SAXSdb — 2v7d

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

14-3-3 PROTEIN ZETA/DELTA

BOS TAURUS

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–245 Chain B； UniProt 1–245	Not recorded	INTEGRIN BETA CHAIN, BETA 2 VARIANT × 2 （Q53HS5）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；18-19% PEG3350, 10MM CACL2, 1MM NICL2, 100MM TRIS PH8.5	Resolution 2.50 Å R-free 0.273
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–245 Chain D； UniProt 1–245	Not recorded	INTEGRIN BETA CHAIN, BETA 2 VARIANT × 2 （Q53HS5）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；18-19% PEG3350, 10MM CACL2, 1MM NICL2, 100MM TRIS PH8.5	Resolution 2.50 Å R-free 0.273

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 2V7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A37 14-3-3 PROTEIN ZETA BOUND TO PS-RAF259 PEPTIDE Deposited 1998-01-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–245（245 aa） Chain B 1–245（245 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 3.60 Å R-free 0.360
1A38 14-3-3 PROTEIN ZETA BOUND TO R18 PEPTIDE Deposited 1998-01-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–245（245 aa） Chain B 1–245（245 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 3.35 Å R-free 0.390
1A4O 14-3-3 PROTEIN ZETA ISOFORM Deposited 1998-02-01	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–245（245 aa） Chain B 1–245（245 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.80 Å R-free 0.345
1A4O 14-3-3 PROTEIN ZETA ISOFORM Deposited 1998-02-01	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–245（245 aa） Chain D 1–245（245 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.80 Å R-free 0.345

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

View Construct and Data Evidence

UniProt name	1433Z_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–247； UniProt 1–245 Author chain B； PDBConstruct 3–247； UniProt 1–245 Author chain C； PDBConstruct 3–247； UniProt 1–245 Author chain D； PDBConstruct 3–247； UniProt 1–245

INTEGRIN BETA CHAIN, BETA 2 VARIANT

OrganismNot specified

UniProt Q53HS5

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain P； UniProt 755–764 Chain Q； UniProt 755–764	Fragment：INTEGRIN CYTOPLASMIC TAIL, RESIDUES 755-764 Non-standard monomer：Yes (specific site not provided by mmCIF)	14-3-3 PROTEIN ZETA/DELTA × 2 （P63103）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；18-19% PEG3350, 10MM CACL2, 1MM NICL2, 100MM TRIS PH8.5	Resolution 2.50 Å R-free 0.273
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain R； UniProt 755–764 Chain S； UniProt 755–764	Fragment：INTEGRIN CYTOPLASMIC TAIL, RESIDUES 755-764 Non-standard monomer：Yes (specific site not provided by mmCIF)	14-3-3 PROTEIN ZETA/DELTA × 2 （P63103）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；18-19% PEG3350, 10MM CACL2, 1MM NICL2, 100MM TRIS PH8.5	Resolution 2.50 Å R-free 0.273

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	Q53HS5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–10； UniProt 755–764 Author chain Q； PDBConstruct 1–10； UniProt 755–764 Author chain R； PDBConstruct 1–10； UniProt 755–764 Author chain S； PDBConstruct 1–10； UniProt 755–764

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	2v7d
Deposition date deposition_date	2007-07-30
Structure title title	14-3-3 protein zeta in complex with Thr758 phosphorylated integrin beta2 peptide
Keywords keywords	;MEMBRANE, INTEGRIN, RECEPTOR, CYTOPLASM, ACETYLATION, TRANSMEMBRANE, BETA2 INTEGRIN, PHOSPHORYLATION, DISEASE MUTATION, PYRROLIDONE CARBOXYLIC ACID, 14-3-3 ZETA, GLYCOPROTEIN, CELL ADHESION, SIGNALING PROTEIN ;; SIGNALING 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	32.60 Å
Radius of gyration Rg (electron density) rg_electron	32.07 Å
Forward intensity I(0) i0	184088000.00
Molecular weight molecular_weight	106900.0 kDa
Excluded volume excluded_volume	133240 Å³
Envelope volume envelope_volume	172280 Å³
Hydration-shell volume shell_volume	45228 Å³
Envelope diameter envelope_diameter	112.6 Å
Shell Rg shell_rg	39.05 Å
Envelope Rg envelope_rg	31.47 Å
Shape Rg shape_rg	32.09 Å
Total Rg total_rg	32.55 Å
Total atoms total_atoms	7490
Residues n_residues	938
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	104.2 Å
Rg (real space) rg_real	32.42 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.8410e+08
I(0) uncertainty (real space) i0_real_error	2.7510e+06
Rg (reciprocal space) rg_reciprocal	32.50 Å
I(0) (reciprocal space) i0_reciprocal	184100000.0000
Solution quality estimate total_estimate	0.8942
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.5 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21610000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.949

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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	14-3-3 PROTEIN ZETA/DELTA
Molecular weight formula_weight	27921.2 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	7645

GSMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN

来源 Source

来源生物 organism	BOS TAURUS
通用名 common_name	BOVINE
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	INTEGRIN BETA CHAIN, BETA 2 VARIANT
Molecular weight formula_weight	1130.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q,R,S

KSATTTVMNP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	155

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2v7da_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.7 — 14-3-3 protein
Family Family family	a.118.7.1 — 14-3-3 protein

Domain ID domain_id	d2v7db_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.7 — 14-3-3 protein
Family Family family	a.118.7.1 — 14-3-3 protein

Domain ID domain_id	d2v7dc_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.7 — 14-3-3 protein
Family Family family	a.118.7.1 — 14-3-3 protein

Domain ID domain_id	d2v7dd_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.7 — 14-3-3 protein
Family Family family	a.118.7.1 — 14-3-3 protein

CATH v4.4 (4 domains)

Domain ID domain_id	2v7dA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily	20 — 14-3-3 domain

Domain ID domain_id	2v7dB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily	20 — 14-3-3 domain

Domain ID domain_id	2v7dC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily	20 — 14-3-3 domain

Domain ID domain_id	2v7dD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily	20 — 14-3-3 domain

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8. Citations (1)

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Unit-cell length a length_a	94.920 Å
Unit-cell length b length_b	94.920 Å
Unit-cell length c length_c	233.600 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	47.600 Å
R factor r_factor	0.2277
R_work r_work	0.2277
R_free r_free	0.2733

fit	/app/data/saxs_computation/v7/2v7d/2v7d.fit
pddf	/app/data/pr_computation/v7/2v7d/2v7d.pr.out
profile	/app/data/saxs_computation/v7/2v7d/2v7d.dat

14-3-3 protein zeta in complex with Thr758 phosphorylated integrin beta2 peptide

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

14-3-3 PROTEIN ZETA/DELTA

State in the Current Structure

Other States of the Same Protein in the Database

INTEGRIN BETA CHAIN, BETA 2 VARIANT

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

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)