9Q9J: Human Mre11-Rad50-Nbs1 (MRN) complex

Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542). Determined by electron microscopy at 2.71 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 2.71 Å
Organism: Homo sapiens
Chains: 8
Atoms: 17,465
Mol. weight: 615.05 kDa
Ligands: MG, ADP, BEF, MN
Released: 1 Oct 2025

Explore 9Q9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q9J contains 79 α-helices and 100 β-strands across 6 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	5
β-strand	12	1	6
α-helix	19-21	3
β-strand	23-26	4	5
β-strand	31-35	5	7
α-helix	42-54	13
α-helix	56-58	3
α-helix	63-66	4
β-strand	67	1	6
α-helix	68-69	2
β-strand	77-87	11	5
β-strand	93-105	13	5
β-strand	108-113	6	5
α-helix	114-115	2
β-strand	116-122	7	5
β-strand	125-131	7	5
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	183-235	53
α-helix	1079-1091	13
α-helix	1095-1098	4
α-helix	1101-1154	54
β-strand	1163-1168	6	8
β-strand	1183-1190	8	8
β-strand	1193-1196	4	8
α-helix	1203-1221	19
β-strand	1227-1231	5	7
α-helix	1239-1257	19
β-strand	1263-1267	5	7
α-helix	1271-1277	7
α-helix	1278-1280	3
β-strand	1285-1291	7	7
β-strand	1297-1303	7	7
β-strand	1305	1	9

Chain B: 18 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	10
β-strand	3-10	8	11
β-strand	12	1	12
α-helix	19-21	3
β-strand	23-26	4	11
β-strand	33-35	3	1
α-helix	42-54	13
α-helix	56-58	3
β-strand	67	1	12
α-helix	68-69	2
β-strand	77-87	11	11
β-strand	93-105	13	11
β-strand	108-113	6	11
β-strand	116-120	5	11
β-strand	121-122	2	13
β-strand	125-126	2	13
β-strand	129-131	3	11
α-helix	133-144	12
α-helix	148-150	3
α-helix	151-155	5
α-helix	159-161	3
α-helix	164-166	3
α-helix	169-179	11
α-helix	183-236	54
α-helix	1079-1091	13
α-helix	1095-1098	4
α-helix	1100-1154	55
β-strand	1163-1168	6	14
β-strand	1183-1190	8	14
β-strand	1193-1196	4	14
α-helix	1203-1221	19
β-strand	1225	1	10
β-strand	1227	1	15
β-strand	1230-1231	2	1
α-helix	1239-1256	18
β-strand	1263	1	15
β-strand	1266-1267	2	1
α-helix	1271-1280	10
β-strand	1285-1291	7	1
β-strand	1297-1303	7	1
α-helix	1304-1309	6

Chain D: 19 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	16
β-strand	20	1	17
β-strand	23	1	18
α-helix	36-49	14
β-strand	54-57	4	16
β-strand	62	1	18
α-helix	69-82	14
β-strand	84	1	19
α-helix	87-89	3
β-strand	92-93	2	20
β-strand	95	1	3
α-helix	97-100	4
β-strand	116	1	21
β-strand	118	1	19
β-strand	122-124	3	16
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	2
α-helix	165-166	2
β-strand	167-171	5	20
β-strand	174-181	8	20
α-helix	186-194	9
β-strand	198-203	6	2
α-helix	207-209	3
β-strand	211-216	6	20
β-strand	240-243	4	20
β-strand	250-255	6	20
β-strand	262-265	4	20
β-strand	268	1	17
α-helix	281-282	2
β-strand	283-290	8	16
β-strand	293-300	8	16
α-helix	305-306	2
β-strand	307-313	7	23
α-helix	314-316	3
α-helix	328-351	24
β-strand	362-368	7	23
α-helix	378-382	5
α-helix	383-385	3
β-strand	396-399	4	23
α-helix	429-443	15
α-helix	450	1
α-helix	453-463	11
α-helix	470-487	18
α-helix	494-507	14

Chain E: 19 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	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	92-93	2	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	4
β-strand	167-171	5	27
β-strand	174-181	8	27
α-helix	186-194	9
β-strand	198-203	6	4
β-strand	213-217	5	27
β-strand	240-244	5	27
β-strand	250	1	29
β-strand	262-264	3	27
β-strand	265	1	29
α-helix	276-279	4
α-helix	281-282	2
β-strand	283-290	8	24
β-strand	293-300	8	24
α-helix	305-306	2
β-strand	307-313	7	30
α-helix	328-351	24
β-strand	362-368	7	30
α-helix	373-375	3
α-helix	378-383	6
β-strand	396-399	4	30
α-helix	429-443	15
α-helix	445-446	2
α-helix	450	1
α-helix	454-464	11
α-helix	469-487	19
α-helix	494-507	14

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	656-660	5	2
β-strand	663	1	3
α-helix	690-692	3
β-strand	708-711	4	4
α-helix	712-714	3
α-helix	717-745	29

Chain J: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	460-462	3	1
α-helix	468-471	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Telomeric repeat-binding factor 2	J	protein	116	Homo sapiens	Q15554 (AlphaFold model)
DNA (64-mer)	P	DNA	64	Homo sapiens
DNA (64-mer)	T	DNA	64	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 (J), FASTA

>9Q9J_1 Telomeric repeat-binding factor 2 (chains J)
GPGGSSGGSSGQPLPGEKNPKVPKGKWNSSNGVEEKETWVEEDELFQVQAAPDEDSTTNI
TKKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKRLGMN

Sequence of entity 2 (P), FASTA

>9Q9J_2 DNA (64-MER) (chains P)
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTT

Sequence of entity 3 (T), FASTA

>9Q9J_3 DNA (64-MER) (chains T)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAA

Sequence of entity 4 (F), FASTA

>9Q9J_4 Nibrin (chains F)
MWKLLPAAGPAGGEPYRLLTGVEYVVGRKNCAILIENDQSISRNHAVLTANFSVTNLSQT
DEIPVLTLKDNSKYGTFVNEEKMQNGFSRTLKSGDGITFGVFGSKFRIEYEPLVACSSCL
DVSGKTALNQAILQLGGFTVNNWTEECTHLVMVSVKVTIKTICALICGRPIVKPEYFTEF
LKAVESKKQPPQIESFYPPLDEPSIGSKNVDLSGRQERKQIFKGKTFIFLNAKQHKKLSS
AVVFGGGEARLITEENEEEHNFFLAPGTCVVDTGITNSQTLIPDCQKKWIQSIMDMLQRQ
GLRPIPEAEIGLAVIFMTTKNYCDPQGHPSTGLKTTTPGPSLSQGVSVDEKLMPSAPVNT
TTYVADTESEQADTWDLSERPKEIKVSKMEQKFRMLSQDAPTVKESCKTSSNNNSMVSNT
LAKMRIPNYQLSPTKLPSINKSKDRASQQQQTNSIRNYFQPSTKKRERDEENQEMSSCKS
ARIETSCSLLEQTQPATPSLWKNKEQHLSENEPVDTNSDNNLFTDTDLKSIVKNSASKSH
AAEKLRSNKKREMDDVAIEDEVLEQLFKDTKPELEIDVKVQKQEEDVNVRKRPRMDIETN
DTFSDEAVPESSKISQENEIGKKRELKEDSLWSAKEISNNDKLQDDSEMLPKKLLLTEFR
SLVIKNSTSRNPSGINDDYGQLKNFKKFKKVTYPGAGKLPHIIGGSDLIAHHARKNTELE
EWLRQEMEVQNQHAKEESLADDLFRYNPYLKRRR

Sequence of entity 5 (A, B), FASTA

>9Q9J_5 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 6 (D, E), FASTA

>9Q9J_6 Double-strand break repair protein MRE11 (chains D, E)
MSTADALDDENTFKILVATDIHLGFMEKDAVRGNDTFVTLDEILRLAQENEVDFILLGGD
LFHENKPSRKTLHTCLELLRKYCMGDRPVQFEILSDQSVNFGFSKFPWVNYQDGNLNISI
PVFSIHGNHDDPTGADALCALDILSCAGFVNHFGRSMSVEKIDISPVLLQKGSTKIALYG
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	4

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 Q15554 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SJM 1.35 Å, Crystal Structure Analysis of TRF2-Dbd-DNA complex
1W0U 1.8 Å, hTRF2 DNA-binding domain in complex with telomeric DNA.
3K6G 1.95 Å, Crystal structure of Rap1 and TRF2 complex
4M7C 2.05 Å, Crystal structure of the TRF2-binding motif of SLX4 in complex with the TRFH domain of…
6J67 2.05 Å, Crystal structure of the compound 34 in a complex with TRF2
3BU8 2.15 Å, Crystal Structure of TRF2 TRFH domain and TIN2 peptide complex
7C5D 2.15 Å, Crystal structure of TRF2 TRFH domain in complex with a MCPH1 peptide
1H6P 2.2 Å, Dimeristion domain from human TRF2
5XYF 2.2 Å, Crystal structure of the human TIN2-TPP1-TRF2 telomeric complex
4RQI 2.44 Å, Structure of TRF2/RAP1 secondary interaction binding site
3BUA 2.5 Å, Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex
9Q9K 2.59 Å, Cryo-EM structure of human Mre11-Rad50 (MR) complex bound to DNA and telomeric factor…

Browse structure collections

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