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2x8a

Human Nuclear Valosin containing protein Like (NVL), C-terminal AAA- ATPase domain

Method: X-RAY DIFFRACTION Dmax: 65.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NUCLEAR VALOSIN-CONTAINING PROTEIN-LIKE

HOMO SAPIENS

UniProt O15381

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 574–845 Fragment：C-TERMINAL AAA-ATPASE DOMAIN, 574-845 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.60 Å R-free 0.250

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 2X8A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6RO1 X-ray crystal structure of the MTR4 NVL complex Deposited 2019-05-10 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 167–216（50 aa）
Not recorded SO4 SULFATE ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1M Tris/HCl pH 8.0, 1.8M Ammonium Sulphate
Resolution 3.07 Å R-free 0.257
9BJI Cryo-EM structure of apo NVL Deposited 2024-04-25 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 × 7 PDB declaration: heptameric
Chain A 1–856（856 aa）
Chain B 1–856（856 aa）
Chain C 1–856（856 aa）
Chain D 1–856（856 aa）
Chain E 1–856（856 aa）
Chain F 1–856（856 aa）
Mutation：E365Q,E682Q Mutation：E365Q,E682Q Mutation：E365Q,E682Q Mutation：E365Q,E682Q Mutation：E365Q,E682Q Mutation：E365Q,E682Q ATP ADENOSINE-5'-TRIPHOSPHATE × 9 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9BJJ Cryo-EM structure of NVL bound the the MM017 inhibitor Deposited 2024-04-25 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 × 7 PDB declaration: heptameric
Chain A 1–856（856 aa）
Chain B 1–856（856 aa）
Chain C 1–856（856 aa）
Chain D 1–856（856 aa）
Chain E 1–856（856 aa）
Chain F 1–856（856 aa）
Mutation：E365Q, E682Q Mutation：E365Q, E682Q Mutation：E365Q, E682Q Mutation：E365Q, E682Q Mutation：E365Q, E682Q Mutation：E365Q, E682Q ATP ADENOSINE-5'-TRIPHOSPHATE × 9 MG MAGNESIUM ION × 8 A1AP0 N-[10-(2-methoxyethyl)-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiazepin-7-yl]furan-3-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
9NYP Cryo-EM structure of NVL bound the the MM927 inhibitor Deposited 2025-03-28 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 × 7 PDB declaration: heptameric
Chain A 1–856（856 aa）
Chain B 1–856（856 aa）
Chain C 1–856（856 aa）
Chain D 1–856（856 aa）
Chain E 1–856（856 aa）
Chain F 1–856（856 aa）
Mutation：E366Q,E683Q Mutation：E366Q,E683Q Mutation：E366Q,E683Q Mutation：E366Q,E683Q Mutation：E366Q,E683Q Mutation：E366Q,E683Q ATP ADENOSINE-5'-TRIPHOSPHATE × 9 MG MAGNESIUM ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1 A1B7F N-[10-(but-2-yn-1-yl)-3-fluoro-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiazepin-7-yl]-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazole-5-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å

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

View Construct and Data Evidence
UniProt name NVL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–274； UniProt 574–845

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 2x8a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2x8a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2x8a
Deposition date deposition_date2010-03-08
Structure title titleHuman Nuclear Valosin containing protein Like (NVL), C-terminal AAA- ATPase domain
Keywords keywordsNUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.36 Å
Radius of gyration Rg (electron density) rg_electron19.32 Å
Forward intensity I(0) i010769000.00
Molecular weight molecular_weight24485.0 kDa
Excluded volume excluded_volume30725 ų
Envelope volume envelope_volume37245 ų
Hydration-shell volume shell_volume16802 ų
Envelope diameter envelope_diameter67.0 Å
Shell Rg shell_rg24.86 Å
Envelope Rg envelope_rg19.50 Å
Shape Rg shape_rg19.31 Å
Total Rg total_rg20.18 Å
Total atoms total_atoms1715
Residues n_residues237
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 dmax65.7 Å
Rg (real space) rg_real20.35 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real1.0770e+07
I(0) uncertainty (real space) i0_real_error1.5520e+05
Rg (reciprocal space) rg_reciprocal20.36 Å
I(0) (reciprocal space) i0_reciprocal10770000.0000
Solution quality estimate total_estimate0.8196
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.6 Å
Skewness Skewness skewness0.290
Kurtosis Kurtosis kurtosis-0.538
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2217000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2x8aa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2x8aA01
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_id2x8aA02
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)