5DA9: PDB entry 5DA9

ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with the Rad50-binding domain of Mre11. Determined by X-ray diffraction at 3.0 Å resolution. Released 2 Mar 2016.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Chaetomium thermophilum var. thermophilum DSM 1495
Chains: 4
Atoms: 7,814
Mol. weight: 128.18 kDa
Ligands: MG, AGS
Released: 2 Mar 2016

Explore 5DA9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DA9 contains 41 α-helices and 32 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: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
β-strand	12	1	2
β-strand	21-24	4	1
β-strand	29-33	5	3
α-helix	40-52	13
α-helix	55-56	2
β-strand	66	1	2
α-helix	67-68	2
α-helix	70-72	3
β-strand	76-86	11	1
β-strand	92-103	12	1
β-strand	109-122	14	1
β-strand	125-130	6	1
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	169-180	12
α-helix	182-223	42
α-helix	1100-1159	60
β-strand	1167-1177	11	4
β-strand	1185-1195	11	4
β-strand	1201-1202	2	4
α-helix	1209-1227	19
β-strand	1232-1237	6	3
α-helix	1245-1263	19
β-strand	1268-1274	7	3
α-helix	1277-1284	8
β-strand	1291-1297	7	3
β-strand	1303-1309	7	3
α-helix	1310	1

Chain B: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	5
β-strand	12	1	6
β-strand	21-24	4	5
α-helix	25-26	2
β-strand	29-34	6	7
α-helix	40-52	13
α-helix	55-56	2
β-strand	66	1	6
α-helix	67-68	2
α-helix	69-71	3
β-strand	76-86	11	5
β-strand	92-103	12	5
α-helix	105-107	3
β-strand	109-122	14	5
β-strand	125-130	6	5
α-helix	133-144	12
α-helix	148-150	3
α-helix	151-155	5
α-helix	164-166	3
α-helix	169-180	12
α-helix	182-202	21
α-helix	1116-1159	44
β-strand	1167-1178	12	8
β-strand	1184-1196	13	8
β-strand	1199-1202	4	8
α-helix	1209-1227	19
β-strand	1232-1237	6	7
α-helix	1245-1263	19
β-strand	1268-1274	7	7
α-helix	1277-1284	8
β-strand	1291-1297	7	7
β-strand	1303-1309	7	7

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	441-451	11
α-helix	459-471	13
α-helix	477-495	19
α-helix	498-503	6
α-helix	506-521	16

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	442-451	10
α-helix	459-471	13
α-helix	477-485	9
α-helix	510-519	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putative uncharacterized protein,Putative uncharacterized protein	A, B	protein	449	Chaetomium thermophilum var. thermophilum DSM 1495	G0SHW7 (AlphaFold model)
Putative double-strand break protein	C, D	protein	108	Chaetomium thermophilum var. thermophilum DSM 1495	G0RYR3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5DA9_1 Putative uncharacterized protein,Putative uncharacterized protein (chains A, B)
MSKIEKLSILGVRSFGPHHPETIAFNTPLTLIVGYNGSGKTTVIECLKYATTGELPPNST
RNGAFIHDPDLVGEKEVRAQVKLSFRSTIGESYVVTRNIQLLVQRNNKRTQKTLEGSLLL
RNNGERTVISTRVAELDKLVSEKLGVPPAILDAVIFCHQDDSLWPMSEPAALKKRFDEIF
EAQKYTKVIENIRLLKKKKGDELKILKEREVQDKANKERAEKVDGGAGGAGGELDLKDAK
AKYKETHIKVETTKAAIEDLGRGMAAVDHAIMQYHSKMMEQINRTIAELWQSTYQGTDID
TIQIRSDVESTTSSDSGTRRNYNYRVSMVKGDTEMDMRGRCSAGQKVLASIIIRLALAES
FCANCGLIALDEPTTNLDSDNIRSLAESLHGIIKARQAQGNLQLIVITHDEEFLKYMQCS
DFCDDFYRVKRDEKQNSVIVRESITRITE

Sequence of entity 2 (C, D), FASTA

>5DA9_2 Putative double-strand break protein (chains C, D)
SDSISVDALVQEFFAQQSLKILPQAPFGDAVNQFVSKDDKHAVEMFVMDSLSSQVRGLLQ
LDDDKINEGLDSHIEDFRKVMEKNFLSGQQKQAQRRRRFKEKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	2

Primary citation

Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50. Seifert, F.U., Lammens, K., Stoehr, G. et al. EMBO J (2016) 35:759-772. DOI 10.15252/embj.201592934 · PubMed

Other PDB entries of the same protein (UniProt G0SHW7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5DAC 2.5 Å, ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with DNA
7ZQY 2.51 Å, Chaetomium thermophilum Rad50 Zn hook
7ZR1 4.0 Å, Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite structure)

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