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9bji

Cryo-EM structure of apo NVL

Method: ELECTRON MICROSCOPY Dmax: 144.4 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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain A； UniProt 1–856 Chain B； UniProt 1–856 Chain C； UniProt 1–856 Chain D； UniProt 1–856 Chain E； UniProt 1–856 Chain F； UniProt 1–856 Mutation：E365Q,E682Q Substrate mimic × 1 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

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 9BJI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2X8A Human Nuclear Valosin containing protein Like (NVL), C-terminal AAA- ATPase domain Deposited 2010-03-08 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 574–845（272 aa） Fragment：C-TERMINAL AAA-ATPASE DOMAIN, 574-845
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.250
6RO1 X-ray crystal structure of the MTR4 NVL complex Deposited 2019-05-10 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 × 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
9BJJ Cryo-EM structure of NVL bound the the MM017 inhibitor Deposited 2024-04-25 Different mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 2
Chains and sequence ranges Author chain A； PDBConstruct 1–856； UniProt 1–856 Author chain B； PDBConstruct 1–856； UniProt 1–856 Author chain C； PDBConstruct 1–856； UniProt 1–856 Author chain D； PDBConstruct 1–856； UniProt 1–856 Author chain E； PDBConstruct 1–856； UniProt 1–856 Author chain F； PDBConstruct 1–856； UniProt 1–856

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 9bji

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9bji
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9bji
Deposition date deposition_date2024-04-25
Structure title titleCryo-EM structure of apo NVL
Keywords keywordsRibosome biogenesis, AAA+ ATPase, TRANSLOCASE; TRANSLOCASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.65 Å
Radius of gyration Rg (electron density) rg_electron45.92 Å
Forward intensity I(0) i02052080000.00
Molecular weight molecular_weight369680.0 kDa
Excluded volume excluded_volume460590 ų
Envelope volume envelope_volume641450 ų
Hydration-shell volume shell_volume109040 ų
Envelope diameter envelope_diameter148.7 Å
Shell Rg shell_rg55.71 Å
Envelope Rg envelope_rg45.17 Å
Shape Rg shape_rg45.93 Å
Total Rg total_rg46.22 Å
Total atoms total_atoms25835
Residues n_residues3312
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 dmax144.4 Å
Rg (real space) rg_real46.29 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real2.0520e+09
I(0) uncertainty (real space) i0_real_error3.1920e+07
Rg (reciprocal space) rg_reciprocal46.65 Å
I(0) (reciprocal space) i0_reciprocal2053000000.0000
Solution quality estimate total_estimate0.8895
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary59.5 Å
Skewness Skewness skewness0.086
Kurtosis Kurtosis kurtosis-0.506
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha225000000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.901
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)