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- PDB-3sui: Crystal structure of ca2+-calmodulin in complex with a trpv1 c-te... -

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Basic information

Entry
Database: PDB / ID: 3sui
TitleCrystal structure of ca2+-calmodulin in complex with a trpv1 c-terminal peptide
Components
  • Calmodulin
  • Transient receptor potential cation channel subfamily V member 1TRPV1
KeywordsCALCIUM-BINDING PROTEIN / CALMODULIN / CALCIUM-CALMODULIN / TRPV1 / TRPV1 C-TERMINUS / CALMODULIN COMPLEX / THERMOSENSOR / TRP CHANNEL / EF HANDS / 1-10 MOTIF / CALCIUM CHANNEL / CALMODULIN-BINDING / ION CHANNEL / CALCIUM BINDING PROTEIN
Function / homology
Function and homology information


temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / : / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus ...temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / : / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / establishment of protein localization to mitochondrial membrane / TRP channels / cellular response to acidic pH / thermoception / fever generation / type 3 metabotropic glutamate receptor binding / detection of temperature stimulus involved in thermoception / glutamate secretion / dendritic spine membrane / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / response to pH / CaM pathway / monoatomic cation transmembrane transporter activity / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / regulation of synaptic vesicle endocytosis / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / cellular response to ATP / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / response to pain / Glycogen breakdown (glycogenolysis) / temperature homeostasis / negative regulation of heart rate / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / cellular response to alkaloid / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / behavioral response to pain / Synthesis of IP3 and IP4 in the cytosol / diet induced thermogenesis / nitric-oxide synthase binding / Phase 0 - rapid depolarisation / extracellular ligand-gated monoatomic ion channel activity / protein phosphatase activator activity / intracellularly gated calcium channel activity / RHO GTPases activate PAKs / cellular response to cytokine stimulus / negative regulation of mitochondrial membrane potential / detection of temperature stimulus involved in sensory perception of pain / calcium ion import across plasma membrane / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / ligand-gated monoatomic ion channel activity / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 1 / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLau, S.-Y. / Gaudet, R.
CitationJournal: J.Gen.Physiol. / Year: 2012
Title: Distinct properties of Ca2+-calmodulin binding to N- and C-terminal regulatory regions of the TRPV1 channel.
Authors: Lau, S.Y. / Procko, E. / Gaudet, R.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Transient receptor potential cation channel subfamily V member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1907
Polymers20,9332
Non-polymers2565
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-24 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.681, 41.681, 341.533
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Calmodulin / / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM, CALM1, CALM2, CALM3, CALML2, CAM, CAM1, CAM2, CAM3, CAMB, CAMC, CAMIII
Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Transient receptor potential cation channel subfamily V member 1 / TRPV1 / TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1 / Vanilloid ...TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1 / Vanilloid receptor type 1-like


Mass: 4080.678 Da / Num. of mol.: 1 / Fragment: Unp residues 767-801
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv1, Vr1, Vr1l / Plasmid: pMALC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O35433
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES PH6.0, 2.2-2.8M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 13912 / Num. obs: 13862 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.2
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.469 / % possible all: 91.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DVE

3dve


Resolution: 1.95→36.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.173 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24837 690 5 %RANDOM
Rwork0.19175 ---
obs0.19437 13172 98.67 %-
all-13912 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 9 91 1368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221372
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.961866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7075182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92626.29681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44715256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.427158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021077
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9721.5830
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72821341
X-RAY DIFFRACTIONr_scbond_it2.5253542
X-RAY DIFFRACTIONr_scangle_it4.1414.5513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 47 -
Rwork0.257 885 -
obs--93.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3932-1.11521.26553.213-1.83765.96370.11250.13-0.0104-0.223-0.0082-0.02180.208-0.2905-0.10430.31920.00090.02720.1938-0.00850.0356-5.942-25.899-17.752
23.2946-1.8878-0.46183.73920.00662.61750.00130.1104-0.0225-0.1786-0.0292-0.15910.11660.08330.02790.3531-0.01160.00950.17270.00790.0478-12.415-9.658-6.211
311.45380.7982-1.64330.86310.539313.1870.1270.276-0.1402-0.8867-0.25840.2787-0.0152-0.27640.13140.31920.03180.02430.2687-0.07020.0575-11.329-17.979-12.683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 80
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION2A81 - 148
4X-RAY DIFFRACTION2A503 - 504
5X-RAY DIFFRACTION3B784 - 798

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