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5vc7

VCP like ATPase from T. acidophilum (VAT) - conformation 1

Method: ELECTRON MICROSCOPY Dmax: 138.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

VCP-like ATPase

Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)

UniProt O05209

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 183–745 Chain C； UniProt 183–745 Chain D； UniProt 183–745 Chain E； UniProt 183–745 Chain F； UniProt 183–745 Chain G； UniProt 183–745 Fragment：UNP residues 183-745 ATP ADENOSINE-5'-TRIPHOSPHATE × 12 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE；Blot for 4 seconds before plunging Resolution 3.90 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 5VC7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CZ4 NMR STRUCTURE OF VAT-N: THE N-TERMINAL DOMAIN OF VAT (VCP-LIKE ATPASE OF THERMOPLASMA) Deposited 1999-09-01 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 1–183（183 aa） Fragment：N-TERMINAL DOMAIN: M1 TO E183 FOLLOWED BY A DIGLYCINE SPACER
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.9；320 K；Ionic strength (raw mmCIF value) 80 mM；Pressure AMBIENT
NMR measurement conditions pH 5.9；320 K；Ionic strength (raw mmCIF value) 80 mM；Pressure AMBIENT
NMR sample composition 1.4 MM VAT-NU-15N,13C; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O
NMR sample composition 1.2 MM VAT-N U-15N; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O
Resolution not provided
1CZ5 NMR STRUCTURE OF VAT-N: THE N-TERMINAL DOMAIN OF VAT (VCP-LIKE ATPASE OF THERMOPLASMA) Deposited 1999-09-01 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 1–183（183 aa） Fragment：N-TERMINAL DOMAIN: M1 TO E183 FOLLOWED BY A DIGLYCINE SPACER
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.9；320 K；Ionic strength (raw mmCIF value) 80 mM；Pressure AMBIENT
NMR measurement conditions pH 5.9；320 K；Ionic strength (raw mmCIF value) 80 mM；Pressure AMBIENT
NMR sample composition 1.4 MM VAT-N U-15N,13C; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O
NMR sample composition 1.2 MM VAT-N U-15N; 40 MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O
Resolution not provided
5G4F Structure of the ADP-bound VAT complex Deposited 2016-05-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–726（726 aa）
Chain B 1–726（726 aa）
Chain C 1–726（726 aa）
Chain D 1–726（726 aa）
Chain E 1–726（726 aa）
Chain P 1–726（726 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 MM HEPES, 100 MM NACL, 5MM ADP；pH 7.5；50 MM HEPES, 100 MM NACL, 5MM ADP
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 4 SECONDS BEFORE PLUNGING, DETAILS- SAMPLE HELD AT 4 DEGREES CELSIUS BEFORE FREEZING
Resolution 7.00 Å
5G4G Structure of the ATPgS-bound VAT complex Deposited 2016-05-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 6–726（721 aa）
Chain B 6–726（721 aa）
Chain C 6–726（721 aa）
Chain D 6–726（721 aa）
Chain E 6–726（721 aa）
Chain F 6–726（721 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 MM HEPES, 100 MM NACL, 5MM ATPGS；pH 7.5；50 MM HEPES, 100 MM NACL, 5MM ATPGS
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT FOR 4 SECONDS BEFORE PLUNGING,
Resolution 7.80 Å
5VCA VCP like ATPase from T. acidophilum (VAT)-Substrate bound conformation Deposited 2017-03-31 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain M 183–745（563 aa） Fragment：UNP residues 183-745
Chain N 183–745（563 aa） Fragment：UNP residues 183-745
Chain O 183–745（563 aa） Fragment：UNP residues 183-745
Chain P 183–745（563 aa） Fragment：UNP residues 183-745
Chain Q 183–745（563 aa） Fragment：UNP residues 183-745
Chain R 183–745（563 aa） Fragment：UNP residues 183-745
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot for 4 seconds before plunging
Resolution 4.80 Å
7DBO DPBB domain of VCP-like ATPase from Thermoplasma acidophilum Deposited 2020-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–91（91 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM citrate / phosphate pH5.0, 1.4M Ammonium sulfate
Resolution 1.90 Å R-free 0.264
7DBO DPBB domain of VCP-like ATPase from Thermoplasma acidophilum Deposited 2020-10-21 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 1–91（91 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM citrate / phosphate pH5.0, 1.4M Ammonium sulfate
Resolution 1.90 Å R-free 0.264

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VAT_THEAC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–564； UniProt 183–745 Author chain C； PDBConstruct 2–564； UniProt 183–745 Author chain D； PDBConstruct 2–564； UniProt 183–745 Author chain E； PDBConstruct 2–564； UniProt 183–745 Author chain F； PDBConstruct 2–564； UniProt 183–745 Author chain G； PDBConstruct 2–564； UniProt 183–745

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

SAXS profile for 5vc7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5vc7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5vc7
Deposition date deposition_date2017-03-31
Structure title titleVCP like ATPase from T. acidophilum (VAT) - conformation 1
Keywords keywordsAAA+, ATPase, unfoldase, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.14 Å
Radius of gyration Rg (electron density) rg_electron45.14 Å
Forward intensity I(0) i01587700000.00
Molecular weight molecular_weight330660.0 kDa
Excluded volume excluded_volume413810 ų
Envelope volume envelope_volume601610 ų
Hydration-shell volume shell_volume104700 ų
Envelope diameter envelope_diameter141.8 Å
Shell Rg shell_rg55.04 Å
Envelope Rg envelope_rg43.88 Å
Shape Rg shape_rg45.18 Å
Total Rg total_rg45.38 Å
Total atoms total_atoms23442
Residues n_residues3264
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax138.4 Å
Rg (real space) rg_real45.74 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real1.5880e+09
I(0) uncertainty (real space) i0_real_error2.5610e+07
Rg (reciprocal space) rg_reciprocal46.14 Å
I(0) (reciprocal space) i0_reciprocal1588000000.0000
Solution quality estimate total_estimate0.8911
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary61.1 Å
Skewness Skewness skewness0.012
Kurtosis Kurtosis kurtosis-0.546
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha277600000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.861
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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) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id5vc7A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7A03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7A04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7C03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7C04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7D03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7D04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7E01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7E02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7E03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7E04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7F01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7F02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7F03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7F04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7G01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7G02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5vc7G03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5vc7G04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
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8. Citations (1)

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9. Files and Curves (10)