6RML: TOPBP1 BRCT0,1,2

Crystal structure of TOPBP1 BRCT0,1,2 in complex with a 53BP1 phosphopeptide. Determined by X-ray diffraction at 2.81 Å resolution. Released 12 Jun 2019.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,605
Mol. weight: 69.54 kDa
Released: 12 Jun 2019

Explore 6RML in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RML contains 32 α-helices and 32 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: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	5
α-helix	21-30	10
α-helix	36-38	3
β-strand	39-42	4	5
α-helix	44-49	6
β-strand	57-59	3	5
α-helix	66-74	9
β-strand	78-79	2	5
α-helix	81-89	9
α-helix	93-95	3
β-strand	101	1	5
β-strand	110-114	5	6
α-helix	118-130	13
β-strand	134-135	2	6
β-strand	145-148	4	6
α-helix	154-161	8
β-strand	166-167	2	6
α-helix	169-180	12
α-helix	192-195	4
β-strand	196	1	6
α-helix	197-198	2
β-strand	204-207	4	7
α-helix	212-224	13
β-strand	228-229	2	7
β-strand	240-242	3	7
α-helix	249-255	7
β-strand	260-262	3	7
α-helix	264-273	10
α-helix	279-282	4
β-strand	283	1	7

Chain B: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	1
α-helix	21-33	13
α-helix	36-38	3
β-strand	39-42	4	1
α-helix	44-48	5
β-strand	57-59	3	1
α-helix	66-74	9
β-strand	77-79	3	1
α-helix	81-89	9
α-helix	93-95	3
β-strand	101	1	1
β-strand	110-114	5	2
α-helix	118-130	13
β-strand	134-135	2	2
β-strand	145-148	4	2
α-helix	154-161	8
β-strand	166-167	2	2
α-helix	169-180	12
α-helix	187-189	3
α-helix	192-195	4
β-strand	196	1	2
α-helix	197-198	2
β-strand	204-207	4	3
α-helix	212-224	13
β-strand	228-229	2	3
β-strand	233-234	2	4
β-strand	240-242	3	3
α-helix	249-256	8
β-strand	260-262	3	3
α-helix	264-273	10
α-helix	279-282	4
β-strand	283	1	3

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	666-667	2	4
α-helix	668-671	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA topoisomerase 2-binding protein 1	A, B	protein	292	Homo sapiens	Q92547 (AlphaFold model)
53BP1	C	protein	15	Homo sapiens	Q12888 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6RML_1 DNA topoisomerase 2-binding protein 1 (chains A, B)
GPMSRNDKEPFFVKFLKSSDNSKCFFKALESIKEFQSEEYLQIITEEEALKIKENDRSLY
ICDPFSGVVFDHLKKLGCRIVGPQVVIFCMHHQRCVPRAEHPVYNMVMSDVTISCTSLEK
EKREEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPSWIKTLWEK
SQEKKITRYTDINMEDFKCPIFLGCIICVTGLCGLDRKEVQQLTVKHGGQYMGQLKMNEC
THLIVQEPKGQKYECAKRWNVHCVTTQWFFDSIEKGFCQDESIYKTEPRPEA

Sequence of entity 2 (C), FASTA

>6RML_2 53BP1 (chains C)
EVEEIPETPCESQGE

Primary citation

Phosphorylation-mediated interactions with TOPBP1 couple 53BP1 and 9-1-1 to control the G1 DNA damage checkpoint. Bigot, N., Day, M., Baldock, R.A. et al. Elife (2019) 8. DOI 10.7554/eLife.44353 · PubMed

Other PDB entries of the same protein (UniProt Q92547 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PD7 1.26 Å, Crystal Structure of the Sixth BRCT Domain of Human TopBP1
3JVE 1.34 Å, Crystal Structure of the Sixth BRCT Domain of TopBP1
9MAT 1.65 Å, TopBP1 BRCT 7-8 Domain
7CMZ 1.7 Å, Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8
3UEN 1.9 Å, Crystal structure of TopBP1 BRCT4/5 domains
3AL2 2.0 Å, Crystal Structure of TopBP1 BRCT7/8
3AL3 2.15 Å, Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex
3OLC 2.4 Å, Crystal structure of the N-terminal region of TopBP1
9MAW 2.45 Å, Crystal structure of TOPBP1BRCT7-8 domain in complex with 1-Adamantaneacetic acid
2XNK 2.6 Å, Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor…
3UEO 2.6 Å, Crystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide
2XNH 2.8 Å, Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor…

Browse structure collections

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