SAXSdb — 5hog

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase alpha-binding protein

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Dna2p × 2 （A0A0D4IHI3） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CTF4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–478； UniProt 450–927 Author chain B； PDBConstruct 1–478； UniProt 450–927 Author chain C； PDBConstruct 1–478； UniProt 450–927

Dna2p

OrganismNot specified

UniProt A0A0D4IHI3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	DNA polymerase alpha-binding protein × 3 （Q01454） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0D4IHI3_YEASX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–17； UniProt 207–223 Author chain E； PDBConstruct 1–17； UniProt 207–223

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5hog
Deposition date deposition_date	2016-01-19
Structure title title	Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.
Keywords keywords	DNA replication, adaptor protein, beta-propeller domain, replication; REPLICATION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5hog__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5hog__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5hog__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.72 Å
Rg (electron density)	33.73 Å
Total Rg	34.36 Å
Atom count	9503
Residues	1180
Excluded volume	169660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5hog__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA polymerase alpha-binding protein
Molecular weight formula_weight	54447.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9598

MGSSHHHHHHSQDPENLYFQGTGKFRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEGEEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQLK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Dna2p
Molecular weight formula_weight	1918.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

SLRNIDDILDDIEGDLT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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Unit-cell length a length_a	88.677 Å
Unit-cell length b length_b	99.551 Å
Unit-cell length c length_c	218.373 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.092 Å
Low-resolution limit resolution_low	48.980 Å
R factor r_factor	0.1826
R_work r_work	0.1802
R_free r_free	0.2260

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase alpha-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Dna2p

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5hog__assembly_1__model_1

5hog__assembly_1__model_1 | I(q)

5hog__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (2)

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase alpha-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Dna2p

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5hog__assembly_1__model_1

5hog__assembly_1__model_1 | I(q)

5hog__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (2)