	6	10
α-helix	360-362	3
α-helix	364-378	15
β-strand	382	1	51
α-helix	384-396	13
α-helix	399-415	17
β-strand	421	1	51
α-helix	423-432	10
β-strand	434	1	27
α-helix	436-445	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RuvB-like 1	A, B, C	protein	459	Homo sapiens	Q9Y265 (AlphaFold model)
RuvB-like 2	D, E, F	protein	481	Homo sapiens	Q9Y230 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9EMA_1 RuvB-like 1 (chains A, B, C)
GSHMKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIK
SKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFR
RAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIF
ESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQD
VTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPG
VLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDR
VMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLA
KINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK

Sequence of entity 2 (D, E, F), FASTA

>9EMA_2 RuvB-like 2 (chains D, E, F)
MADLNWISAGHAIADVGTMATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQA
SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTA
IAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLT
LKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQT
KFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAE
WREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQS
PHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYA
IQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDT
S

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
A1H5V	5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,…	C29 H34 Cl F N4 O5	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	6

Primary citation

Mechanism of allosteric inhibition of RUVBL1-RUVBL2 by the small-molecule CB-6644. Garcia-Martin, C., Lopez-Perrote, A., Boskovic, J. et al. Cell Rep Phys Sci (2024). DOI 10.1016/j.xcrp.2024.101982

Other PDB entries of the same protein (UniProt Q9Y265 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2C9O 2.2 Å, 3D Structure of the human RuvB-like helicase RuvBL1
8QR1 2.4 Å, Cryo-EM structure of the human Tip60 complex
6K0R 2.5 Å, Ruvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin
9C57 2.75 Å, Reconstituted P400 Subcomplex of the human TIP60 complex
2XSZ 3.0 Å, The dodecameric human RuvBL1:RuvBL2 complex with truncated domains II
9CAE 3.07 Å, Cryo-EM structure of the reconstituted RuvBL lobe of the human TIP60 complex (composite…
7ZI4 3.2 Å, Cryo-EM structure of the human INO80 complex bound to a WT nucleosome
8X15 3.2 Å, Structure of nucleosome-bound SRCAP-C in the apo state
8X19 3.2 Å, Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
8X1C 3.2 Å, Structure of nucleosome-bound SRCAP-C in the ADP-bound state
8XVT 3.2 Å, The core subcomplex of human NuA4/TIP60 complex
9SN2 3.2 Å, Cryo-EM reconstruction of the RUVBL1-RUVBL2-CCDC103 (R2C) complex

Browse structure collections

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