SAXSdb — 7zy4

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

Cleavage stimulation factor subunit 3

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 241–549	Not recorded	hFip1 × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；278.15 K；0.1 M Bicine pH 9.0, 10% w/v PEG 20k, 2% v/v Dioxane	Resolution 2.55 Å R-free 0.247
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 241–549	Not recorded	hFip1 × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；278.15 K；0.1 M Bicine pH 9.0, 10% w/v PEG 20k, 2% v/v Dioxane	Resolution 2.55 Å R-free 0.247

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 7ZY4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6B3X Crystal structure of CstF-50 in complex with CstF-77 Deposited 2017-09-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 581–600（20 aa） Fragment：UNP residues 581-600	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M MES pH6.0-6.5, 1.6-1.9M ammonium sulfate, 2-5% PEG400, 0.2M NaCl	Resolution 2.30 Å R-free 0.262
6URO Cryo-EM structure of human CPSF160-WDR33-CPSF30-PAS RNA-CstF77 complex Deposited 2019-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric	Chain E 1–717（717 aa） Chain F 1–717（717 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSTF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–312； UniProt 241–549 Author chain B； PDBConstruct 4–312； UniProt 241–549

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	7zy4
Deposition date deposition_date	2022-05-23
Structure title title	Crystal structure of human CstF77 in complex with hFip1
Keywords keywords	;Complex, 3' end processing, CstF, CPSF, GENE REGULATION ;; GENE REGULATION
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	31.10 Å
Radius of gyration Rg (electron density) rg_electron	30.52 Å
Forward intensity I(0) i0	83868200.00
Molecular weight molecular_weight	74614.0 kDa
Excluded volume excluded_volume	94216 Å³
Envelope volume envelope_volume	120930 Å³
Hydration-shell volume shell_volume	33880 Å³
Envelope diameter envelope_diameter	107.7 Å
Shell Rg shell_rg	36.92 Å
Envelope Rg envelope_rg	30.26 Å
Shape Rg shape_rg	30.47 Å
Total Rg total_rg	31.27 Å
Total atoms total_atoms	10471
Residues n_residues	628
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	103.3 Å
Rg (real space) rg_real	31.21 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	8.3870e+07
I(0) uncertainty (real space) i0_real_error	1.2150e+06
Rg (reciprocal space) rg_reciprocal	31.17 Å
I(0) (reciprocal space) i0_reciprocal	83870000.0000
Solution quality estimate total_estimate	0.8786
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.394
Kurtosis Kurtosis kurtosis	-0.391
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15110000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.899; Smooth: 0.881

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cleavage stimulation factor subunit 3
Molecular weight formula_weight	36598.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10507

SNANTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDTRTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFKEEYEGKETALLVDRYKFMDLYPCSASELKALGYKDV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	hFip1
Molecular weight formula_weight	4133.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SNAMSAGEVERLVSELSGGTGGDEEEEWLYGDENEVER

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

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8. Citations (1)

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Unit-cell length a length_a	157.612 Å
Unit-cell length b length_b	157.612 Å
Unit-cell length c length_c	161.005 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	hexagonal

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	56.310 Å
R factor r_factor	0.2138
R_work r_work	0.2121
R_free r_free	0.2469

fit	/app/data/saxs_computation/zy/7zy4/7zy4.fit
pddf	/app/data/pr_computation/zy/7zy4/7zy4.pr.out
profile	/app/data/saxs_computation/zy/7zy4/7zy4.dat

Crystal structure of human CstF77 in complex with hFip1

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

Cleavage stimulation factor subunit 3

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)