9nvp

Structure of Nanchung-Inactive-Calmodulin in complex with Nicotinamide, EDTA

Method: ELECTRON MICROSCOPY Dmax: 149.8 Å Quality: GOOD

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

Inactive

Halyomorpha halys

UniProt A0A9P0HI19

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 11–902 Chain D; UniProt 11–902 Not recorded Nanchung × 2 Calmodulin-1 × 2 (P0DP23) 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 14 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 6 NCA NICOTINAMIDE × 2 D39 (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.85 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.

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

View Construct and Data Evidence
UniProt name A0A9P0HI19_NEZVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 93–984; UniProt 11–902 Author chain D; PDBConstruct 93–984; UniProt 11–902

Inactive

Halyomorpha halys

UniProt A0A9P0MRC5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 78–139 Chain D; UniProt 78–139 Not recorded Nanchung × 2 Calmodulin-1 × 2 (P0DP23) 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 14 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 6 NCA NICOTINAMIDE × 2 D39 (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.85 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.

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

View Construct and Data Evidence
UniProt name A0A9P0MRC5_NEZVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 31–92; UniProt 78–139 Author chain D; PDBConstruct 31–92; UniProt 78–139

Calmodulin-1

Homo sapiens

UniProt P0DP23

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 1–149 Chain F; UniProt 1–149 Not recorded Inactive × 2 (A0A9P0MRC5,A0A9P0HI19) Nanchung × 2 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 14 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 6 NCA NICOTINAMIDE × 2 D39 (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.85 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.

213 other PDB entries and 279 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–149; UniProt 1–149 Author chain F; PDBConstruct 1–149; UniProt 1–149

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 9nvp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9nvp
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id9nvp
Deposition date deposition_date2025-03-21
Structure title titleStructure of Nanchung-Inactive-Calmodulin in complex with Nicotinamide, EDTA
Keywords keywordsMembrane protein, membrane channel, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier50.56
Radius of gyration Rg (electron density) rg_electron49.65
Forward intensity I(0) i01609510000.00
Molecular weight molecular_weight351130.0 kDa
Excluded volume excluded_volume445780 ų
Envelope volume envelope_volume669490 ų
Hydration-shell volume shell_volume108380 ų
Envelope diameter envelope_diameter152.5
Shell Rg shell_rg57.89
Envelope Rg envelope_rg47.55
Shape Rg shape_rg49.68
Total Rg total_rg49.81
Total atoms total_atoms48920
Residues n_residues3052
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax149.8
Rg (real space) rg_real50.25
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real1.6100e+09
I(0) uncertainty (real space) i0_real_error2.8800e+07
Rg (reciprocal space) rg_reciprocal50.81
I(0) (reciprocal space) i0_reciprocal1611000000.0000
Solution quality estimate total_estimate0.8774
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary67.7
Skewness Skewness skewness-0.049
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha108200000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.665

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)