3OQ4: Motif N of Saccharomyces cerevisiae Dbf4

Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4. Determined by X-ray diffraction at 2.4 Å resolution. Released 7 Sept 2011.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Saccharomyces cerevisiae
Chains: 5
Atoms: 4,592
Mol. weight: 78.11 kDa
Released: 7 Sept 2011

Explore 3OQ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3OQ4 contains 24 α-helices and 24 β-strands across 5 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, 4 β-strands

Element	Residues	Length	Sheet
β-strand	125-128	4	1
α-helix	138-157	20
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	204-213	10
α-helix	218-221	4
α-helix	233-241	9

Chain B: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	125-128	4	2
β-strand	134-135	2	1
α-helix	138-156	19
β-strand	161-163	3	2
β-strand	172-175	4	2
α-helix	179-184	6
α-helix	190-196	7
β-strand	200-203	4	2
α-helix	204-213	10
α-helix	218-222	5

Chain C: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	125-128	4	3
β-strand	134-135	2	2
α-helix	138-158	21
β-strand	161-163	3	3
β-strand	172-175	4	3
α-helix	179-184	6
α-helix	190-196	7
β-strand	200-203	4	3
α-helix	204-213	10

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	125-128	4	4
β-strand	134-135	2	3
α-helix	138-157	20
β-strand	161-163	3	4
β-strand	172-175	4	4
α-helix	179-184	6
α-helix	190-196	7
β-strand	200-203	4	4
α-helix	204-213	10

Chain E: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	122-124	3
β-strand	125-128	4	5
β-strand	134-135	2	4
α-helix	138-157	20
β-strand	161-162	2	5
β-strand	172-175	4	5
α-helix	182-184	3
α-helix	190-196	7
β-strand	200-203	4	5
α-helix	209-214	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DBF4	A, B, C, D, E	protein	134	Saccharomyces cerevisiae	P32325 (AlphaFold model)

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

>3OQ4_1 DBF4 (chains A, B, C, D, E)
GSHMKRDSRIYFDITDDVEMNTYNKSKMDKRRDLLKRGFLTLGAQITQFFDTTVTIVITR
RSVENIYLLKDTDILSRAKKNYMKVWSYEKAARFLKNLDVDLDHLSKTKSASLAAPTLSN
LLHNEKLYGPTDRD

Primary citation

Crystal Structure of Saccharomyces cerevisiae Dbf4-motif N. Matthews, L.A., Jones, D.R., Prasad, A.A. et al. To be published.

Other PDB entries of the same protein (UniProt P32325 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5T2S 2.4 Å, Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4…
5T2F 2.66 Å, Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4
3QBZ 2.69 Å, Crystal structure of the Rad53-recognition domain of Saccharomyces cerevisiae Dbf4
3OQ0 2.7 Å, Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4
7V3V 2.9 Å, Cryo-EM structure of MCM double hexamer bound with DDK in State I
7PT6 3.2 Å, Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III
7P5Z 3.3 Å, Structure of a DNA-loaded MCM double hexamer engaged with the Dbf4-dependent kinase
6MF6 3.4 Å, Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4…
7PT7 3.8 Å, Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I

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