1xb4

Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II

Method: X-RAY DIFFRACTION D_max: 110.9 Å Quality: REASONABLE

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

Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region

Saccharomyces cerevisiae

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–202 Chain B； UniProt 1–202	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG 8000, Magnesium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.10 Å R-free 0.327
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–202 Chain D； UniProt 1–202	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG 8000, Magnesium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.10 Å R-free 0.327

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 1XB4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U5T Structure of the ESCRT-II endosomal trafficking complex Deposited 2004-07-28	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–202（202 aa） Chain D 1–202（202 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；Naacetate, hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.60 Å R-free 0.288
1W7P The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36) Deposited 2004-09-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–202（202 aa） Chain C 1–202（202 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；3.1% PEG35000, 0.1 M TRIS ACETATE PH 8.5, 1.36 M SODIUM FORMIATE, 19% GLYCEROL	Resolution 3.60 Å R-free 0.330

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

View Construct and Data Evidence

UniProt name	VPS25_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–202； UniProt 1–202 Author chain B； PDBConstruct 1–202； UniProt 1–202 Author chain C； PDBConstruct 1–202； UniProt 1–202 Author chain D； PDBConstruct 1–202； UniProt 1–202

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1xb4
Deposition date deposition_date	2004-08-27
Structure title title	Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II
Keywords keywords	winged helix, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	32.34 Å
Radius of gyration Rg (electron density) rg_electron	31.80 Å
Forward intensity I(0) i0	101305000.00
Molecular weight molecular_weight	81731.0 kDa
Excluded volume excluded_volume	103190 Å³
Envelope volume envelope_volume	134040 Å³
Hydration-shell volume shell_volume	36278 Å³
Envelope diameter envelope_diameter	117.1 Å
Shell Rg shell_rg	37.49 Å
Envelope Rg envelope_rg	31.64 Å
Shape Rg shape_rg	31.78 Å
Total Rg total_rg	32.41 Å
Total atoms total_atoms	5757
Residues n_residues	693
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	110.9 Å
Rg (real space) rg_real	32.34 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	1.0130e+08
I(0) uncertainty (real space) i0_real_error	1.6070e+06
Rg (reciprocal space) rg_reciprocal	32.34 Å
I(0) (reciprocal space) i0_reciprocal	101300000.0000
Solution quality estimate total_estimate	0.7072
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.7 Å
Skewness Skewness skewness	0.321
Kurtosis Kurtosis kurtosis	-0.317
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	17220000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.981; Smooth: 0.979

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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) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1xb4a1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.54 — Vacuolar sorting protein domain

Domain ID domain_id	d1xb4a2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.54 — Vacuolar sorting protein domain

Domain ID domain_id	d1xb4b1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.54 — Vacuolar sorting protein domain

Domain ID domain_id	d1xb4b2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.54 — Vacuolar sorting protein domain

Domain ID domain_id	d1xb4c1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.54 — Vacuolar sorting protein domain

Domain ID domain_id	d1xb4c2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.54 — Vacuolar sorting protein domain

Domain ID domain_id	d1xb4d1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.54 — Vacuolar sorting protein domain

Domain ID domain_id	d1xb4d2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.54 — Vacuolar sorting protein domain

CATH v4.4 (8 domains)

Domain ID domain_id	1xb4A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	570 — "Winged helix" DNA-binding domain. Chain C. Domain 1

Domain ID domain_id	1xb4A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1xb4B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	570 — "Winged helix" DNA-binding domain. Chain C. Domain 1

Domain ID domain_id	1xb4B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1xb4C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	570 — "Winged helix" DNA-binding domain. Chain C. Domain 1

Domain ID domain_id	1xb4C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1xb4D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	570 — "Winged helix" DNA-binding domain. Chain C. Domain 1

Domain ID domain_id	1xb4D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	53.360 Å
Unit-cell length b length_b	123.660 Å
Unit-cell length c length_c	140.300 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	16

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2730
R_work r_work	0.3270
R_free r_free	0.3270

Description description	Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
Molecular weight formula_weight	23582.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5773

Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II

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

Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

fit	/app/data/saxs_computation/xb/1xb4/1xb4.fit
pddf	/app/data/pr_computation/xb/1xb4/1xb4.pr.out
profile	/app/data/saxs_computation/xb/1xb4/1xb4.dat