8U5Y: Human RADX trimer

human RADX trimer bound to ssDNA. Determined by electron microscopy at 3.01 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 3.01 Å
Organism: Homo sapiens
Chains: 4
Atoms: 17,339
Mol. weight: 300.6 kDa
Released: 11 Oct 2023

Explore 8U5Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U5Y contains 85 α-helices and 146 β-strands across 3 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: 30 helices, 44 β-strands

Element	Residues	Length	Sheet
α-helix	45-55	11
α-helix	61-63	3
β-strand	69-72	4	9
β-strand	73	1	10
β-strand	74-78	5	9
α-helix	89-91	3
β-strand	93-100	8	9
β-strand	105-110	6	9
α-helix	112-114	3
α-helix	116-119	4
β-strand	127	1	11
β-strand	128-129	2	9
β-strand	131-137	7	9
β-strand	147-153	7	9
β-strand	158	1	11
α-helix	166-167	2
β-strand	168	1	9
β-strand	189	1	9
β-strand	218	1	12
α-helix	221-226	6
β-strand	236	1	12
β-strand	237-244	8	13
β-strand	248-249	2	14
β-strand	261-262	2	14
β-strand	263-269	7	13
β-strand	272-278	7	13
α-helix	283-286	4
β-strand	295-298	4	13
β-strand	304-305	2	13
α-helix	306-307	2
α-helix	312-315	4
β-strand	322-327	6	13
β-strand	330	1	13
β-strand	339-342	4	13
α-helix	344-346	3
α-helix	349-351	3
α-helix	353-356	4
β-strand	360-361	2	15
α-helix	363-368	6
β-strand	374-391	18	15
β-strand	399-408	10	15
β-strand	416-421	6	15
α-helix	426-429	4
β-strand	437-448	12	15
β-strand	455-460	6	15
β-strand	466-467	2	15
α-helix	474-476	3
α-helix	480-494	15
α-helix	499-501	3
β-strand	502-503	2	15
α-helix	516-521	6
α-helix	525-527	3
α-helix	535-541	7
β-strand	546	1	15
β-strand	547-562	16	16
β-strand	679-681	3	16
α-helix	683-688	6
β-strand	694-697	4	16
α-helix	703-705	3
β-strand	708-709	2	15
α-helix	715-722	8
α-helix	724-726	3
β-strand	728	1	10
α-helix	736-738	3
α-helix	739-741	3
α-helix	743	1
β-strand	744	1	15
β-strand	750-757	8	16
β-strand	762-768	7	16
α-helix	774-779	6
β-strand	787	1	16
α-helix	810-821	12
β-strand	827-835	9	16
β-strand	841-849	9	16

Chain B: 28 helices, 45 β-strands

Element	Residues	Length	Sheet
α-helix	45-52	8
β-strand	57	1	1
β-strand	61	1	2
β-strand	69-72	4	2
β-strand	73	1	3
β-strand	74-78	5	2
β-strand	93-100	8	2
β-strand	105-110	6	2
α-helix	112-114	3
α-helix	115-119	5
β-strand	127	1	4
β-strand	128-129	2	2
β-strand	131-135	5	2
β-strand	136	1	1
β-strand	149-153	5	2
β-strand	158	1	4
β-strand	168	1	2
α-helix	171-173	3
β-strand	189	1	2
α-helix	221-226	6
β-strand	237-244	8	5
α-helix	245-247	3
β-strand	248-249	2	6
β-strand	261-262	2	6
β-strand	263-269	7	5
β-strand	272-278	7	5
α-helix	283-286	4
β-strand	295-298	4	5
β-strand	302-304	3	5
α-helix	311-315	5
α-helix	321	1
β-strand	322-330	9	5
β-strand	341-342	2	5
α-helix	344-346	3
α-helix	349-351	3
α-helix	353-355	3
β-strand	360-361	2	7
α-helix	363-366	4
α-helix	369-370	2
β-strand	375-384	10	7
β-strand	388-391	4	7
β-strand	399-408	10	7
β-strand	416-421	6	7
α-helix	426-429	4
β-strand	437-448	12	7
β-strand	455-460	6	7
β-strand	466-469	4	7
α-helix	480-494	15
β-strand	502-503	2	7
α-helix	516-520	5
α-helix	525-528	4
β-strand	530	1	8
α-helix	535-541	7
β-strand	546	1	7
β-strand	547-561	15	8
β-strand	679-681	3	8
α-helix	683-688	6
β-strand	694-695	2	8
α-helix	703-705	3
β-strand	708-709	2	7
α-helix	712-714	3
α-helix	715-720	6
α-helix	724-726	3
β-strand	728	1	3
α-helix	731-732	2
β-strand	744	1	7
α-helix	749-750	2
β-strand	751-757	7	8
β-strand	762-768	7	8
α-helix	774-779	6
α-helix	808-821	14
β-strand	827-835	9	8
β-strand	841-849	9	8

Chain C: 27 helices, 57 β-strands

Element	Residues	Length	Sheet
α-helix	45-53	9
β-strand	57	1	17
β-strand	61	1	17
β-strand	69-72	4	17
β-strand	73	1	18
β-strand	74-78	5	17
β-strand	93-100	8	17
β-strand	105	1	17
β-strand	109-110	2	17
α-helix	112-114	3
α-helix	116-119	4
β-strand	127	1	19
β-strand	128-129	2	17
β-strand	133-137	5	17
β-strand	147-152	6	17
β-strand	158	1	19
α-helix	166-167	2
β-strand	168	1	17
α-helix	171-174	4
α-helix	188	1
β-strand	189	1	17
α-helix	190	1
β-strand	218	1	20
α-helix	221-226	6
β-strand	236	1	20
β-strand	239-244	6	21
α-helix	245-247	3
β-strand	248-249	2	22
β-strand	261-262	2	22
β-strand	263-268	6	21
β-strand	272-273	2	23
β-strand	274-278	5	21
α-helix	280-282	3
α-helix	283-286	4
β-strand	295-298	4	21
β-strand	302-305	4	21
α-helix	306-307	2
α-helix	312-315	4
β-strand	321-322	2	23
β-strand	326-330	5	21
β-strand	339-342	4	21
β-strand	360	1	24
α-helix	363-366	4
β-strand	375-384	10	25
β-strand	388	1	25
β-strand	389	1	26
β-strand	391	1	27
β-strand	399	1	27
β-strand	402-408	7	25
β-strand	418-421	4	25
α-helix	426-429	4
β-strand	437-446	10	25
β-strand	457-460	4	25
β-strand	466-468	3	25
α-helix	474-476	3
α-helix	480-494	15
β-strand	502-503	2	25
α-helix	516-522	7
β-strand	529	1	28
α-helix	535-541	7
β-strand	546	1	26
β-strand	547-562	16	28
β-strand	679-681	3	28
β-strand	694-697	4	28
α-helix	703-705	3
β-strand	708-709	2	25
β-strand	711	1	29
β-strand	714	1	29
α-helix	716-721	6
α-helix	724-726	3
β-strand	728	1	18
α-helix	739-741	3
α-helix	743	1
β-strand	744	1	25
β-strand	750-751	2	28
β-strand	754-757	4	28
β-strand	762-765	4	28
β-strand	767-768	2	28
α-helix	774-779	6
β-strand	787	1	28
α-helix	806-807	2
α-helix	808-821	14
β-strand	827-837	11	28
β-strand	840-849	10	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RPA-related protein RADX	A, B, C	protein	855	Homo sapiens	Q6NSI4 (AlphaFold model)
DNA (25-mer)	D	DNA	25	Homo sapiens

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

>8U5Y_1 RPA-related protein RADX (chains A, B, C)
MSGESGQPEAGPSHAGLDWPNPERNRAGVPGGVIRRAGSQGPRSWIQKVLEQIMDSPRQC
VTPSEVVPVTVLAVQRYLLEDEPRDTVPKPPLYCYDVTISDGVYQEKCYLDPSLNSLVYQ
NILKVGIQMRISRVSCLYNEKRIGQGILCIDNVHCGETSDSISLETPFRNRAHQEKPERP
LRGGKSHYLALWNNEDPYGDIWLTDKQPEEHNFSDTKIISLSHLEMTWTNRRNFPALLVR
ILHKSKLRYYGKPDKKMIEPYQTFLEVADSSGTVSVIMWNALCPEWYKSLRVGLVLLLQD
YSVKKSYPFRIQPVPVDPQIKLISTMEICLNLRDPPTNIIIIPEKQVKPEWRLPKLNHRF
TTRSELDDMPENCICDVIGLLVFVGRVQRSKKKENREDFWSYRWIHIADGTSEQPFIVEL
FSTSQPEIFENIYPMAYFVCTQLKVVRNDNQVPKLLYLTTTNESGVFITGHRGQPYTYDA
KVKNFIQWIRTKSDSGEQKNMVIGGYYPYPPVPETFSKYSSSIKVESLLTAISEVRKEIE
DLQYREQKRIAIQGIITAIKYIPHSSATESASASETLRNANRPSTSQAARVEIQERNGKR
HQDDEPVNSQYFQTTSTNLSLSNKIRILQGPHANPVAVPQPGASVQTKGIKPGMPSIFNR
RANINANLQGKARKTISDRWESQLWREKKFGLIDHLHYSRVYPESIPRKFMFEHRKFLSD
QYNSQPAKYVPPEGRPPKLDDFKSARSLGHFEVTILGLNHEIAIDVAFLPMYCPEDIRTS
QIDTLLTSMNYSCAYPQDTTGNDRLPGPRAVAGDIIKAATELDRVHIVGILDICNLGNNK
VEVYLHKIYSPENTS

Sequence of entity 2 (D), FASTA

>8U5Y_2 DNA (25-MER) (chains D)
TTTTTTTTTTTTTTTTTTTTTTTTT

Primary citation

Structure of RADX and mechanism for regulation of RAD51 nucleofilaments. Balakrishnan, S., Adolph, M., Tsai, M.S. et al. bioRxiv (2023). DOI 10.1101/2023.09.19.558089 · PubMed

Other PDB entries of the same protein (UniProt Q6NSI4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SRK 2.5 Å, Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide YPPVPETF
7STG 2.7 Å, Consequences of HLA single chain trimer mutations on peptide presentation and binding…
8U61 4.0 Å, Human RADX tetramer bound to ssDNA

Browse structure collections

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