SAXSdb — 9umg

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

Vacuolar transporter chaperone complex subunit 1

Saccharomyces cerevisiae S288C

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 5–122 Chain B； UniProt 21–123 Chain C； UniProt 21–123	Not recorded	Vacuolar transporter chaperone complex subunit 4 × 1 （P47075） Vacuolar transporter chaperone 3 complex subunit 3 × 1 （Q02725） Vacuole transporter chaperone complex subunit 5 × 1 （P38966） 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

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 9UMG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7YTJ Cryo-EM structure of VTC complex Deposited 2022-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 2–129（128 aa） Chain B 2–129（128 aa） Chain C 2–129（128 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 conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–129（129 aa） Chain B 1–129（129 aa） Chain C 1–129（129 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

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

View Construct and Data Evidence

UniProt name	VTC1_YEAST
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 5–122 Author chain B； PDBConstruct 1–103； UniProt 21–123 Author chain C； PDBConstruct 1–103； UniProt 21–123

Vacuolar transporter chaperone complex subunit 4

Saccharomyces cerevisiae S288C

UniProt P47075

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 196–721	Mutation：R264A,R266A,E426A	Vacuolar transporter chaperone complex subunit 1 × 1 （P40046） Vacuolar transporter chaperone complex subunit 1 × 2 （P40046） Vacuolar transporter chaperone 3 complex subunit 3 × 1 （Q02725） Vacuole transporter chaperone complex subunit 5 × 1 （P38966） 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

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 9UMG	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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
3G3U Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate Deposited 2009-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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	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
3G3U Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate Deposited 2009-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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	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
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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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

10 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VTC4_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–526； UniProt 196–721

Vacuolar transporter chaperone 3 complex subunit 3

Saccharomyces cerevisiae S288C

UniProt Q02725

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 203–806	Not recorded	Vacuolar transporter chaperone complex subunit 1 × 1 （P40046） Vacuolar transporter chaperone complex subunit 1 × 2 （P40046） Vacuolar transporter chaperone complex subunit 4 × 1 （P47075） Vacuole transporter chaperone complex subunit 5 × 1 （P38966） 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

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 9UMG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7YTJ Cryo-EM structure of VTC complex Deposited 2022-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–835（835 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 conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–835（835 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

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

View Construct and Data Evidence

UniProt name	VTC3_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–604； UniProt 203–806

Vacuole transporter chaperone complex subunit 5

Saccharomyces cerevisiae S288C

UniProt P38966

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain F； UniProt 760–869	Not recorded	Vacuolar transporter chaperone complex subunit 1 × 1 （P40046） Vacuolar transporter chaperone complex subunit 1 × 2 （P40046） Vacuolar transporter chaperone complex subunit 4 × 1 （P47075） Vacuolar transporter chaperone 3 complex subunit 3 × 1 （Q02725） 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

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	VTC5_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–110； UniProt 760–869

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	9umg
Deposition date deposition_date	2025-04-21
Structure title title	Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)
Keywords keywords	Transporter, Complex, polyP synthesis, Vacuolar membrane, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	43.63 Å
Radius of gyration Rg (electron density) rg_electron	44.44 Å
Forward intensity I(0) i0	259342000.00
Molecular weight molecular_weight	140140.0 kDa
Excluded volume excluded_volume	178890 Å³
Envelope volume envelope_volume	249910 Å³
Hydration-shell volume shell_volume	49049 Å³
Envelope diameter envelope_diameter	156.8 Å
Shell Rg shell_rg	46.20 Å
Envelope Rg envelope_rg	43.85 Å
Shape Rg shape_rg	44.46 Å
Total Rg total_rg	44.43 Å
Total atoms total_atoms	9877
Residues n_residues	1200
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	150.4 Å
Rg (real space) rg_real	44.02 Å
Rg uncertainty (real space) rg_real_error	2.04 Å
I(0) (real space) i0_real	2.5930e+08
I(0) uncertainty (real space) i0_real_error	5.0870e+06
Rg (reciprocal space) rg_reciprocal	43.63 Å
I(0) (reciprocal space) i0_reciprocal	259200000.0000
Solution quality estimate total_estimate	0.7997
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.474
Kurtosis Kurtosis kurtosis	-0.573
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	47300000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.658; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.665; Smooth: 0.753

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Vacuolar transporter chaperone complex subunit 1
Molecular weight formula_weight	13253.8 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	9877

PLLQRTPGKKIALPTRVEPKVFFANERTFLSWLNFTVMLGGLGVGLLNFGDKIGRVSAGLFTFVAMGTMIYALVTYHWRAAAIRRRGSGPYDDRLGPTLLCFFLLVAVIINFILRLKY

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Vacuolar transporter chaperone complex subunit 1
Molecular weight formula_weight	11592.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

VEPKVFFANERTFLSWLNFTVMLGGLGVGLLNFGDKIGRVSAGLFTFVAMGTMIYALVTYHWRAAAIRRRGSGPYDDRLGPTLLCFFLLVAVIINFILRLKYN

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Vacuolar transporter chaperone complex subunit 4
Molecular weight formula_weight	60283.6 kDa
EC 编号 ec_number	2.7.4.1
Mutation mutation	R264A,R266A,E426A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

RQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNENLDLYYGRLRKDEGAEAHALAWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVLNVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQMDVDIRKPPLPTNIEITRPGRSDNEDNDFDEDDEDDAALVAAMTNAPGNSLDIEESVGYGATSAPTSNTNHVVESANAAYYQRKIRNAENPISKKYYEIVAFFDHYFNGDQISKIPKGTTFDTQIRAPPGKTICVPVRVEPKVYFATERTYLSWLSISILLGGVSTTLLTYGSPTAMIGSIGFFITSLAVLIRTVMVYAKRVVNIRLKRAVDYEDKIGPGMVSVFLILSILFSFFCNLVAKL

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Vacuolar transporter chaperone 3 complex subunit 3
Molecular weight formula_weight	69612.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

ASFKSYKFWVHDDNIMEVKARILRHLPALVYASVPNENDDFVDNLESDVRVQPEARLNIGSKSNSLSSDGNSNQDVEIGKSKSVIFPQSYDPTITTLYFDNDFFDLYNNRLLKISGAPTLRLRWIGKLLDKPDIFLEKRTFTENTETGNSSFEEIRLQMKAKFINNFIFKNDPSYKNYLINQLRERGTQKEELEKLSRDFDNIQNFIVEEKLQPVLRATYNRTAFQIPGDQSIRVTIDSNIMYIREDSLDKNRPIRNPENWHRDDIDSNIPNPLRFLRAGEYSKFPYSVMEIKVINQDNSQMPNYEWIKDLTNSHLVNEVPKFSLYLQGVASLFGEDDKYVNILPFWLPDLETDIRKNPQEAYEEEKKTLQKQKSIHDKLDNMRRLSKISVPDGKTTERQGQKDQNTRHVIADLEDHESSDEEGTALPKKSAVKKGKKFKTNAAFLKILAGKNISENGNDPYSDDTDSASSFQLPPGVKKPVHLLKNAGPVKVEAKVWLANERTFNRWLSVTTLLSVLTFSIYNSVQKAEFPQLADLLAYVYFFLTLFCGVWAYRTYLKRLTLIKGRSGKHLDAPVGPILVAVVLIVTLVVNFSVAFKEAARRE

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Vacuole transporter chaperone complex subunit 5
Molecular weight formula_weight	12434.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

SIYEYRHDEVVTFLYLSALLTSCIMASVCLGIVLSLFRGQSNNEIDLEIQNILIAIIIISLLVSLILICACLLLLFSRFTLAPIWHYVGCFTMFFSVTGTVCYGMIEIFF

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Homo sapiens

Entity 6 Entity 6 non-polymer

Description description	INOSITOL HEXAKISPHOSPHATE
Molecular weight formula_weight	660.0 kDa
Source method src_method	syn
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.040 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.04 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	186553

fit	/app/data/saxs_computation/um/9umg/9umg.fit
pddf	/app/data/pr_computation/um/9umg/9umg.pr.out
profile	/app/data/saxs_computation/um/9umg/9umg.dat

Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)

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

Vacuolar transporter chaperone complex subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar transporter chaperone complex subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar transporter chaperone 3 complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Vacuole transporter chaperone complex subunit 5

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

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

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)