SAXSdb — 2d9n

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

Cleavage and polyadenylation specificity factor, 30 kDa subunit

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 61–126	Fragment：CCCH-type zinc finger motif	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition：20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 50uM ZnCl2+1mM IDA, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2D9N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2RHK Crystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A Deposited 2007-10-09	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 × 4 PDB declaration: tetrameric	Chain C 61–121（61 aa） Fragment：F2F3 Zinc-binding domains (UNP residues 61-121) Chain D 61–121（61 aa） Fragment：F2F3 Zinc-binding domains (UNP residues 61-121)	Mutation：P94S Mutation：P94S	NO3 NITRATE ION × 5 ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293 K；0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50	Resolution 1.95 Å R-free 0.234
2RHK Crystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A Deposited 2007-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 61–121（61 aa） Fragment：F2F3 Zinc-binding domains (UNP residues 61-121) Chain D 61–121（61 aa） Fragment：F2F3 Zinc-binding domains (UNP residues 61-121)	Mutation：P94S Mutation：P94S	NO3 NITRATE ION × 9 ZN ZINC ION × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293 K；0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50	Resolution 1.95 Å R-free 0.234
2RHK Crystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A Deposited 2007-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 61–121（61 aa） Fragment：F2F3 Zinc-binding domains (UNP residues 61-121) Chain D 61–121（61 aa） Fragment：F2F3 Zinc-binding domains (UNP residues 61-121)	Mutation：P94S Mutation：P94S	NO3 NITRATE ION × 5 ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293 K；0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50	Resolution 1.95 Å R-free 0.234
2RHK Crystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A Deposited 2007-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 61–121（61 aa） Fragment：F2F3 Zinc-binding domains (UNP residues 61-121)	Mutation：P94S	NO3 NITRATE ION × 4 ZN ZINC ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293 K；0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50	Resolution 1.95 Å R-free 0.234
6DNH Cryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex at 3.4 A resolution Deposited 2018-06-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain C 1–244（244 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；25 mM Tris-HCl, pH 7.9, 380 mM NaCl, 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6FUW Cryo-EM structure of the human CPSF160-WDR33-CPSF30 complex bound to the PAS AAUAAA motif at 3.1 Angstrom resolution Deposited 2018-02-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain C 1–178（178 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；15 seconds wait time prior to blotting	Resolution 3.07 Å
6URG Cryo-EM structure of human CPSF160-WDR33-CPSF30-CPSF100 PIM complex Deposited 2019-10-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–244（244 aa）	Not recorded	ZN ZINC ION × 1	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 3.00 Å
6URO Cryo-EM structure of human CPSF160-WDR33-CPSF30-PAS RNA-CstF77 complex Deposited 2019-10-23	Different construct 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 C 1–244（244 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
7ZYH Crystal structure of human CPSF30 in complex with hFip1 Deposited 2022-05-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–178（61 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292.15 K；1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5	Resolution 2.20 Å R-free 0.264
7ZYH Crystal structure of human CPSF30 in complex with hFip1 Deposited 2022-05-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 118–178（61 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292.15 K；1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5	Resolution 2.20 Å R-free 0.264
7ZYH Crystal structure of human CPSF30 in complex with hFip1 Deposited 2022-05-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 118–178（61 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292.15 K；1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5	Resolution 2.20 Å R-free 0.264
7ZYH Crystal structure of human CPSF30 in complex with hFip1 Deposited 2022-05-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 118–178（61 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292.15 K；1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5	Resolution 2.20 Å R-free 0.264
8E3I CRYO-EM STRUCTURE OF the human MPSF IN COMPLEX WITH THE AUUAAA poly(A) signal Deposited 2022-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain C 1–244（244 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；25 mM Tris (pH 8.0), 150 mM NaCl, and 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8E3Q CRYO-EM STRUCTURE OF the human MPSF Deposited 2022-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–244（244 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；25 mM Tris (pH 8.0), 150 mM NaCl, and 5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.68 Å
8R8R Cryo-EM structure of the human mPSF with PAPOA C-terminus peptide (PAPOAc) Deposited 2023-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain C 2–244（243 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.79 Å
9OXE CRYO-EM STRUCTURE OF the human mPSF IN COMPLEX WITH THE AGUAAA poly(A) signal Deposited 2025-06-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain C 1–244（244 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
9OXS CRYO-EM STRUCTURE OF the human mPSF IN COMPLEX WITH THE AAUAAU poly(A) signal Deposited 2025-06-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain C 1–244（244 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å

11 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CPSF4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–71； UniProt 61–126

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	2d9n
Deposition date deposition_date	2005-12-12
Structure title title	Solution structure of CCCH type zinc-finger domain 2 in Cleavage and polyadenylation specificity factor
Keywords keywords	;CCCH Zinc-finger, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.62 Å
Radius of gyration Rg (electron density) rg_electron	15.40 Å
Forward intensity I(0) i0	493211000.00
Molecular weight molecular_weight	175710.0 kDa
Excluded volume excluded_volume	214020 Å³
Envelope volume envelope_volume	28593 Å³
Hydration-shell volume shell_volume	14129 Å³
Envelope diameter envelope_diameter	61.9 Å
Shell Rg shell_rg	22.87 Å
Envelope Rg envelope_rg	18.06 Å
Shape Rg shape_rg	15.42 Å
Total Rg total_rg	15.51 Å
Total atoms total_atoms	23300
Residues n_residues	1540
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	53.8 Å
Rg (real space) rg_real	15.65 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	4.9320e+08
I(0) uncertainty (real space) i0_real_error	6.2560e+06
Rg (reciprocal space) rg_reciprocal	15.64 Å
I(0) (reciprocal space) i0_reciprocal	493200000.0000
Solution quality estimate total_estimate	0.8648
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.8 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.586
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	89420.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.758; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2d9nA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1000 — CCCH zinc finger
Homologous superfamily homologous superfamily	10 — Zinc finger, CCCH-type

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8. Citations (1)

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Description description	Cleavage and polyadenylation specificity factor, 30 kDa subunit
Molecular weight formula_weight	8685.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	23300

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

fit	/app/data/saxs_computation/d9/2d9n/2d9n.fit
pddf	/app/data/pr_computation/d9/2d9n/2d9n.pr.out
profile	/app/data/saxs_computation/d9/2d9n/2d9n.dat

Solution structure of CCCH type zinc-finger domain 2 in Cleavage and polyadenylation specificity factor

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

Cleavage and polyadenylation specificity factor, 30 kDa subunit

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)