6FO1: RuvB-like 1

Name: PDB 6FO1: Human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain from RPAP3.
Published: 2018-04-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Human R2TP subcomplex containing 1 RUVBL1-RUVBL2 hexamer bound to 1 RBD domain from RPAP3. Determined by electron microscopy at 3.57 Å resolution. Released 4 Apr 2018.

Method: Electron microscopy
Resolution: 3.57 Å
Organism: Homo sapiens
Chains: 7
Atoms: 15,645
Mol. weight: 382.95 kDa
Ligands: ADP
Released: 4 Apr 2018

Explore 6FO1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FO1 contains 114 α-helices and 108 β-strands across 7 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, 17 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
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	76-86	11
β-strand	93-97	5	3
α-helix	98-100	3
α-helix	108-117	10
β-strand	120-123	4	4
β-strand	237-239	3	4
α-helix	240-246	7
α-helix	273-288	16
β-strand	293-296	4	4
β-strand	298-302	5	3
α-helix	304-306	3
α-helix	309-319	11
β-strand	326-331	6	3
β-strand	335-337	3	5
β-strand	345-347	3	5
α-helix	352-355	4
β-strand	358-362	5	3
α-helix	364-367	4
α-helix	368-381	14
β-strand	385-386	2	6
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	424-425	2	6
α-helix	427-436	10
β-strand	437-438	2	7
α-helix	440-454	15

Chain B: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	16-18	3
β-strand	26	1	8
β-strand	32	1	8
β-strand	35-36	2	9
β-strand	39-40	2	9
α-helix	43-57	15
β-strand	65-69	5	10
α-helix	76-86	11
β-strand	93-97	5	10
α-helix	98-100	3
α-helix	108-119	12
β-strand	120-122	3	11
β-strand	239	1	11
α-helix	242-248	7
α-helix	273-289	17
β-strand	294-296	3	11
β-strand	298-302	5	10
α-helix	304-306	3
α-helix	309-318	10
α-helix	324-325	2
β-strand	326-331	6	10
β-strand	335-337	3	12
α-helix	338	1
β-strand	345-347	3	12
α-helix	352-355	4
β-strand	358-362	5	10
α-helix	365-367	3
α-helix	368-381	14
β-strand	386	1	13
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	425	1	13
α-helix	427-436	10
β-strand	437-438	2	14
α-helix	440-451	12

Chain C: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
β-strand	26	1	15
α-helix	31	1
β-strand	32	1	15
α-helix	33	1
β-strand	35-36	2	16
β-strand	39-40	2	16
α-helix	43-57	15
β-strand	65-69	5	17
α-helix	76-87	12
β-strand	93-97	5	17
α-helix	98-100	3
α-helix	108-119	12
β-strand	120-123	4	18
β-strand	237-239	3	18
α-helix	240-245	6
α-helix	273-288	16
β-strand	294-296	3	18
β-strand	298-302	5	17
α-helix	304-306	3
α-helix	309-318	10
α-helix	324-325	2
β-strand	326-331	6	17
β-strand	335-337	3	19
β-strand	345-347	3	19
α-helix	352-355	4
β-strand	358-362	5	17
α-helix	365-367	3
α-helix	368-382	15
β-strand	386	1	20
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	425	1	20
α-helix	427-436	10
β-strand	437-438	2	21
α-helix	440-450	11

Chain D: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	22
β-strand	39	1	22
β-strand	42-43	2	23
β-strand	46-47	2	23
α-helix	50-64	15
β-strand	72-77	6	14
α-helix	83-94	12
β-strand	100-104	5	14
α-helix	105-108	4
α-helix	115-125	11
β-strand	127-130	4	24
β-strand	241-243	3	24
α-helix	244-252	9
α-helix	270-286	17
β-strand	290-293	4	24
β-strand	295-299	5	14
α-helix	301-303	3
β-strand	305	1	25
α-helix	306-315	10
β-strand	323-328	6	14
β-strand	332-334	3	26
α-helix	335	1
β-strand	336	1	25
β-strand	341-343	3	26
α-helix	348-351	4
β-strand	354-359	6	14
α-helix	360-362	3
α-helix	364-377	14
β-strand	382	1	27
α-helix	384-396	13
α-helix	399-413	15
β-strand	421	1	27
α-helix	423-432	10
β-strand	434	1	3
α-helix	436-451	16

Chain E: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	28
β-strand	33	1	29
β-strand	39	1	29
β-strand	45	1	28
α-helix	50-64	15
β-strand	72-76	5	21
α-helix	83-94	12
β-strand	100-104	5	21
α-helix	115-125	11
β-strand	127-130	4	30
β-strand	241-243	3	30
α-helix	244-247	4
α-helix	270-286	17
β-strand	290-293	4	30
β-strand	295-299	5	21
α-helix	301-303	3
α-helix	306-313	8
β-strand	323-328	6	21
β-strand	332-334	3	31
β-strand	336	1	32
β-strand	338	1	32
β-strand	341-343	3	31
α-helix	348-351	4
β-strand	354-358	5	21
α-helix	360-362	3
α-helix	364-377	14
β-strand	382	1	33
α-helix	384-396	13
α-helix	399-413	15
α-helix	414-416	3
β-strand	421	1	33
α-helix	423-432	10
β-strand	434	1	10
α-helix	436-452	17

Chain F: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	34
β-strand	39	1	34
β-strand	42-43	2	35
β-strand	46-47	2	35
α-helix	50-64	15
β-strand	72-77	6	7
α-helix	83-94	12
β-strand	100-104	5	7
α-helix	115-125	11
β-strand	127-130	4	36
β-strand	241-243	3	36
α-helix	244-252	9
α-helix	270-286	17
β-strand	291-293	3	36
β-strand	295-299	5	7
α-helix	301-303	3
α-helix	306-316	11
β-strand	323-328	6	7
β-strand	332-334	3	37
β-strand	336	1	38
β-strand	338	1	38
β-strand	341-343	3	37
α-helix	348-351	4
β-strand	354-359	6	7
α-helix	360-362	3
α-helix	364-377	14
β-strand	382	1	39
α-helix	384-396	13
α-helix	399-416	18
β-strand	421	1	39
α-helix	423-432	10
β-strand	433-434	2	17
α-helix	435	1
α-helix	436-450	15

Chain G: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	550-559	10
α-helix	563-565	3
α-helix	567-572	6
α-helix	577-582	6
α-helix	588-602	15
α-helix	608-619	12
α-helix	624-630	7
α-helix	635-648	14
α-helix	654-661	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RuvB-like 1	A, B, C	protein	456	Homo sapiens	Q9Y265 (AlphaFold model)
RuvB-like 2	D, E, F	protein	463	Homo sapiens	Q9Y230 (AlphaFold model)
RNA polymerase II-associated protein 3	G	protein	665	Homo sapiens	Q9H6T3 (AlphaFold model)

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

>6FO1_1 RuvB-like 1 (chains A, B, C)
MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKK
MAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAI
GLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESL
QKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL
HDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLF
VDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMI
IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKIN
GKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK

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

>6FO1_2 RuvB-like 2 (chains D, E, F)
MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVL
EMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALT
QAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIE
SLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVH
TVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDE
VHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTT
PYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTE
VQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS

Sequence of entity 3 (G), FASTA

>6FO1_3 RNA polymerase II-associated protein 3 (chains G)
MTSANKAIELQLQVKQNAEELQDFMRDLENWEKDIKQKDMELRRQNGVPEENLPPIRNGN
FRKKKKGKAKESSKKTREENTKNRIKSYDYEAWAKLDVDRILDELDKDDSTHESLSQESE
SEEDGIHVDSQKALVLKEKGNKYFKQGKYDEAIDCYTKGMDADPYNPVLPTNRASAYFRL
KKFAVAESDCNLAVALNRSYTKAYSRRGAARFALQKLEEAKKDYERVLELEPNNFEATNE
LRKISQALASKENSYPKEADIVIKSTEGERKQIEAQQNKQQAISEKDRGNGFFKEGKYER
AIECYTRGIAADGANALLPANRAMAYLKIQKYEEAEKDCTQAILLDGSYSKAFARRGTAR
TFLGKLNEAKQDFETVLLLEPGNKQAVTELSKIKKELIEKGHWDDVFLDSTQRQNVVKPI
DNPPHPGSTKPLKKVIIEETGNLIQTIDVPDSTTAAAPENNPINLANVIAATGTTSKKNS
SQDDLFPTSDTPRAKVLKIEEVSDTSSLQPQASLKQDVCQSYSEKMPIEIEQKPAQFATT
VLPPIPANSFQLESDFRQLKSSPDMLYQYLKQIEPSLYPKLFQKNLDPDVFNQIVKILHD
FYIEKEKPLLIFEILQRLSELKRFDMAVMFMSETEKKIARALFNHIDKSGLKDSSVEELK
KRYGG

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	6

Primary citation

RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone complex. Martino, F., Pal, M., Munoz-Hernandez, H. et al. Nat Commun (2018) 9:1501-1501. DOI 10.1038/s41467-018-03942-1 · 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
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

Browse structure collections

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