SAXSdb — 2cay

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

VACUOLAR PROTEIN SORTING PROTEIN 36

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–99 Chain A； UniProt 252–289 Chain B； UniProt 1–99 Chain B； UniProt 252–289	Fragment：PH DOMAIN, RESIDUES 1-99 AND 252-289	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

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 2CAY	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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 396–564（169 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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
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 mutation/modification 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 mutation/modification 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–107； UniProt 1–99 Author chain A； PDBConstruct 108–145； UniProt 252–289 Author chain B； PDBConstruct 9–107； UniProt 1–99 Author chain B； PDBConstruct 108–145； UniProt 252–289

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	2cay
Deposition date deposition_date	2005-12-23
Structure title title	Vps36 N-terminal PH domain
Keywords keywords	;TRANSPORT, VPS36, PH DOMAIN, ESCRT-II, LIPID-BINDING, MULTIVESICULAR BODIES, MEMBRANE, METAL-BINDING, PROTEIN TRANSPORT, ZINC, ZINC-FINGER ;; TRANSPORT
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	21.79 Å
Radius of gyration Rg (electron density) rg_electron	20.86 Å
Forward intensity I(0) i0	16396200.00
Molecular weight molecular_weight	30494.0 kDa
Excluded volume excluded_volume	38160 Å³
Envelope volume envelope_volume	45714 Å³
Hydration-shell volume shell_volume	19094 Å³
Envelope diameter envelope_diameter	77.6 Å
Shell Rg shell_rg	26.32 Å
Envelope Rg envelope_rg	21.02 Å
Shape Rg shape_rg	20.81 Å
Total Rg total_rg	21.80 Å
Total atoms total_atoms	2155
Residues n_residues	262
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	74.1 Å
Rg (real space) rg_real	21.87 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.6400e+07
I(0) uncertainty (real space) i0_real_error	2.2950e+05
Rg (reciprocal space) rg_reciprocal	21.85 Å
I(0) (reciprocal space) i0_reciprocal	16400000.0000
Solution quality estimate total_estimate	0.8620
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.440
Kurtosis Kurtosis kurtosis	-0.296
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2414000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.933

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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	VACUOLAR PROTEIN SORTING PROTEIN 36
Molecular weight formula_weight	16893.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2331

MAHHHHHHMEYWHYVETTSSGQPLLREGEKDIFIDQSVGLYHGKSKILQRQRGRIFLTSQRIIYIDDAKPTQNSLGLELDDLAYVNYSSGFLTRSPRLILFFKDPSSSTEFVQLSFRKSDGVLFSQATERALENILTEKNKHIFN

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(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2caya1
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.12 — VPS36 N-terminal domain-like

Domain ID domain_id	d2caya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2cayb1
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.12 — VPS36 N-terminal domain-like

Domain ID domain_id	d2cayb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2cayA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	2cayB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	94.451 Å
Unit-cell length b length_b	88.375 Å
Unit-cell length c length_c	45.888 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	44.190 Å
R factor r_factor	0.1930
R_work r_work	0.1910
R_free r_free	0.2280

fit	/app/data/saxs_computation/ca/2cay/2cay.fit
pddf	/app/data/pr_computation/ca/2cay/2cay.pr.out
profile	/app/data/saxs_computation/ca/2cay/2cay.dat

Vps36 N-terminal PH domain

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

VACUOLAR PROTEIN SORTING PROTEIN 36

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