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- PDB-6dah: 2.5 Angstrom crystal structure of the N97S CaM mutant -

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Basic information

Entry
Database: PDB / ID: 6dah
Title2.5 Angstrom crystal structure of the N97S CaM mutant
ComponentsCalmodulin-1
KeywordsCALCIUM BINDING PROTEIN / calmodulin / mutant
Function / homology
Function and homology information


CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation ...CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / 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 / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / 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 / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway
Similarity search - Function
EF-hand domain pair / 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 / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsWang, K. / Van Petegem, F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Arrhythmia mutations in calmodulin cause conformational changes that affect interactions with the cardiac voltage-gated calcium channel.
Authors: Wang, K. / Holt, C. / Lu, J. / Brohus, M. / Larsen, K.T. / Overgaard, M.T. / Wimmer, R. / Van Petegem, F.
History
DepositionMay 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
B: Calmodulin-1
C: Calmodulin-1
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,72420
Polymers68,0834
Non-polymers64116
Water61334
1
A: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1815
Polymers17,0211
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1815
Polymers17,0211
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1815
Polymers17,0211
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1815
Polymers17,0211
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.117, 94.414, 60.977
Angle α, β, γ (deg.)90.000, 94.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Calmodulin-1 /


Mass: 17020.719 Da / Num. of mol.: 4 / Mutation: N97S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG3350, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→47.207 Å / Num. obs: 43340 / % possible obs: 95.4 % / Redundancy: 1.81 % / Biso Wilson estimate: 44.56 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.057 / Net I/σ(I): 14.23
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.5-2.652.4369110.8450.424193.6
2.65-2.841
2.84-3.061
3.06-3.351
3.35-3.751
3.75-4.321
4.32-5.281
5.28-7.431
7.43-47.2071

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CLL

1cll


Resolution: 2.502→47.207 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.2 / Phase error: 31.8
RfactorNum. reflection% reflection
Rfree0.279 2159 4.98 %
Rwork0.2181 --
obs0.2212 43334 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.09 Å2 / Biso mean: 56.8088 Å2 / Biso min: 22.07 Å2
Refinement stepCycle: final / Resolution: 2.502→47.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 16 34 4288
Biso mean--54.09 46.93 -
Num. residues----579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5016-2.55980.3631410.28392636277791
2.5598-2.62380.30931390.27182726286595
2.6238-2.69480.34061470.25712761290896
2.6948-2.77410.26841470.25392776292396
2.7741-2.86360.30471490.24582739288896
2.8636-2.96590.34091440.26132778292296
2.9659-3.08470.35671440.26222733287795
3.0847-3.2250.36091390.2552702284194
3.225-3.3950.36361500.23542801295197
3.395-3.60760.29891400.22432765290596
3.6076-3.88610.27011500.19922789293997
3.8861-4.27690.29181400.17982749288995
4.2769-4.89520.23241460.17532777292397
4.8952-6.16530.26251380.23562709284794
6.1653-47.21540.1931450.1922734287995
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)
12.01781.9585-0.08086.44951.73833.35070.038-0.0878-0.05040.11840.19890.173-0.05410.2989-0.25280.21120.0314-0.0020.29410.0420.309914.5128-27.41763.068
25.4652-0.4062-2.91883.1540.54645.7427-0.0375-0.45720.95250.22420.3865-0.4634-0.11760.2406-0.3320.37580.0627-0.06650.3952-0.12410.4928-22.1597-28.179914.9468
35.06331.028-0.91947.82810.3483.01520.0526-0.0850.2303-0.0047-0.0004-0.6939-0.36-0.2048-0.06490.29010.0436-0.00370.41290.00930.352811.3493-19.573531.6302
47.17090.8132-3.3864.82630.18174.88990.0174-0.21071.11870.45920.60371.2041-0.0917-0.0436-0.57530.39550.06920.07720.61050.08760.7296-24.6542-22.551143.0968
52.284-0.31291.01411.7818-1.46541.74840.1552-0.1144-0.43650.1168-0.3257-0.69920.28540.32550.20870.44390.0052-0.02270.37460.06250.669654.27595.8394.5662
62.98271.7692-1.33455.8991-2.35074.9125-0.2150.17870.2419-0.42330.22580.60410.4774-0.3899-0.03860.3498-0.04530.01070.27070.01140.392519.99450.1313-6.1178
74.0351-0.53131.16833.8577-0.09732.48850.0990.2611-0.74590.0334-0.03920.11760.11720.3204-0.06070.31970.0594-0.00980.41190.00890.342853.81857.589731.1353
83.51191.06932.10772.575-1.75694.1124-0.0687-0.0632-0.4886-0.1840.2667-0.21190.6241-0.4903-0.19310.3649-0.08670.10760.3863-0.10790.382118.27953.932920.5369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid -2 through 78 ) or (resid 501 through 502))A0
2X-RAY DIFFRACTION2chain 'A' and ((resid 79 through 145 ) or (resid 503 through 504))A0
3X-RAY DIFFRACTION3chain 'B' and ((resid 12 through 78 ) or (resid 501 through 502))B0
4X-RAY DIFFRACTION4chain 'B' and ((resid 79 through 146 ) or (resid 503 through 504))B0
5X-RAY DIFFRACTION5chain 'C' and ((resid -2 through 78 ) or (resid 501 through 502))C0
6X-RAY DIFFRACTION6chain 'C' and ((resid 79 through 146 ) or (resid 503 through 504))C0
7X-RAY DIFFRACTION7chain 'D' and ((resid -2 through 78 ) or (resid 501 through 502))D0
8X-RAY DIFFRACTION8chain 'D' and ((resid 79 through 144 ) or (resid 503 through 504))D0

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