SAXSdb — 6b3x

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

Cleavage stimulation factor subunit 1

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 80–431	Fragment：UNP residues 80-431	Cleavage stimulation factor subunit 3 × 1 （Q12996）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CSTF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–358； UniProt 80–431

Cleavage stimulation factor subunit 3

OrganismNot specified

UniProt Q12996

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 B； UniProt 581–600	Fragment：UNP residues 581-600	Cleavage stimulation factor subunit 1 × 1 （Q05048）	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

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 6B3X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
7ZY4 Crystal structure of human CstF77 in complex with hFip1 Deposited 2022-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 241–549（309 aa）	Not recorded	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
7ZY4 Crystal structure of human CstF77 in complex with hFip1 Deposited 2022-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 241–549（309 aa）	Not recorded	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

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSTF3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–20； UniProt 581–600

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	6b3x
Deposition date deposition_date	2017-09-25
Structure title title	Crystal structure of CstF-50 in complex with CstF-77
Keywords keywords	WD40 fold, Scaffold protein, 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	20.04 Å
Radius of gyration Rg (electron density) rg_electron	18.95 Å
Forward intensity I(0) i0	26779100.00
Molecular weight molecular_weight	38555.0 kDa
Excluded volume excluded_volume	47691 Å³
Envelope volume envelope_volume	53974 Å³
Hydration-shell volume shell_volume	22904 Å³
Envelope diameter envelope_diameter	60.5 Å
Shell Rg shell_rg	26.25 Å
Envelope Rg envelope_rg	19.14 Å
Shape Rg shape_rg	18.95 Å
Total Rg total_rg	19.86 Å
Total atoms total_atoms	2708
Residues n_residues	341
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	59.6 Å
Rg (real space) rg_real	19.89 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.6780e+07
I(0) uncertainty (real space) i0_real_error	3.0480e+05
Rg (reciprocal space) rg_reciprocal	19.92 Å
I(0) (reciprocal space) i0_reciprocal	26780000.0000
Solution quality estimate total_estimate	0.9075
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.068
Kurtosis Kurtosis kurtosis	-0.510
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7451000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cleavage stimulation factor subunit 1
Molecular weight formula_weight	40331.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2810

GSHMEFGIDLEFDADVQTMSPEASEYETCYVTSHKGPCRVATYSRDGQLIATGSADASIKILDTERMLAKSAMPIEVMMNETAQQNMENHPVIRTLYDHVDEVTCLAFHPTEQILASGSRDYTLKLFDYSKPSAKRAFKYIQEAEMLRSISFHPSGDFILVGTQHPTLRLYDINTFQCFVSCNPQDQHTDAICSVNYNSSANMYVTGSKDGCIKLWDGVSNRCITTFEKAHDGAEVCSAIFSKNSKYILSSGKDSVAKLWEISTGRTLVRYTGAGLSGRQVHRTQAVFNHTEDYVLLPDERTISLCCWDSRTAERRNLLSLGHNNIVRCIVHSPTNPGFMTCSDDFRARFWYRRSTTD

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	unidentified baculovirus

Entity 2 Entity 2 polymer

Description description	Cleavage stimulation factor subunit 3
Molecular weight formula_weight	2364.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

YPKPDTQQMIPFQPRHLAPP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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8. Citations (1)

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Unit-cell length a length_a	43.863 Å
Unit-cell length b length_b	74.491 Å
Unit-cell length c length_c	95.105 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	47.000 Å
R factor r_factor	0.2165
R_work r_work	0.2141
R_free r_free	0.2615

fit	/app/data/saxs_computation/b3/6b3x/6b3x.fit
pddf	/app/data/pr_computation/b3/6b3x/6b3x.pr.out
profile	/app/data/saxs_computation/b3/6b3x/6b3x.dat

Crystal structure of CstF-50 in complex with CstF-77

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

Cleavage stimulation factor subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)