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- PDB-1cll: CALMODULIN STRUCTURE REFINED AT 1.7 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1cll
TitleCALMODULIN STRUCTURE REFINED AT 1.7 ANGSTROMS RESOLUTION
ComponentsCALMODULIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


: / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway ...: / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of peptidyl-threonine phosphorylation / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / positive regulation of DNA binding / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / activation of adenylate cyclase activity / Protein methylation / calcium channel inhibitor activity / presynaptic cytosol / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / positive regulation of nitric-oxide synthase activity / titin binding / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / nitric-oxide synthase regulator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / regulation of cytokinesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / spindle microtubule / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / Stimuli-sensing channels / RAF activation / Transcriptional activation of mitochondrial biogenesis
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / 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 ...EF-hand / : / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHANOL / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsChattopadhyaya, R. / Quiocho, F.A.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Calmodulin structure refined at 1.7 A resolution.
Authors: Chattopadhyaya, R. / Meador, W.E. / Means, A.R. / Quiocho, F.A.
#1: Journal: Science / Year: 1992
Title: Target Enzyme Recognition by Calmodulin: 2.4 Angstroms Structure of a Calmodulin-Peptide Complex
Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of Calmodulin Refined at 2.2 Angstroms Resolution
Authors: Babu, Y.S. / Bugg, C.E. / Cook, W.J.
History
DepositionSep 29, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE ANTI-PARALLEL BETA SHEETS ARE EXTREMELY SHORT IN THIS STRUCTURE. THERE IS ADDITIONAL ...SHEET THE ANTI-PARALLEL BETA SHEETS ARE EXTREMELY SHORT IN THIS STRUCTURE. THERE IS ADDITIONAL CONNECTIVITY VIA WATERS BETWEEN THE TWO STRANDS OF EACH SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9286
Polymers16,7211
Non-polymers2065
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.170, 53.600, 25.140
Angle α, β, γ (deg.)93.62, 97.30, 89.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
312 mg/mlprotein1drop
450 mM1dropMgCl2
55 mM1dropCaCl2
650 mMNaOAc1drop
717.5 %(v/v)MPD1drop
87.5 %(v/v)ethanol1drop
935 %MPD1reservoir
1peptide1drop
2calmodulin1drop
1015 %ethanol1reservoir
1150 mMNaOAc1reservoir
1250 mM1reservoirMgCl2
135 mM1reservoirCaCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. all: 46091 / Num. obs: 15417 / Rmerge(I) obs: 0.329 / Biso Wilson estimate: 25 Å2

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Processing

Software
NameClassification
MERLOTphasing
PROLSQrefinement
RefinementResolution: 1.7→10 Å / σ(F): 0.5
Details: CRYSTAL PACKING IS EXTENSIVELY STUDIED IN THE CHATTOPADHYAYA ET AL. PAPER ON CALMODULIN, AND FACILE CRYSTAL GROWTH ALONG THE Z-DIRECTION EXPLAINED. THE AUTHORS ALSO HAVE REPORTED IN DETAIL ...Details: CRYSTAL PACKING IS EXTENSIVELY STUDIED IN THE CHATTOPADHYAYA ET AL. PAPER ON CALMODULIN, AND FACILE CRYSTAL GROWTH ALONG THE Z-DIRECTION EXPLAINED. THE AUTHORS ALSO HAVE REPORTED IN DETAIL ABOUT THE HYDROGEN BONDING WITHIN VARIOUS STRUCTURAL ELEMENTS IN THAT PUBLICATION. HYDRATION IS ALSO DESCRIBED. THESE ARE AREAS WHICH WERE NOT DEALT WITH IN THE BABU ET AL. (1988) PUBLICATION.
RfactorNum. reflection
obs0.216 14469
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 4 142 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it24
X-RAY DIFFRACTIONp_mcangle_it2.55
X-RAY DIFFRACTIONp_scbond_it35
X-RAY DIFFRACTIONp_scangle_it4.26
X-RAY DIFFRACTIONp_plane_restr0.0070.02
X-RAY DIFFRACTIONp_chiral_restr0.1520.15
X-RAY DIFFRACTIONp_singtor_nbd0.1990.5
X-RAY DIFFRACTIONp_multtor_nbd0.3040.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2810.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.63
X-RAY DIFFRACTIONp_staggered_tor21.415
X-RAY DIFFRACTIONp_orthonormal_tor26.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 14469 / σ(F): 0.5 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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