9Q9I: Human Mre11-Rad50-Nbs1 complex

Cryo-EM structure of human Mre11-Rad50-Nbs1 complex bound to DNA. Determined by electron microscopy at 2.79 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 2.79 Å
Organism: Homo sapiens
Chains: 7
Atoms: 17,121
Mol. weight: 593.32 kDa
Ligands: MG, ADP, BEF, MN
Released: 1 Oct 2025

Explore 9Q9I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q9I contains 75 α-helices and 103 β-strands across 5 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	4
β-strand	12	1	5
β-strand	15	1	6
α-helix	19-21	3
β-strand	23-26	4	4
β-strand	31-35	5	6
α-helix	42-54	13
α-helix	56-58	3
α-helix	63-66	4
β-strand	67	1	5
α-helix	68-69	2
α-helix	70-73	4
β-strand	77-87	11	4
β-strand	93-105	13	4
β-strand	108-112	5	4
α-helix	113-115	3
β-strand	116-119	4	4
β-strand	121-122	2	7
β-strand	125-126	2	7
β-strand	129-131	3	4
α-helix	135-144	10
α-helix	148-150	3
α-helix	151-155	5
α-helix	169-179	11
α-helix	183-235	53
α-helix	1079-1092	14
α-helix	1095-1098	4
α-helix	1101-1139	39
α-helix	1141-1154	14
β-strand	1163-1168	6	8
β-strand	1183-1190	8	8
β-strand	1193-1196	4	8
α-helix	1203-1220	18
β-strand	1226-1231	6	6
α-helix	1239-1256	18
β-strand	1262-1267	6	6
α-helix	1271-1278	8
β-strand	1285-1291	7	6
β-strand	1297-1303	7	6
β-strand	1305	1	9

Chain B: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	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	42-54	13
α-helix	56-58	3
β-strand	67	1	11
α-helix	68-69	2
β-strand	79-87	9	10
β-strand	93-96	4	10
β-strand	99-101	3	10
β-strand	104-105	2	13
β-strand	108-109	2	13
β-strand	112-114	3	10
β-strand	116-119	4	10
β-strand	128-131	4	10
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	183-236	54
α-helix	1079-1093	15
α-helix	1095-1098	4
α-helix	1100-1154	55
β-strand	1162-1167	6	14
β-strand	1184-1190	7	14
β-strand	1193-1196	4	14
α-helix	1203-1221	19
β-strand	1227	1	15
β-strand	1230-1231	2	12
α-helix	1239-1256	18
β-strand	1263	1	15
β-strand	1266-1267	2	12
α-helix	1271-1276	6
β-strand	1285-1291	7	12
β-strand	1297-1303	7	12
α-helix	1304-1309	6

Chain D: 18 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	15-17	3	16
β-strand	20	1	17
β-strand	23	1	18
α-helix	36-50	15
β-strand	54-57	4	16
β-strand	62	1	18
α-helix	69-82	14
β-strand	84	1	19
β-strand	92-93	2	20
β-strand	95	1	2
α-helix	97-100	4
α-helix	110-112	3
β-strand	116	1	21
β-strand	118	1	19
β-strand	122-124	3	16
α-helix	128-130	3
β-strand	133	1	22
β-strand	138	1	22
α-helix	140-147	8
β-strand	151-152	2	16
β-strand	162-164	3	1
β-strand	167-171	5	20
β-strand	174-181	8	20
α-helix	186-194	9
β-strand	198-203	6	1
β-strand	211-216	6	20
α-helix	231-233	3
β-strand	240-242	3	20
β-strand	250-254	5	20
β-strand	262-265	4	20
β-strand	268	1	17
α-helix	281-282	2
β-strand	283-287	5	16
β-strand	296-300	5	16
α-helix	305-306	2
β-strand	307-313	7	23
α-helix	314-316	3
α-helix	328-350	23
β-strand	362-368	7	23
α-helix	378-382	5
β-strand	396-399	4	23
α-helix	429-443	15
α-helix	450	1
α-helix	454-463	10
α-helix	469-487	19
α-helix	494-503	10

Chain E: 20 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	24
β-strand	23	1	25
α-helix	35-49	15
β-strand	54-57	4	24
β-strand	62	1	25
α-helix	69-82	14
β-strand	84	1	26
α-helix	87-89	3
β-strand	92	1	27
α-helix	97-100	4
α-helix	110-112	3
β-strand	116	1	21
β-strand	118	1	26
β-strand	122-124	3	24
β-strand	133	1	28
β-strand	134	1	9
β-strand	138	1	28
α-helix	140-147	8
β-strand	151-152	2	24
β-strand	162-164	3	29
β-strand	167-171	5	27
β-strand	174-181	8	27
α-helix	186-194	9
β-strand	198-200	3	29
β-strand	201-203	3	3
α-helix	207-209	3
β-strand	213-217	5	27
β-strand	240-244	5	27
β-strand	250-254	5	27
β-strand	262-265	4	27
α-helix	276-279	4
α-helix	281-282	2
β-strand	283-284	2	30
β-strand	287-290	4	24
β-strand	293-296	4	24
β-strand	299-300	2	30
α-helix	305-306	2
β-strand	307-313	7	31
α-helix	314-316	3
α-helix	328-350	23
β-strand	362-368	7	31
α-helix	378-381	4
α-helix	382-385	4
β-strand	396-399	4	31
α-helix	429-441	13
α-helix	450	1
α-helix	454-464	11
α-helix	469-487	19
α-helix	494-506	13

Chain F: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	656-660	5	1
β-strand	663	1	2
β-strand	708-710	3	3
α-helix	717-745	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (50-mer)	P	DNA	50	Homo sapiens
DNA (50-mer)	T	DNA	50	Homo sapiens
Nibrin	F	protein	754	Homo sapiens	O60934 (AlphaFold model)
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)

Sequence of entity 1 (P), FASTA

>9Q9I_1 DNA (50-MER) (chains P)
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Sequence of entity 2 (T), FASTA

>9Q9I_2 DNA (50-MER) (chains T)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Sequence of entity 3 (F), FASTA

>9Q9I_3 Nibrin (chains F)
MWKLLPAAGPAGGEPYRLLTGVEYVVGRKNCAILIENDQSISRNHAVLTANFSVTNLSQT
DEIPVLTLKDNSKYGTFVNEEKMQNGFSRTLKSGDGITFGVFGSKFRIEYEPLVACSSCL
DVSGKTALNQAILQLGGFTVNNWTEECTHLVMVSVKVTIKTICALICGRPIVKPEYFTEF
LKAVESKKQPPQIESFYPPLDEPSIGSKNVDLSGRQERKQIFKGKTFIFLNAKQHKKLSS
AVVFGGGEARLITEENEEEHNFFLAPGTCVVDTGITNSQTLIPDCQKKWIQSIMDMLQRQ
GLRPIPEAEIGLAVIFMTTKNYCDPQGHPSTGLKTTTPGPSLSQGVSVDEKLMPSAPVNT
TTYVADTESEQADTWDLSERPKEIKVSKMEQKFRMLSQDAPTVKESCKTSSNNNSMVSNT
LAKMRIPNYQLSPTKLPSINKSKDRASQQQQTNSIRNYFQPSTKKRERDEENQEMSSCKS
ARIETSCSLLEQTQPATPSLWKNKEQHLSENEPVDTNSDNNLFTDTDLKSIVKNSASKSH
AAEKLRSNKKREMDDVAIEDEVLEQLFKDTKPELEIDVKVQKQEEDVNVRKRPRMDIETN
DTFSDEAVPESSKISQENEIGKKRELKEDSLWSAKEISNNDKLQDDSEMLPKKLLLTEFR
SLVIKNSTSRNPSGINDDYGQLKNFKKFKKVTYPGAGKLPHIIGGSDLIAHHARKNTELE
EWLRQEMEVQNQHAKEESLADDLFRYNPYLKRRR

Sequence of entity 4 (A, B), FASTA

>9Q9I_4 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 5 (D, E), FASTA

>9Q9I_5 Double-strand break repair protein MRE11 (chains D, E)
MSTADALDDENTFKILVATDIHLGFMEKDAVRGNDTFVTLDEILRLAQENEVDFILLGGD
LFHENKPSRKTLHTCLELLRKYCMGDRPVQFEILSDQSVNFGFSKFPWVNYQDGNLNISI
PVFSIHGNNDDPTGADALCALDILSCAGFVNHFGRSMSVEKIDISPVLLQKGSTKIALYG
LGSIPDERLYRMFVNKKVTMLRPKEDENSWFNLFVIHQNRSKHGSTNFIPEQFLDDFIDL
VIWGHEHECKIAPTKNEQQLFYISQPGSSVVTSLSPGEAVKKHVGLLRIKGRKMNMHKIP
LHTVRQFFMEDIVLANHPDIFNPDNPKVTQAIQSFCLEKIEEMLENAERERLGNSHQPEK
PLVRLRVDYSGGFEPFSVLRFSQKFVDRVANPKDIIHFFRHREQKEKTGEEINFGKLITK
PSEGTTLRVEDLVKQYFQTAEKNVQLSLLTERGMGEAVQEFVDKEEKDAIEELVKYQLEK
TQRFLKERHIDALEDKIDEEVRRFRETRQKNTNEEDDEVREAMTRARALRSQSEESASAF
SADDLMSIDLAEQMANDSDDSISAATNKGRGRGRGRRGGRGQNSASRGGSQRGRADTGLE
TSTRSRNSKTAVSASRNMSIIDAFKSTRQQPSRNVTTKNYSEVIEVDESDVEEDIFPTTS
KTDQRWSSTSSSKIMSQSQVSKGVDFESSEDDDDDPFMNTSSLRRNRRSGGSLEVLFQGP
DYKDDDDKGTDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
BEF	Beryllium trifluoride ion	Be F3	2
MN	Manganese (II) ion	Mn	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 O60934 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SID 2.53 Å, Human ATM Dimer Bound to Nbs1
9Q9J 2.71 Å, Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric…
9Q9M 2.81 Å, Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric…
5WQD 3.0 Å, Crystal structure of TRF2 TRFH in complex with an NBS1 peptide
9ULO 3.91 Å, Cryo-EM structure of Human Mre11-Nbs1 complex
8BAH 4.13 Å, Human Mre11-Nbs1 complex

Browse structure collections

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