6K0R: Ruvbl1-Ruvbl2 with truncated domain II

Ruvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin. Determined by X-ray diffraction at 2.5 Å resolution. Released 6 May 2020.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 12
Atoms: 27,180
Mol. weight: 479.67 kDa
Ligands: CU0, 3AT, MG, CUU
Released: 6 May 2020

Explore 6K0R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K0R contains 207 α-helices and 227 β-strands across 12 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: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
β-strand	26	1	1
α-helix	31	1
β-strand	32	1	1
α-helix	33	1
β-strand	35-36	2	2
β-strand	39-40	2	2
α-helix	43-57	15
β-strand	65-69	5	3
α-helix	76-87	12
β-strand	93-97	5	3
α-helix	98-101	4
α-helix	108-118	11
β-strand	120-123	4	4
β-strand	237-239	3	4
α-helix	240-246	7
α-helix	273-289	17
β-strand	294-296	3	4
β-strand	298-302	5	3
α-helix	304-306	3
β-strand	308	1	5
α-helix	309-319	11
α-helix	324-325	2
β-strand	326-331	6	3
β-strand	335-337	3	6
α-helix	338	1
β-strand	339	1	5
β-strand	345-347	3	6
α-helix	352-355	4
β-strand	358-362	5	3
α-helix	365-367	3
α-helix	368-382	15
β-strand	386	1	7
α-helix	388-400	13
α-helix	403-419	17
β-strand	425	1	7
α-helix	427-436	10
β-strand	438	1	8
α-helix	440-450	11

Chain B: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	26	1	9
α-helix	31	1
β-strand	32	1	9
α-helix	33	1
β-strand	35-36	2	10
β-strand	39-40	2	10
α-helix	43-58	16
β-strand	65-69	5	11
α-helix	76-87	12
β-strand	93-97	5	11
α-helix	108-118	11
β-strand	120-123	4	12
β-strand	238-239	2	12
α-helix	240-246	7
α-helix	273-289	17
β-strand	293-296	4	12
β-strand	298-302	5	11
α-helix	304-306	3
β-strand	308	1	13
α-helix	309-319	11
β-strand	326-331	6	11
β-strand	335-337	3	14
α-helix	338	1
β-strand	339	1	13
β-strand	345-347	3	14
α-helix	352-355	4
β-strand	358-362	5	11
α-helix	365-367	3
α-helix	368-382	15
β-strand	386	1	15
α-helix	388-400	13
α-helix	403-407	5
α-helix	410-420	11
β-strand	425	1	15
α-helix	427-436	10
β-strand	437-438	2	16
α-helix	440-450	11

Chain C: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	26	1	17
β-strand	32	1	17
β-strand	35-36	2	18
β-strand	39-40	2	18
α-helix	43-57	15
β-strand	65-69	5	19
α-helix	76-87	12
β-strand	93-97	5	19
α-helix	98-101	4
α-helix	108-117	10
β-strand	120-123	4	20
β-strand	237-239	3	20
α-helix	241-248	8
α-helix	273-288	16
β-strand	293-296	4	20
β-strand	298-302	5	19
α-helix	304-306	3
β-strand	308	1	21
α-helix	309-319	11
β-strand	326-331	6	19
β-strand	335-337	3	22
α-helix	338	1
β-strand	339	1	21
β-strand	345-347	3	22
α-helix	352-355	4
β-strand	358-362	5	19
α-helix	365-367	3
α-helix	368-382	15
β-strand	385-386	2	23
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	424-425	2	23
α-helix	427-436	10
β-strand	438	1	24
α-helix	440-449	10

Chain D: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	25
β-strand	33	1	26
β-strand	39	1	26
β-strand	42-43	2	27
β-strand	45	1	25
β-strand	46-47	2	27
α-helix	50-64	15
β-strand	72-76	5	16
α-helix	83-92	10
β-strand	100-104	5	16
α-helix	105-107	3
α-helix	117-125	9
β-strand	127-130	4	28
β-strand	241-243	3	28
α-helix	244-250	7
α-helix	270-286	17
β-strand	290-293	4	28
β-strand	295-299	5	16
β-strand	305	1	29
α-helix	306-316	11
β-strand	323-328	6	16
β-strand	332-334	3	30
β-strand	336	1	29
β-strand	341-343	3	30
α-helix	348-351	4
β-strand	354-358	5	16
α-helix	360-362	3
α-helix	364-375	12
β-strand	382	1	31
α-helix	384-396	13
α-helix	399-415	17
β-strand	421	1	31
α-helix	424-432	9
β-strand	434	1	19
α-helix	435	1
α-helix	436-449	14

Chain E: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	32
β-strand	39	1	32
α-helix	50-64	15
β-strand	72-77	6	24
α-helix	83-93	11
β-strand	100-104	5	24
α-helix	105-108	4
α-helix	115-125	11
β-strand	127-130	4	33
β-strand	241-243	3	33
α-helix	244-250	7
α-helix	270-286	17
β-strand	290-293	4	33
β-strand	295-299	5	24
α-helix	301-303	3
β-strand	305	1	34
α-helix	306-316	11
β-strand	323-328	6	24
β-strand	332-334	3	35
α-helix	335	1
β-strand	336	1	34
β-strand	341-343	3	35
α-helix	348-351	4
β-strand	354-359	6	24
α-helix	360-363	4
α-helix	364-377	14
β-strand	382	1	36
α-helix	384-396	13
α-helix	399-415	17
β-strand	421	1	36
α-helix	423-432	10
β-strand	434	1	3
α-helix	436-447	12

Chain F: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	37
β-strand	39	1	37
β-strand	43	1	38
β-strand	46	1	38
α-helix	50-65	16
β-strand	72-77	6	8
α-helix	83-94	12
β-strand	100-104	5	8
α-helix	105-108	4
α-helix	115-126	12
β-strand	127-130	4	39
β-strand	241-243	3	39
α-helix	244-253	10
α-helix	270-286	17
β-strand	290-293	4	39
β-strand	295-299	5	8
α-helix	301-303	3
β-strand	305	1	40
α-helix	306-315	10
β-strand	323-328	6	8
β-strand	332-334	3	41
α-helix	335	1
β-strand	336	1	40
β-strand	341-343	3	41
α-helix	348-351	4
β-strand	354-359	6	8
α-helix	360-362	3
α-helix	364-377	14
β-strand	382	1	42
α-helix	384-396	13
α-helix	399-413	15
β-strand	421	1	42
α-helix	423-432	10
β-strand	434	1	11
α-helix	436-449	14

Chain G: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
β-strand	26	1	43
α-helix	31	1
β-strand	32	1	43
α-helix	33	1
β-strand	35-36	2	44
β-strand	39-40	2	44
α-helix	43-57	15
β-strand	66-69	4	45
α-helix	76-86	11
β-strand	93-97	5	45
α-helix	99-101	3
α-helix	108-118	11
β-strand	120-123	4	46
β-strand	237-239	3	46
α-helix	242-247	6
α-helix	273-289	17
β-strand	294-296	3	46
β-strand	298-302	5	45
α-helix	304-306	3
β-strand	308	1	47
α-helix	309-319	11
β-strand	326-331	6	45
β-strand	335-337	3	48
α-helix	338	1
β-strand	339	1	47
β-strand	345-347	3	48
β-strand	359-362	4	45
α-helix	365-367	3
α-helix	368-382	15
β-strand	386	1	49
α-helix	388-400	13
α-helix	403-420	18
β-strand	425	1	49
α-helix	427-436	10
β-strand	437-438	2	50
α-helix	440-450	11

Chain H: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	51
β-strand	26	1	52
β-strand	32	1	52
β-strand	35-36	2	53
β-strand	38	1	51
β-strand	39-40	2	53
α-helix	43-56	14
β-strand	65-69	5	54
α-helix	76-87	12
β-strand	93-97	5	54
α-helix	98-101	4
α-helix	108-118	11
β-strand	120-123	4	55
β-strand	237-239	3	55
α-helix	240-246	7
α-helix	273-288	16
β-strand	293-296	4	55
β-strand	298-302	5	54
α-helix	304-306	3
β-strand	308	1	56
α-helix	311-317	7
β-strand	326-331	6	54
β-strand	335-337	3	57
α-helix	338	1
β-strand	339	1	56
β-strand	345-347	3	57
α-helix	352-355	4
β-strand	358-362	5	54
α-helix	365-367	3
α-helix	368-382	15
β-strand	386	1	58
α-helix	388-398	11
α-helix	403-408	6
α-helix	410-420	11
β-strand	425	1	58
α-helix	427-436	10
α-helix	440-450	11

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RuvB-like 1,RuvB-like 1	A, B, C, G, H, I	protein	355	Homo sapiens	Q9Y265 (AlphaFold model)
RuvB-like 2,RuvB-like 2	D, E, F, J, K, L	protein	366	Homo sapiens	Q9Y230 (AlphaFold model)

Sequence of entity 1 (A, B, C, G, H, I), FASTA

>6K0R_1 RuvB-like 1,RuvB-like 1 (chains A, B, C, G, H, I)
GPSKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKS
KKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRR
AIGLRIKEGPPGIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINK
VVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGT
EDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKT
TLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK

Sequence of entity 2 (D, E, F, J, K, L), FASTA

>6K0R_2 RuvB-like 2,RuvB-like 2 (chains D, E, F, J, K, L)
GGSMATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAG
VVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTE
ALTQAFRRSIGVRIKEGPPGVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQIN
AKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRG
TSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLET
SLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKG
ETMDTS

Ligands and cofactors

ID	Name	Formula	Copies
CU0	[(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen…	C5 H12 O10 P2	1
3AT	3'-deoxyadenosine-5'-triphosphate	C10 H16 N5 O12 P3	2
MG	Magnesium ion	Mg	2
CUU	[(2~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl…	C10 H15 N5 O9 P2	8
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals. Ju, D., Zhang, W., Yan, J. et al. Sci Transl Med (2020) 12. DOI 10.1126/scitranslmed.aba0769 · PubMed

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
9EMA 2.4 Å, RUVBL1/2 in complex with ATP and CB-6644 inhibitor
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

About this viewer

MolViewer shows 6K0R directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.