SAXSdb — 2v8c

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

PROFILIN-2

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 1–140	Not recorded	VASODILATOR-STIMULATED PHOSPHOPROTEIN × 1 （P70460） SO4 SULFATE ION × 3 IPA ISOPROPYL ALCOHOL × 2 NA SODIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.98 Å R-free 0.181

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 2V8C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V8F Mouse Profilin IIa in complex with a double repeat from the FH1 domain of mDia1 Deposited 2007-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–140（140 aa） Chain B 1–140（140 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 5 NA SODIUM ION × 1 GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.10 Å R-free 0.173

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PROF2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–140； UniProt 1–140

VASODILATOR-STIMULATED PHOSPHOPROTEIN

OrganismNot specified

UniProt P70460

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 C； UniProt 165–184	Fragment：PROLINE-RICH PEPTIDE, UNP RESIDUES 165-184	PROFILIN-2 × 1 （Q3V171） SO4 SULFATE ION × 3 IPA ISOPROPYL ALCOHOL × 2 NA SODIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.98 Å R-free 0.181

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	VASP_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–20； UniProt 165–184

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	2v8c
Deposition date deposition_date	2007-08-06
Structure title title	Mouse Profilin IIa in complex with the proline-rich domain of VASP
Keywords keywords	ALTERNATIVE SPLICING, PROTEIN-BINDING, CYTOPLASM, ACETYLATION, CYTOSKELETON, ACTIN-BINDING, PROTEIN BINDING; PROTEIN BINDING
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	15.55 Å
Radius of gyration Rg (electron density) rg_electron	14.16 Å
Forward intensity I(0) i0	5644250.00
Molecular weight molecular_weight	16568.0 kDa
Excluded volume excluded_volume	20497 Å³
Envelope volume envelope_volume	22715 Å³
Hydration-shell volume shell_volume	13383 Å³
Envelope diameter envelope_diameter	46.9 Å
Shell Rg shell_rg	20.23 Å
Envelope Rg envelope_rg	14.49 Å
Shape Rg shape_rg	14.15 Å
Total Rg total_rg	15.33 Å
Total atoms total_atoms	1153
Residues n_residues	152
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	48.2 Å
Rg (real space) rg_real	15.43 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	5.6440e+06
I(0) uncertainty (real space) i0_real_error	5.6630e+04
Rg (reciprocal space) rg_reciprocal	15.45 Å
I(0) (reciprocal space) i0_reciprocal	5644000.0000
Solution quality estimate total_estimate	0.8867
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.083
Kurtosis Kurtosis kurtosis	-0.362
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1499000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	PROFILIN-2
Molecular weight formula_weight	15048.2 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	1283

MAGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPVEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDSGF

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	VASODILATOR-STIMULATED PHOSPHOPROTEIN
Molecular weight formula_weight	1816.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPPPPPGPPPPPGPPPPPGL

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	119

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2v8ca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.1 — Profilin (actin-binding protein)
Family Family family	d.110.1.1 — Profilin (actin-binding protein)

CATH v4.4 (1 domains)

Domain ID domain_id	2v8cA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

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8. Citations (1)

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Unit-cell length a length_a	43.730 Å
Unit-cell length b length_b	47.090 Å
Unit-cell length c length_c	68.580 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	1.980 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1460
R_work r_work	0.1450
R_free r_free	0.1810

fit	/app/data/saxs_computation/v8/2v8c/2v8c.fit
pddf	/app/data/pr_computation/v8/2v8c/2v8c.pr.out
profile	/app/data/saxs_computation/v8/2v8c/2v8c.dat

Mouse Profilin IIa in complex with the proline-rich domain of VASP

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

PROFILIN-2

State in the Current Structure

Other States of the Same Protein in the Database

VASODILATOR-STIMULATED PHOSPHOPROTEIN

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)