SAXSdb — 2pf4

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

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

Mus musculus

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 1–589	Not recorded	Small T antigen × 1 （Q9W9P1） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00	Resolution 3.10 Å R-free 0.304
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–589	Not recorded	Small T antigen × 1 （Q9W9P1） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00	Resolution 3.10 Å R-free 0.304
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–589	Not recorded	Small T antigen × 1 （Q9W9P1） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00	Resolution 3.10 Å R-free 0.304
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–589	Not recorded	Small T antigen × 1 （Q9W9P1） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00	Resolution 3.10 Å R-free 0.304

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 2PF4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2IAE Crystal structure of a protein phosphatase 2A (PP2A) holoenzyme. Deposited 2006-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 0–588（589 aa） Fragment：Aalpha subunit	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M MES, pH 7.0, 50mM NaCl, 1.4M ammonium sulfate, 0.2M LiCl, 2% 1,6-diaminohexane, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.316
2IAE Crystal structure of a protein phosphatase 2A (PP2A) holoenzyme. Deposited 2006-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 0–588（589 aa） Fragment：Aalpha subunit	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M MES, pH 7.0, 50mM NaCl, 1.4M ammonium sulfate, 0.2M LiCl, 2% 1,6-diaminohexane, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.316
3FGA Structural Basis of PP2A and Sgo interaction Deposited 2008-12-05	Different construct 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 2–589（588 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；295 K；0.2 M SCTD, 20% w/v Polyethylene glycol 3,350, pH 7, EVAPORATION, temperature 295K	Resolution 2.70 Å R-free 0.277
6EF4 Crystal structure of mouse PP2A Aalpha P179R mutant Deposited 2018-08-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–589（589 aa）	Mutation：P179R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350	Resolution 3.40 Å R-free 0.235

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	2AAA_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–589； UniProt 1–589 Author chain B； PDBConstruct 1–589； UniProt 1–589 Author chain C； PDBConstruct 1–589； UniProt 1–589 Author chain D； PDBConstruct 1–589； UniProt 1–589

Small T antigen

Simian virus 40

UniProt Q9W9P1

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 E； UniProt 1–174	Not recorded	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （Q76MZ3） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00	Resolution 3.10 Å R-free 0.304
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 1–174	Not recorded	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （Q76MZ3） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00	Resolution 3.10 Å R-free 0.304
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 1–174	Not recorded	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （Q76MZ3） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00	Resolution 3.10 Å R-free 0.304
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–174	Not recorded	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （Q76MZ3） ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00	Resolution 3.10 Å R-free 0.304

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	Q9W9P1_SV40
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–174； UniProt 1–174 Author chain F； PDBConstruct 1–174； UniProt 1–174 Author chain G； PDBConstruct 1–174； UniProt 1–174 Author chain H； PDBConstruct 1–174； UniProt 1–174

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	2pf4
Deposition date deposition_date	2007-04-03
Structure title title	Crystal structure of the full-length simian virus 40 small t antigen complexed with the protein phosphatase 2A Aalpha subunit
Keywords keywords	PP2A, SV40, small t, DnaJ, Aalpha subunit, HYDROLASE REGULATOR-VIRAL PROTEIN COMPLEX; HYDROLASE REGULATOR/VIRAL PROTEIN
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	46.94 Å
Radius of gyration Rg (electron density) rg_electron	46.31 Å
Forward intensity I(0) i0	1482650000.00
Molecular weight molecular_weight	326150.0 kDa
Excluded volume excluded_volume	410940 Å³
Envelope volume envelope_volume	582040 Å³
Hydration-shell volume shell_volume	99773 Å³
Envelope diameter envelope_diameter	140.7 Å
Shell Rg shell_rg	55.23 Å
Envelope Rg envelope_rg	44.78 Å
Shape Rg shape_rg	46.34 Å
Total Rg total_rg	46.55 Å
Total atoms total_atoms	22802
Residues n_residues	2904
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	140.8 Å
Rg (real space) rg_real	46.50 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.4830e+09
I(0) uncertainty (real space) i0_real_error	2.5380e+07
Rg (reciprocal space) rg_reciprocal	46.93 Å
I(0) (reciprocal space) i0_reciprocal	1483000000.0000
Solution quality estimate total_estimate	0.8869
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	66.3 Å
Skewness Skewness skewness	-0.008
Kurtosis Kurtosis kurtosis	-0.510
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	178100000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.855

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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	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Molecular weight formula_weight	65392.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	22802

MAAADGDDSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIYDEDEVLLALAEQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHSPSDLEAHFVPLVKRLAGGDWFTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPMVRRAAASKLGEFAKVLELDNVKSEIIPMFSNLASDEQDSVRLLAVEACVNIAQLLPQEDLEALVMPTLRQAAEDKSWRVRYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRAAASHKVKEFCENLSADCRENVIMTQILPCIKELVSDANQHVKSALASVIMGLSPILGKDNTIEHLLPLFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVRLAIIEYMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHATIIPKVLAMSGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQKIGPILDNSTLQSEVKPILEKLTQDQDVDVKYFAQEALTVLSLA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Small T antigen
Molecular weight formula_weight	20519.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MDKVLNREESLQLMDLLGLERSAWGNIPLMRKAYLKKCKEFHPDKGGDEEKMKKMNTLYKKMEDGVKYAHQPDFGGFWDATEVFASSLNPGVDAIYCKQWPECVKKMSTNCICLLCLLRMKHENRKLYRKDPLVWVDCYCFDCFRMWFGLDLCEGTLLLWCDIIGQTTYRDLKL

来源 Source

来源生物 organism	Simian virus 40
NCBI Class编号 ncbi_taxonomy_id	10633
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2pf4a_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.2 — HEAT repeat

Domain ID domain_id	d2pf4b_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.2 — HEAT repeat

Domain ID domain_id	d2pf4c_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.2 — HEAT repeat

Domain ID domain_id	d2pf4d_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.2 — HEAT repeat

CATH v4.4 (11 domains)

Domain ID domain_id	2pf4A01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	2pf4B01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	2pf4C01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	2pf4D01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	2pf4E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	110 — DnaJ domain

Domain ID domain_id	2pf4E02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1860 — Small t-antigen, unique domain

Domain ID domain_id	2pf4F01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	110 — DnaJ domain

Domain ID domain_id	2pf4F02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1860 — Small t-antigen, unique domain

Domain ID domain_id	2pf4G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	110 — DnaJ domain

Domain ID domain_id	2pf4H01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	110 — DnaJ domain

Domain ID domain_id	2pf4H02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1860 — Small t-antigen, unique domain

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8. Citations (1)

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Unit-cell length a length_a	94.711 Å
Unit-cell length b length_b	105.501 Å
Unit-cell length c length_c	111.937 Å
Unit-cell angle α angle_alpha	115.64 °
Unit-cell angle β angle_beta	109.55 °
Unit-cell angle γ angle_gamma	94.11 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2470
R_work r_work	0.2440
R_free r_free	0.3040

fit	/app/data/saxs_computation/pf/2pf4/2pf4.fit
pddf	/app/data/pr_computation/pf/2pf4/2pf4.pr.out
profile	/app/data/saxs_computation/pf/2pf4/2pf4.dat

Crystal structure of the full-length simian virus 40 small t antigen complexed with the protein phosphatase 2A Aalpha subunit

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

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

State in the Current Structure

Other States of the Same Protein in the Database

Small T antigen

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

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (4 domains)

CATH v4.4 (11 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)