SAXSdb — 4c8h

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

CTF4

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 471–927 Chain B； UniProt 471–927 Chain C； UniProt 471–927	Fragment：C-TERMINAL DOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 2.69 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4C8H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4C8S Crystal structure of the C-terminal region of yeast Ctf4 Deposited 2013-10-01	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain B 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain C 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 3.00 Å R-free 0.205
4C93 Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha. Deposited 2013-10-02	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain B 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain C 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 2.69 Å R-free 0.210
4C95 Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Sld5 Deposited 2013-10-02	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain B 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927 Chain C 471–927（457 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 471-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000	Resolution 2.69 Å R-free 0.214
5HOG Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2. Deposited 2016-01-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 450–927（478 aa） Fragment：UNP residues 450-927 Chain B 450–927（478 aa） Fragment：UNP residues 450-927 Chain C 450–927（478 aa） Fragment：UNP residues 450-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl.	Resolution 3.09 Å R-free 0.226
5HOI Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Tof2. Deposited 2016-01-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 472–927（456 aa） Fragment：UNP residues 472-927 Chain B 472–927（456 aa） Fragment：UNP residues 472-927 Chain C 472–927（456 aa） Fragment：UNP residues 472-927	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl	Resolution 3.30 Å R-free 0.224
5NXQ Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP Deposited 2017-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 471–927（457 aa） Fragment：UNP residues 471-927 Chain B 471–927（457 aa） Fragment：UNP residues 471-927 Chain C 471–927（457 aa） Fragment：UNP residues 471-927	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M tri-sodium citrate pH 6.2 7.5-9% (w/v) PEG 8000 0.40-0.65 M NaCI	Resolution 2.41 Å R-free 0.211
6PTJ Structure of Ctf4 trimer in complex with one CMG helicase Deposited 2019-07-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain E 1–927（927 aa） Chain F 1–927（927 aa） Chain G 1–927（927 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6PTN Structure of Ctf4 trimer in complex with two CMG helicases Deposited 2019-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain E 1–927（927 aa） Chain F 1–927（927 aa） Chain G 1–927（927 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
6PTO Structure of Ctf4 trimer in complex with three CMG helicases Deposited 2019-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain X 1–927（927 aa） Chain Y 1–927（927 aa） Chain Z 1–927（927 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
6SKL Cryo-EM structure of the CMG Fork Protection Complex at a replication fork - Conformation 1 Deposited 2019-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain F 1–927（927 aa） Fragment：Mcm6 Chain G 1–927（927 aa） Fragment：Mcm6 Chain H 1–927（927 aa） Fragment：Mcm6	Not recorded	ZN ZINC ION × 5 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Three microlitres of sample was applied on a grid and incubated for 15-30 s at 4 degC before manually blotting with filter paper for 10 s and plunge-freezing in liquid ethane.	Resolution 3.70 Å
7PMN S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II) Deposited 2021-09-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain F 1–927（927 aa） Fragment：Mcm6 Chain G 1–927（927 aa） Fragment：Mcm6 Chain H 1–927（927 aa） Fragment：Mcm6	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Manual plunger	Resolution 3.20 Å
8B9A S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain H 1–927（927 aa） Chain K 1–927（927 aa） Chain L 1–927（927 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8B9B S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain H 1–927（927 aa） Chain K 1–927（927 aa） Chain L 1–927（927 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8KG6 Yeast replisome in state I Deposited 2023-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 5 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 3.07 Å
8KG8 Yeast replisome in state II Deposited 2023-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 5 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 4.23 Å
8KG9 Yeast replisome in state III Deposited 2023-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 4.52 Å
8W7M Yeast replisome in state V Deposited 2023-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 5 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 4.12 Å
8W7S Yeast replisome in state IV Deposited 2023-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: hexadecameric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；blot with filter paper for 3-4 seconds before plunging.	Resolution 7.39 Å
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain F 1–927（927 aa） Chain G 1–927（927 aa） Chain H 1–927（927 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTF4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–478； UniProt 471–927 Author chain B； PDBConstruct 22–478； UniProt 471–927 Author chain C； PDBConstruct 22–478； UniProt 471–927

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	4c8h
Deposition date deposition_date	2013-10-01
Structure title title	Crystal structure of the C-terminal region of yeast Ctf4, selenomethionine protein.
Keywords keywords	DNA REPLICATION, ADAPTOR PROTEIN, BETA PROPELLER DOMAIN; DNA REPLICATION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.60 Å
Radius of gyration Rg (electron density) rg_electron	33.63 Å
Forward intensity I(0) i0	324137000.00
Molecular weight molecular_weight	146790.0 kDa
Excluded volume excluded_volume	183670 Å³
Envelope volume envelope_volume	235860 Å³
Hydration-shell volume shell_volume	55533 Å³
Envelope diameter envelope_diameter	109.1 Å
Shell Rg shell_rg	42.50 Å
Envelope Rg envelope_rg	33.80 Å
Shape Rg shape_rg	33.64 Å
Total Rg total_rg	34.23 Å
Total atoms total_atoms	10253
Residues n_residues	1244
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.3 Å
Rg (real space) rg_real	34.43 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	3.2410e+08
I(0) uncertainty (real space) i0_real_error	5.0310e+06
Rg (reciprocal space) rg_reciprocal	34.54 Å
I(0) (reciprocal space) i0_reciprocal	324200000.0000
Solution quality estimate total_estimate	0.6828
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.137
Kurtosis Kurtosis kurtosis	-0.589
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	69500000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.985; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	CTF4
Molecular weight formula_weight	55010.2 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	10421

MGSSHHHHHHSQDPENLYFQGTGKFRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEGEEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQLK

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	163

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8. Citations (1)

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Unit-cell length a length_a	107.294 Å
Unit-cell length b length_b	118.428 Å
Unit-cell length c length_c	155.697 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	2.691 Å
Low-resolution limit resolution_low	49.188 Å
R factor r_factor	0.1913
R_work r_work	0.1895
R_free r_free	0.2248

fit	/app/data/saxs_computation/c8/4c8h/4c8h.fit
pddf	/app/data/pr_computation/c8/4c8h/4c8h.pr.out
profile	/app/data/saxs_computation/c8/4c8h/4c8h.dat

Crystal structure of the C-terminal region of yeast Ctf4, selenomethionine protein.

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

CTF4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)