6zbi

Ternary complex of Calmodulin bound to 2 molecules of NHE1

Method: SOLUTION NMR Dmax: 69.2 Å Quality: REASONABLE

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

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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 2–149 Not recorded Sodium/hydrogen exchanger 1 × 2 (P19634) CA CALCIUM ION × 4 SOLUTION NMR NMR measurement conditions:pH 7.5;310 K;Ionic strength (raw mmCIF value) 120;Pressure 1 NMR sample composition:0.5 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.15 mM Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 95% H2O/5% D2O | 95% H2O/5% D2O NMR sample composition:1 mM [U-99% 13C; U-99% 15N] Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 0.5 mM Calmodulin, 95% H2O/5% D2O | 95% H2O/5% D2O Resolution not provided

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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–148; UniProt 2–149

Sodium/hydrogen exchanger 1

Homo sapiens

UniProt P19634

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 622–657 Chain C; UniProt 622–657 Not recorded Calmodulin-1 × 1 (P0DP23) CA CALCIUM ION × 4 SOLUTION NMR NMR measurement conditions:pH 7.5;310 K;Ionic strength (raw mmCIF value) 120;Pressure 1 NMR sample composition:0.5 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.15 mM Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 95% H2O/5% D2O | 95% H2O/5% D2O NMR sample composition:1 mM [U-99% 13C; U-99% 15N] Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 0.5 mM Calmodulin, 95% H2O/5% D2O | 95% H2O/5% D2O Resolution not provided

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.

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

View Construct and Data Evidence
UniProt name SL9A1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–36; UniProt 622–657 Author chain C; PDBConstruct 1–36; UniProt 622–657

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 6zbi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6zbi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6zbi
Deposition date deposition_date2020-06-08
Structure title titleTernary complex of Calmodulin bound to 2 molecules of NHE1
Keywords keywordsComplex, NHE1, Calmodulin, Signaling, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier25.82
Radius of gyration Rg (electron density) rg_electron25.61
Forward intensity I(0) i04121220000.00
Molecular weight molecular_weight512810.0 kDa
Excluded volume excluded_volume629420 ų
Envelope volume envelope_volume137450 ų
Hydration-shell volume shell_volume37637 ų
Envelope diameter envelope_diameter117.5
Shell Rg shell_rg37.16
Envelope Rg envelope_rg31.99
Shape Rg shape_rg25.62
Total Rg total_rg25.76
Total atoms total_atoms70740
Residues n_residues4400
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 dmax69.2
Rg (real space) rg_real24.43
Rg uncertainty (real space) rg_real_error0.13
I(0) (real space) i0_real3.9390e+09
I(0) uncertainty (real space) i0_real_error4.6110e+07
Rg (reciprocal space) rg_reciprocal26.01
I(0) (reciprocal space) i0_reciprocal4121000000.0000
Solution quality estimate total_estimate0.6560
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.4
Skewness Skewness skewness0.338
Kurtosis Kurtosis kurtosis-0.808
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha2.5810
Highest regularization parameter α highest_alpha61830000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 0.990; Sysdev: 0.000; Positv: 1.000; Valcen: 0.825; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6zbia_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like

CATH v4.4 (1 domains)

Domain ID domain_id6zbiA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand

8. Citations (1)

9. Files and Curves (10)