1u5t

Structure of the ESCRT-II endosomal trafficking complex

Method: X-RAY DIFFRACTION D_max: 126.1 Å Quality: GOOD

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

appears to be functionally related to SNF7; Snf8p

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–233	Not recorded	Defective in vacuolar protein sorting; Vps36p × 1 （Q06696） Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region × 2 （P47142）	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

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 1U5T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W7P The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36) Deposited 2004-09-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–233（233 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

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

View Construct and Data Evidence

UniProt name	SNF8_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–233； UniProt 1–233

Defective in vacuolar protein sorting; Vps36p

Saccharomyces cerevisiae

UniProt Q06696

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 B； UniProt 396–564	Not recorded	appears to be functionally related to SNF7; Snf8p × 1 （Q12483） Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region × 2 （P47142）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1U5T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W7P The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36) Deposited 2004-09-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–566（566 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
2CAY Vps36 N-terminal PH domain Deposited 2005-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–99（99 aa） Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289 Chain A 252–289（38 aa） Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289 Chain B 1–99（99 aa） Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289 Chain B 252–289（38 aa） Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；1M AMSO4, 0.2M NACL, 6% GLYCEROL 0.1M TRIS PH 9.5	Resolution 1.90 Å R-free 0.228
2J9U 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II Deposited 2006-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 110–171（62 aa） Fragment：RESIDUES 110-176	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% ETHANOL, 0.1M KCL, pH 7.40	Resolution 2.00 Å R-free 0.260
2J9U 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II Deposited 2006-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 110–171（62 aa） Fragment：RESIDUES 110-176	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% ETHANOL, 0.1M KCL, pH 7.40	Resolution 2.00 Å R-free 0.260

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

View Construct and Data Evidence

UniProt name	VPS36_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–169； UniProt 396–564

Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region

Saccharomyces cerevisiae

UniProt P47142

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 C； UniProt 1–202 Chain D； UniProt 1–202	Not recorded	appears to be functionally related to SNF7; Snf8p × 1 （Q12483） Defective in vacuolar protein sorting; Vps36p × 1 （Q06696）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1U5T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W7P The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36) Deposited 2004-09-07	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
1XB4 Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II Deposited 2004-08-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–202（202 aa） Chain B 1–202（202 aa）	Not recorded	No recorded non-water small molecule	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
1XB4 Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II Deposited 2004-08-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	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, 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 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS25_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	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	1u5t
Deposition date deposition_date	2004-07-28
Structure title title	Structure of the ESCRT-II endosomal trafficking complex
Keywords keywords	escrt, endosomal, trafficking, protein complex, TRANSPORT PROTEIN; TRANSPORT 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	35.87 Å
Radius of gyration Rg (electron density) rg_electron	35.77 Å
Forward intensity I(0) i0	112398000.00
Molecular weight molecular_weight	86121.0 kDa
Excluded volume excluded_volume	108410 Å³
Envelope volume envelope_volume	151460 Å³
Hydration-shell volume shell_volume	37965 Å³
Envelope diameter envelope_diameter	130.3 Å
Shell Rg shell_rg	38.55 Å
Envelope Rg envelope_rg	36.79 Å
Shape Rg shape_rg	35.77 Å
Total Rg total_rg	35.99 Å
Total atoms total_atoms	6055
Residues n_residues	738
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	126.1 Å
Rg (real space) rg_real	36.08 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	1.1240e+08
I(0) uncertainty (real space) i0_real_error	1.9350e+06
Rg (reciprocal space) rg_reciprocal	35.96 Å
I(0) (reciprocal space) i0_reciprocal	112400000.0000
Solution quality estimate total_estimate	0.8526
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.0 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.230
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15980000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.836; Smooth: 0.867

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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	appears to be functionally related to SNF7; Snf8p
Molecular weight formula_weight	26988.1 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	6055

MKQFGLAAFDELKDGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSLFDRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKVHFRKLNVGLDDLEKSIDMLKSLECFEIFQIRGKKFLRSVPNELTSDQTKILEICSILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPSWITRQL

来源 Source

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 BL21

Entity 2 Entity 2 polymer

Description description	Defective in vacuolar protein sorting; Vps36p
Molecular weight formula_weight	19657.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

LDREKFLNKELFLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIGTGLISPMEMREACERFEHLGLNELKLVKVNKRILCVTSEKFDVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQLSGIYYYKNSYWPS

来源 Source

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 BL21

Entity 3 Entity 3 polymer

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MSALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDNELDSGSTDNDDSKKISKNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTRYFILWKSLDSWASLILQWFEDSGKLNQVITLYELSEGDETVNWEFHRMPESLLYYCLKPLCDRNRATMLKDENDKVIAIKVV

来源 Source

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 BL21

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7. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1u5ta1
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	d1u5ta2
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	d1u5tb1
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	d1u5tb2
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	d1u5tc1
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	d1u5tc2
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	d1u5td1
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	d1u5td2
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 (9 domains)

Domain ID domain_id	1u5tA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	1u5tA02
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	1u5tA03
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	1u5tB01
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	1u5tB02
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	1u5tC01
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	1u5tC02
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	1u5tD01
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	1u5tD02
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 (2)

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Unit-cell length a length_a	150.040 Å
Unit-cell length b length_b	150.040 Å
Unit-cell length c length_c	185.760 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 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2362
R_work r_work	0.2259
R_free r_free	0.2885

fit	/app/data/saxs_computation/u5/1u5t/1u5t.fit
pddf	/app/data/pr_computation/u5/1u5t/1u5t.pr.out
profile	/app/data/saxs_computation/u5/1u5t/1u5t.dat

Structure of the ESCRT-II endosomal trafficking complex

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

appears to be functionally related to SNF7; Snf8p

State in the Current Structure

Other States of the Same Protein in the Database

Defective in vacuolar protein sorting; Vps36p

State in the Current Structure

Other States of the Same Protein in the Database

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 (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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (8 domains)

CATH v4.4 (9 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)