6RMM: TOPBP1 BRCT4,5

Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide. Determined by X-ray diffraction at 3.53 Å resolution. Released 12 Jun 2019.

Method: X-ray diffraction
Resolution: 3.53 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,078
Mol. weight: 89.29 kDa
Released: 12 Jun 2019

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

Secondary structure: helices and β-sheets

6RMM contains 37 α-helices and 48 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: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	557-560	4	1
α-helix	565-577	13
β-strand	581-582	2	1
β-strand	591-596	6	1
β-strand	607-612	6	1
α-helix	613-622	10
β-strand	650-653	4	2
α-helix	658-670	13
β-strand	674-675	2	2
β-strand	684	1	3
β-strand	689	1	3
β-strand	694-697	4	2
α-helix	703-710	8
β-strand	715-717	3	2
α-helix	718-727	10
α-helix	733-736	4
β-strand	737	1	2

Chain B: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	557-560	4	4
α-helix	565-577	13
β-strand	581-582	2	4
β-strand	591-596	6	4
β-strand	607-612	6	4
α-helix	613-622	10
α-helix	636-638	3
β-strand	650-653	4	5
α-helix	658-670	13
β-strand	674-675	2	5
β-strand	684	1	6
β-strand	689	1	6
β-strand	694-697	4	5
α-helix	703-710	8
β-strand	715-717	3	5
α-helix	718-727	10
α-helix	733-736	4
β-strand	737	1	5

Chains C and D: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	557-560	4	7
α-helix	565-577	13
β-strand	581-582	2	7
α-helix	583-584	2
β-strand	593-596	4	7
β-strand	610-612	3	7
α-helix	613-621	9
α-helix	628-630	3
α-helix	632-634	3
α-helix	636-638	3
β-strand	650-653	4	8
α-helix	658-670	13
β-strand	674-675	2	8
β-strand	679-680	2	9
β-strand	684	1	10
β-strand	689	1	10
α-helix	690-692	3
β-strand	694-697	4	8
α-helix	703-711	9
β-strand	715-717	3	8
α-helix	718-727	10
α-helix	733-736	4
β-strand	737	1	8
α-helix	738-740	3

Chains P and R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	362-363	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA topoisomerase 2-binding protein 1	A, B, C, D	protein	196	Homo sapiens	Q92547 (AlphaFold model)
53BP1	P, R	protein	15	Homo sapiens	Q12888 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6RMM_1 DNA topoisomerase 2-binding protein 1 (chains A, B, C, D)
HSTEEGLFSQKSFLVLGFSNENESNIANIIKENAGKIMSLLSRTVADYAVVPLLGCEVEA
TVGEVVTNTWLVTCIDYQTLFDPKSNPLFTPVPVMTGMTPLEDCVISFSQCAGAEKESLT
FLANLLGASVQEYFVRKSNAKKGMFASTHLILKERGGSKYEAAKKWNLPAVTIAWLLETA
RTGKRADESHFLIENS

Sequence of entity 2 (P, R), FASTA

>6RMM_2 53BP1 (chains P, R)
SSDLVAPSPDAFRST

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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