5T2F: FHA1 domain of Rad53

Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4. Determined by X-ray diffraction at 2.66 Å resolution. Released 15 Mar 2017.

Method: X-ray diffraction
Resolution: 2.66 Å
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 7,719
Mol. weight: 124.59 kDa
Released: 15 Mar 2017

Explore 5T2F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T2F contains 40 α-helices and 63 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: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	106-122	17
β-strand	125-128	4	1
α-helix	142-157	16
α-helix	160	1
β-strand	161-163	3	1
β-strand	172-175	4	1
α-helix	179-184	6
α-helix	190-196	7
β-strand	200-203	4	1
α-helix	204-212	9
β-strand	239-246	8	2
β-strand	254-258	5	2
α-helix	260-265	6
β-strand	270-277	8	3
β-strand	284-285	2	3
β-strand	297-302	6	3
α-helix	303-305	3
β-strand	307-311	5	3
β-strand	318-319	2	2
β-strand	322-323	2	2
α-helix	324-325	2
β-strand	326	1	3
β-strand	330-331	2	3
β-strand	336-340	5	2
β-strand	349-355	7	2
α-helix	357-360	4

Chain B: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	106-123	18
β-strand	125-128	4	4
α-helix	138-157	20
β-strand	161-163	3	4
β-strand	172-174	3	4
α-helix	182-184	3
α-helix	190-196	7
β-strand	200-202	3	4
α-helix	204-213	10
α-helix	238	1
β-strand	239-246	8	5
β-strand	254-258	5	5
α-helix	260-265	6
β-strand	272-277	6	6
β-strand	284-285	2	6
β-strand	297-301	5	6
α-helix	303-305	3
β-strand	307-311	5	6
β-strand	318-319	2	5
β-strand	322-323	2	5
α-helix	324-325	2
β-strand	330-331	2	6
α-helix	332-333	2
β-strand	336-340	5	5
β-strand	349-355	7	5
α-helix	357-363	7

Chain C: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	106-122	17
β-strand	125-128	4	7
α-helix	138-157	20
β-strand	161-163	3	7
β-strand	172-175	4	7
α-helix	182-184	3
α-helix	190-196	7
β-strand	200-203	4	7
α-helix	204-213	10
β-strand	239-246	8	8
β-strand	254-258	5	8
α-helix	260-265	6
β-strand	270-277	8	9
β-strand	284-285	2	9
β-strand	297-302	6	9
α-helix	303-305	3
β-strand	306-311	6	9
β-strand	318-319	2	8
β-strand	322-323	2	8
α-helix	324-325	2
β-strand	326	1	9
β-strand	329-331	3	9
β-strand	336-340	5	8
β-strand	349-355	7	8
α-helix	357-364	8

Chain D: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	106-122	17
β-strand	125-128	4	10
α-helix	140-157	18
β-strand	161-163	3	10
β-strand	172-175	4	10
α-helix	179-181	3
α-helix	190-196	7
β-strand	200-203	4	10
α-helix	204-212	9
β-strand	239-246	8	11
β-strand	254-258	5	11
α-helix	260-265	6
β-strand	272-277	6	12
β-strand	284-285	2	12
β-strand	297-301	5	12
α-helix	303-305	3
β-strand	307-311	5	12
β-strand	317-319	3	11
β-strand	322-323	2	11
α-helix	324-325	2
β-strand	326	1	12
β-strand	330-331	2	12
β-strand	337-340	4	11
α-helix	345-347	3
β-strand	349-355	7	11
α-helix	357-364	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein	A, B, C, D	protein	269	Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22216 (AlphaFold model), P32325 (AlphaFold model)

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

>5T2F_1 DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein (chains A, B, C, D)
SHMTPKELLEWQTNWKKIMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQ
ITQFFDTTVTIVITRRSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHV
DSGASGGSKFSQEQIGENIVCRVICTTGQIPIRDLSADISQVLKEKRSIKKVWTFGRNPA
CDYHLGNISRLSNKHFQILLGEDGNLLLNDISTNGTWLNGQKVEKNSNQLLSQGDEITVG
VGVESDILSLVIFINDKFKQCLEQNKVDR

Primary citation

'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7. Almawi, A.W., Matthews, L.A., Myrox, P. et al. Sci Rep (2016) 6:34237-34237. DOI 10.1038/srep34237 · PubMed

Other PDB entries of the same protein (UniProt P22216 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1G6G 1.6 Å, X-ray structure of the N-terminal fha domain from S. Cerevisiae RAD53P in complex with a…
5T2S 2.4 Å, Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4…
4PDP 2.59 Å, Crystal structure of Rad53 kinase domain and SCD2
6C4U 2.6 Å, Engineered FHA with Myc-pTBD peptide
5XZW 2.8 Å, Crystal structure of Rad53 1-466
4PDS 2.9 Å, Crystal structure of Rad53 kinase domain and SCD2 in complex with AMPPNP
2YGV 2.94 Å, Conserved N-terminal domain of the yeast Histone Chaperone Asf1 in complex with the…
5XZV 3.1 Å, Crystal structure of Rad53 1-466 in complex with AMP-PNP
1DMZ A refined NMR structure of a new phophopeptide-binding domain containing the FHA2 of RAD53
1FHQ Refined solution structure of the FHA2 domain of RAD53
1FHR Solution structure of the FHA2 domain of RAD53 complexed with a phosphotyrosyl peptide
1G3G NMR structure of the FHA1 domain of yeast RAD53

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