9Q9H: Human Mre11-Rad50 complex

Cryo-EM structure of human Mre11-Rad50 complex bound to DNA. Determined by electron microscopy at 3.11 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 3.11 Å
Organism: Homo sapiens
Chains: 6
Atoms: 16,786
Mol. weight: 508.4 kDa
Ligands: MN, BEF, ADP, MG
Released: 1 Oct 2025

Explore 9Q9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q9H contains 74 α-helices and 101 β-strands across 4 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: 18 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	3-10	8	2
β-strand	12	1	3
β-strand	23-26	4	2
β-strand	31	1	4
β-strand	34-35	2	5
α-helix	42-53	12
α-helix	56-58	3
α-helix	63-66	4
β-strand	67	1	3
α-helix	68-69	2
α-helix	70-73	4
β-strand	79-87	9	2
β-strand	93-101	9	2
β-strand	105	1	6
β-strand	108	1	6
β-strand	112-117	6	2
β-strand	120	1	2
β-strand	127	1	2
β-strand	130-131	2	2
α-helix	133-144	12
α-helix	148-150	3
α-helix	151-155	5
β-strand	156	1	7
α-helix	164-166	3
α-helix	169-173	5
α-helix	183-241	59
α-helix	1070-1092	23
α-helix	1095-1098	4
α-helix	1100-1154	55
β-strand	1163-1166	4	8
β-strand	1185-1190	6	8
β-strand	1193-1196	4	8
α-helix	1203-1220	18
β-strand	1225	1	1
β-strand	1227-1228	2	4
β-strand	1229	1	7
β-strand	1231	1	9
α-helix	1239-1256	18
β-strand	1263-1264	2	4
β-strand	1267	1	9
α-helix	1271-1279	9
β-strand	1285-1290	6	5
β-strand	1298-1303	6	5
α-helix	1307-1309	3

Chain B: 19 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	10
β-strand	12	1	11
α-helix	19-21	3
β-strand	23-26	4	10
β-strand	33-35	3	12
α-helix	43-54	12
α-helix	57-58	2
α-helix	63-66	4
β-strand	67	1	11
α-helix	68-69	2
α-helix	70-73	4
β-strand	77-87	11	10
β-strand	93-94	2	10
β-strand	97-105	9	10
β-strand	108-117	10	10
β-strand	118	1	13
β-strand	120	1	10
β-strand	121-122	2	14
β-strand	125-126	2	14
β-strand	129	1	13
α-helix	133-144	12
α-helix	148-150	3
α-helix	151-155	5
α-helix	164-166	3
α-helix	169-179	11
α-helix	183-244	62
α-helix	1072-1092	21
α-helix	1100-1154	55
β-strand	1162-1168	7	15
β-strand	1183-1190	8	15
β-strand	1193-1196	4	15
α-helix	1197-1200	4
α-helix	1203-1220	18
β-strand	1228-1231	4	12
α-helix	1239-1256	18
β-strand	1264-1267	4	12
α-helix	1273-1279	7
β-strand	1285-1291	7	12
β-strand	1297-1303	7	12
α-helix	1304-1306	3

Chain D: 18 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	15-18	4	16
α-helix	36-50	15
β-strand	54-57	4	16
α-helix	69-82	14
β-strand	84	1	17
α-helix	87-89	3
β-strand	92-93	2	18
α-helix	97-100	4
α-helix	110-112	3
β-strand	116	1	19
β-strand	118	1	17
β-strand	122-124	3	16
β-strand	133	1	20
β-strand	138	1	20
α-helix	140-147	8
β-strand	151-152	2	16
β-strand	162-164	3	21
β-strand	167-171	5	18
β-strand	174-181	8	18
α-helix	186-194	9
β-strand	198-200	3	21
α-helix	207-209	3
β-strand	211-218	8	18
α-helix	231-233	3
β-strand	240-244	5	18
β-strand	250-254	5	22
β-strand	263-265	3	22
α-helix	281-282	2
β-strand	283-284	2	23
β-strand	287-290	4	16
β-strand	293-296	4	16
β-strand	299-300	2	23
β-strand	307-313	7	24
α-helix	314-316	3
α-helix	328-350	23
β-strand	362-368	7	24
α-helix	383-385	3
β-strand	396-399	4	24
α-helix	429-443	15
α-helix	450	1
α-helix	455-463	9
α-helix	469-488	20
α-helix	494-508	15

Chain E: 19 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	25
β-strand	23	1	26
α-helix	36-49	14
β-strand	54-57	4	25
β-strand	62	1	26
α-helix	69-78	10
α-helix	79-83	5
β-strand	84	1	27
α-helix	87-89	3
β-strand	92-93	2	28
α-helix	97-100	4
α-helix	110-112	3
β-strand	116	1	19
β-strand	118	1	27
β-strand	122-124	3	25
β-strand	133	1	29
β-strand	138	1	29
α-helix	140-147	8
β-strand	151-152	2	25
β-strand	162-164	3	30
β-strand	168-171	4	28
β-strand	174-177	4	28
β-strand	178-181	4	31
α-helix	186-194	9
β-strand	198-200	3	30
α-helix	201-203	3
β-strand	213-217	5	31
β-strand	240-244	5	31
β-strand	250-254	5	31
β-strand	262-265	4	31
α-helix	276-279	4
α-helix	281-282	2
β-strand	283-284	2	32
β-strand	287-290	4	25
β-strand	293-296	4	25
β-strand	299-300	2	32
α-helix	305-306	2
β-strand	307-312	6	33
α-helix	328-351	24
β-strand	362-367	6	33
α-helix	378-381	4
β-strand	396-398	3	33
α-helix	429-443	15
α-helix	450	1
α-helix	453-463	11
α-helix	471-487	17
α-helix	495-506	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair protein RAD50	A, B	protein	1312	Homo sapiens	Q92878 (AlphaFold model)
Double-strand break repair protein MRE11	D, E	protein	738	Homo sapiens	P49959 (AlphaFold model)
DNA (50-mer)	P	DNA	50	Homo sapiens
DNA (50-mer)	T	DNA	50	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>9Q9H_1 DNA repair protein RAD50 (chains A, B)
MSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPG
TKGNTFVHDPKVAQETDVRAQIRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITR
TKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKALKQKFDEIF
SATRYIKALETLRQVRQTQGQKVKEYQMELKYLKQYKEKACEIRDQITSKEAQLTSSKEI
VKSYENELDPLKNRLKEIEHNLSKIMKLDNEIKALDSRKKQMEKDNSELEEKMEKVFQGT
DEQLNDLYHNHQRTVREKERKLVDCHRELEKLNKESRLLNQEKSELLVEQGRLQLQADRH
QEHIRARDSLIQSLATQLELDGFERGPFSERQIKNFHKLVRERQEGEAKTANQLMNDFAE
KETLKQKQIDEIRDKKTGLGRIIELKSEILSKKQNELKNVKYELQQLEGSSDRILELDQE
LIKAERELSKAEKNSNVETLKMEVISLQNEKADLDRTLRKLDQEMEQLNHHTTTRTQMEM
LTKDKADKDEQIRKIKSRHSDELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKLNKE
LASSEQNKNHINNELKRKEEQLSSYEDKLFDVCGSQDFESDLDRLKEEIEKSSKQRAMLA
GATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEVISDLQSKLRLAPDKLKSTESELK
KKEKRRDEMLGLVPMRQSIIDLKEKEIPELRNKLQNVNRDIQRLKNDIEEQETLLGTIMP
EEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGIDLDRTVQQVNQEKQEKQHKLD
TVSSKIELNRKLIQDQQEQIQHLKSTTNELKSEKLQISTNLQRRQQLEEQTVELSTEVQS
LYREIKDAKEQVSPLETTLEKFQQEKEELINKKNTSNKIAQDKLNDIKEKVKNIHGYMKD
IENYIQDGKDDYKKQKETELNKVIAQLSECEKHKEKINEDMRLMRQDIDTQKIQERWLQD
NLTLRKRNEELKEVEEERKQHLKEMGQMQVLQMKSEHQKLEENIDNIKRNHNLALGRQKG
YEEEIIHFKKELREPQFRDAEEKYREMMIVMRTTELVNKDLDIYYKTLDQAIMKFHSMKM
EEINKIIRDLWRSTYRGQDIEYIEIRSDADENVSASDKRRNYNYRVVMLKGDTALDMRGR
CSAGQKVLASLIIRLALAETFCLNCGIIALDEPTTNLDRENIESLAHALVEIIKSRSQQR
NFQLLVITHDEDFVELLGRSEYVEKFYRIKKNIDQCSEIVKCSVSSLGFNVH

Sequence of entity 2 (D, E), FASTA

>9Q9H_2 Double-strand break repair protein MRE11 (chains D, E)
MSTADALDDENTFKILVATDIHLGFMEKDAVRGNDTFVTLDEILRLAQENEVDFILLGGD
LFHENKPSRKTLHTCLELLRKYCMGDRPVQFEILSDQSVNFGFSKFPWVNYQDGNLNISI
PVFSIHGNHDDPTGADALCALDILSCAGFVNHFGRSMSVEKIDISPVLLQKGSTKIALYG
LGSIPDERLYRMFVNKKVTMLRPKEDENSWFNLFVIHQNRSKHGSTNFIPEQFLDDFIDL
VIWGHEHECKIAPTKNEQQLFYISQPGSSVVTSLSPGEAVKKHVGLLRIKGRKMNMHKIP
LHTVRQFFMEDIVLANHPDIFNPDNPKVTQAIQSFCLEKIEEMLENAERERLGNSHQPEK
PLVRLRVDYSGGFEPFSVLRFSQKFVDRVANPKDIIHFFRHREQKEKTGEEINFGKLITK
PSEGTTLRVEDLVKQYFQTAEKNVQLSLLTERGMGEAVQEFVDKEEKDAIEELVKYQLEK
TQRFLKERHIDALEDKIDEEVRRFRETRQKNTNEEDDEVREAMTRARALRSQSEESASAF
SADDLMSIDLAEQMANDSDDSISAATNKGRGRGRGRRGGRGQNSASRGGSQRGRADTGLE
TSTRSRNSKTAVSASRNMSIIDAFKSTRQQPSRNVTTKNYSEVIEVDESDVEEDIFPTTS
KTDQRWSSTSSSKIMSQSQVSKGVDFESSEDDDDDPFMNTSSLRRNRRSGGSLEVLFQGP
DYKDDDDKGTDYKDDDDK

Sequence of entity 3 (P), FASTA

>9Q9H_3 DNA (50-MER) (chains P)
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Sequence of entity 4 (T), FASTA

>9Q9H_4 DNA (50-MER) (chains T)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	4
BEF	Beryllium trifluoride ion	Be F3	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2

Primary citation

Structural basis for DNA break sensing by human MRE11-RAD50-NBS1 and its regulation by telomeric factor TRF2. Fan, Y., Kuybu, F., Cui, H. et al. Nat Commun (2025) 16:8320-8320. DOI 10.1038/s41467-025-64082-x · PubMed

Other PDB entries of the same protein (UniProt Q92878 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GOX 2.4 Å, Eukaryotic Rad50 Functions as A Rod-shaped Dimer
9Q9K 2.59 Å, Cryo-EM structure of human Mre11-Rad50 (MR) complex bound to DNA and telomeric factor…
9Q9J 2.71 Å, Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric…
9Q9I 2.79 Å, Cryo-EM structure of human Mre11-Rad50-Nbs1 complex bound to DNA
9Q9M 2.81 Å, Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric…

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