SAXSdb — 3g3u

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

Vacuolar transporter chaperone 4

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 189–480	Fragment：UNP residues 189-480	POP PYROPHOSPHATE 2- × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；15 % PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, 10 % Jeffamine M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.07 Å R-free 0.241
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 189–480	Fragment：UNP residues 189-480	POP PYROPHOSPHATE 2- × 1 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；15 % PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, 10 % Jeffamine M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.07 Å R-free 0.241

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 3G3U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3G3Q Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer Deposited 2009-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 189–480（292 aa） Fragment：UNP residues 189-480	Not recorded	PO4 PHOSPHATE ION × 14 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；22% PEG 3350, 0.15 M (NH4)2SO4, 0.1 M Bis-Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.64 Å R-free 0.250
3G3Q Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer Deposited 2009-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 189–480（292 aa） Fragment：UNP residues 189-480	Not recorded	PO4 PHOSPHATE ION × 15 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；22% PEG 3350, 0.15 M (NH4)2SO4, 0.1 M Bis-Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.64 Å R-free 0.250
3G3Q Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer Deposited 2009-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 189–480（292 aa） Fragment：UNP residues 189-480 Chain B 189–480（292 aa） Fragment：UNP residues 189-480	Not recorded	PO4 PHOSPHATE ION × 29 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；22% PEG 3350, 0.15 M (NH4)2SO4, 0.1 M Bis-Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.64 Å R-free 0.250
3G3R Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+ Deposited 2009-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 189–480（292 aa） Fragment：UNP residues 189-480	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；15% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, 10% Jeffamine M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.253
3G3R Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+ Deposited 2009-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 189–480（292 aa） Fragment：UNP residues 189-480	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；15% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, 10% Jeffamine M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.253
3G3T Crystal structure of a eukaryotic polyphosphate polymerase in complex with orthophosphate Deposited 2009-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 189–480（292 aa） Fragment：UNP residues 189-480	Not recorded	PO4 PHOSPHATE ION × 4 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；1 M Na+/K+ phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.85 Å R-free 0.235
5IIG Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form A). Deposited 2016-03-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–480（479 aa） Fragment：SPX domain, UNP residues 2-480	Mutation：E426N	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES, 1.5M Li2SO4	Resolution 2.99 Å R-free 0.273
5IIQ Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B). Deposited 2016-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–480（479 aa） Fragment：SPX domain- TTM domain, UNP residues 2-480	Not recorded	SO4 SULFATE ION × 3 POP PYROPHOSPHATE 2- × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES, 1.5M AmSO4, 4% PEG 1000	Resolution 3.03 Å R-free 0.262
5IIT Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–178（178 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG 3350, 0.1M AmSO4, 0.1M MES	Resolution 2.13 Å R-free 0.247
5IIT Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–178（178 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG 3350, 0.1M AmSO4, 0.1M MES	Resolution 2.13 Å R-free 0.247
5IIT Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–178（178 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG 3350, 0.1M AmSO4, 0.1M MES	Resolution 2.13 Å R-free 0.247
5IIT Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–178（178 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG 3350, 0.1M AmSO4, 0.1M MES	Resolution 2.13 Å R-free 0.247
5LNC Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–178（178 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8.75% PEG 6000, 2.75M NaCl	Resolution 3.29 Å R-free 0.302
5LNC Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1 Deposited 2016-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–178（178 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8.75% PEG 6000, 2.75M NaCl	Resolution 3.29 Å R-free 0.302
7YTJ Cryo-EM structure of VTC complex Deposited 2022-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 2–721（720 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 3 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8I6V Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1) Deposited 2023-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–721（721 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 PO4 PHOSPHATE ION × 3 3PO TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.06 Å
9UMG Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1) Deposited 2025-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 196–721（526 aa）	Mutation：R264A,R266A,E426A	IHP INOSITOL HEXAKISPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；150mM NaCl, 25mM Tris-HCL, 0.0002m/v GDN, 1mM IP6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VTC4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–295； UniProt 189–480 Author chain B； PDBConstruct 4–295； UniProt 189–480

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	3g3u
Deposition date deposition_date	2009-02-02
Structure title title	Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate
Keywords keywords	;polyphosphate polymerase, polyphosphate kinase, VTC complex, vacuolar transporter chaperone, tunnel enzyme, Membrane, Phosphoprotein, Transmembrane, Vacuole, BIOSYNTHETIC PROTEIN ;; BIOSYNTHETIC 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	28.44 Å
Radius of gyration Rg (electron density) rg_electron	27.51 Å
Forward intensity I(0) i0	77575800.00
Molecular weight molecular_weight	67841.0 kDa
Excluded volume excluded_volume	84583 Å³
Envelope volume envelope_volume	109410 Å³
Hydration-shell volume shell_volume	33371 Å³
Envelope diameter envelope_diameter	90.1 Å
Shell Rg shell_rg	34.64 Å
Envelope Rg envelope_rg	26.93 Å
Shape Rg shape_rg	27.53 Å
Total Rg total_rg	28.21 Å
Total atoms total_atoms	4773
Residues n_residues	571
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	88.7 Å
Rg (real space) rg_real	28.37 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	7.7580e+07
I(0) uncertainty (real space) i0_real_error	1.1020e+06
Rg (reciprocal space) rg_reciprocal	28.40 Å
I(0) (reciprocal space) i0_reciprocal	77580000.0000
Solution quality estimate total_estimate	0.9031
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.252
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17090000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.891

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Vacuolar transporter chaperone 4
Molecular weight formula_weight	34773.8 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	5183

GAMGKQQNFVRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQ

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

Entity 2 Entity 2 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	3

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	8

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	380

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3g3uA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	30 — VTC, catalytic tunnel domain

Domain ID domain_id	3g3uB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	30 — VTC, catalytic tunnel domain

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8. Citations (1)

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Unit-cell length a length_a	68.440 Å
Unit-cell length b length_b	100.730 Å
Unit-cell length c length_c	102.490 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.070 Å
Low-resolution limit resolution_low	19.768 Å
R factor r_factor	0.2010
R_work r_work	0.1988
R_free r_free	0.2412

fit	/app/data/saxs_computation/g3/3g3u/3g3u.fit
pddf	/app/data/pr_computation/g3/3g3u/3g3u.pr.out
profile	/app/data/saxs_computation/g3/3g3u/3g3u.dat

Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate

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

Vacuolar transporter chaperone 4

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