6e2f

Cryo-EM structure of human TRPV6 in complex with Calmodulin

Method: ELECTRON MICROSCOPY Dmax: 149.0 Å Quality: GOOD

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

Transient receptor potential cation channel subfamily V member 6

Homo sapiens

UniProt Q9H1D0

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 41–765 Chain B; UniProt 41–765 Chain C; UniProt 41–765 Chain D; UniProt 41–765 Not recorded Calmodulin-1 × 1 (P0DP23) CA CALCIUM ION × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE 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.

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRPV6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–725; UniProt 41–765 Author chain B; PDBConstruct 1–725; UniProt 41–765 Author chain C; PDBConstruct 1–725; UniProt 41–765 Author chain D; PDBConstruct 1–725; UniProt 41–765

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 1–149 Not recorded Transient receptor potential cation channel subfamily V member 6 × 4 (Q9H1D0) CA CALCIUM ION × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE 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.

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 2
Chains and sequence ranges Author chain E; 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 6e2f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6e2f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6e2f
Deposition date deposition_date2018-07-11
Structure title titleCryo-EM structure of human TRPV6 in complex with Calmodulin
Keywords keywordsTRPV6, TRP channels, Calcium channels, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier48.04
Radius of gyration Rg (electron density) rg_electron47.08
Forward intensity I(0) i01245030000.00
Molecular weight molecular_weight302070.0 kDa
Excluded volume excluded_volume381810 ų
Envelope volume envelope_volume567300 ų
Hydration-shell volume shell_volume97249 ų
Envelope diameter envelope_diameter151.8
Shell Rg shell_rg54.40
Envelope Rg envelope_rg45.89
Shape Rg shape_rg47.08
Total Rg total_rg47.38
Total atoms total_atoms21204
Residues n_residues2640
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 dmax149.0
Rg (real space) rg_real47.63
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real1.2450e+09
I(0) uncertainty (real space) i0_real_error2.4260e+07
Rg (reciprocal space) rg_reciprocal48.03
I(0) (reciprocal space) i0_reciprocal1246000000.0000
Solution quality estimate total_estimate0.8912
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.030
Kurtosis Kurtosis kurtosis-0.552
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha101400000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6e2fC01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily20 — Ankyrin repeat-containing domain
Domain ID domain_id6e2fD01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily20 — Ankyrin repeat-containing domain
Domain ID domain_id6e2fE01
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)