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- PDB-1iwq: Crystal Structure of MARCKS calmodulin binding domain peptide com... -

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Basic information

Entry
Database: PDB / ID: 1iwq
TitleCrystal Structure of MARCKS calmodulin binding domain peptide complexed with Ca2+/Calmodulin
Components
  • CALMODULIN
  • MARCKS
KeywordsMETAL BINDING PROTEIN/PROTEIN BINDING / calmodulin-target peptide complex / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / METAL BINDING PROTEIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


organelle / Acetylcholine regulates insulin secretion / Acetylcholine regulates insulin secretion / actin crosslink formation / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane ...organelle / Acetylcholine regulates insulin secretion / Acetylcholine regulates insulin secretion / actin crosslink formation / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / germinal vesicle / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of peptidyl-threonine phosphorylation / positive regulation of ryanodine-sensitive calcium-release channel activity / neural tube development / 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 / response to corticosterone / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of ryanodine-sensitive calcium-release channel activity / 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 / actin filament bundle / 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 / positive regulation of protein autophosphorylation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / actin filament bundle assembly / 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 / calcium channel inhibitor activity / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / 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 / voltage-gated potassium channel complex / neurogenesis / regulation of calcium-mediated signaling / 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 / protein kinase C binding / nitric-oxide synthase regulator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to endoplasmic reticulum stress / actin filament organization / adenylate cyclase activator activity
Similarity search - Function
Myristoylated alanine-rich C-kinase substrate MARCKS / MARCKS family / MARCKS family signature 1. / MARCKS family phosphorylation site domain. / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...Myristoylated alanine-rich C-kinase substrate MARCKS / MARCKS family / MARCKS family signature 1. / MARCKS family phosphorylation site domain. / 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
Calmodulin-1 / Myristoylated alanine-rich C-kinase substrate / Myristoylated alanine-rich C-kinase substrate / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYamauchi, E. / Nakatsu, T. / Matsubara, M. / Kato, H. / Taniguchi, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: NAT.STRUCT.BIOL. / Year: 2003
Title: Crystal structure of a MARCKS peptide containing the calmodulin-binding domain in complex with Ca(2+)-calmodulin
Authors: Yamauchi, E. / Nakatsu, T. / Matsubara, M. / Kato, H. / Taniguchi, H.
#1: Journal: FEBS LETT. / Year: 1998
Title: MARCKS, a major protein kinase C substrate, assumes non-helical conformations both in solution and in complex with Ca2+-calmodulin
Authors: Matsubara, M. / Yamauchi, E. / Hayashi, N. / Taniguchi, H.
History
DepositionMay 31, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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_conn.ptnr2_label_seq_id / _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: MARCKS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2166
Polymers19,0552
Non-polymers1604
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-73 kcal/mol
Surface area8240 Å2
MethodPISA
2
A: CALMODULIN
B: MARCKS
hetero molecules

A: CALMODULIN
B: MARCKS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,43112
Polymers38,1104
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area7530 Å2
ΔGint-157 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.229, 40.229, 343.468
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1026-

HOH

21A-1045-

HOH

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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) / Plasmid: pACYC/hCaM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide MARCKS / Myristoylated alanine-rich C-kinase substrate


Mass: 2333.857 Da / Num. of mol.: 1 / Fragment: calmodulin binding domain / Source method: obtained synthetically
Details: This sequence occurs naturally in humans, mouse, rat and bovine.
References: UniProt: P26645, UniProt: P29966*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.1 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, sodium acetate, calcium chrolide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %(w/v)PEG60001reservoir
25 mM1reservoirCaCl2
3100 mMsodium acetate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 19, 2000
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2→200 Å / Num. all: 12467 / Num. obs: 11956 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 31.55 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.27 / Num. unique all: 1149 / % possible all: 98
Reflection
*PLUS
Num. measured all: 91390

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QIV

1qiv


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.425 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.213 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26686 569 4.8 %RANDOM
Rwork0.22308 ---
obs0.22513 11336 96.7 %-
all-11722 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.144 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.37 Å20 Å2
2--0.75 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 4 86 1315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221240
X-RAY DIFFRACTIONr_bond_other_d0.0010.021092
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9581659
X-RAY DIFFRACTIONr_angle_other_deg0.8732552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1013154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45515228
X-RAY DIFFRACTIONr_chiral_restr0.10.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021399
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02251
X-RAY DIFFRACTIONr_nbd_refined0.2620.3393
X-RAY DIFFRACTIONr_nbd_other0.2280.31169
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.575
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.518
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.338
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2991.5772
X-RAY DIFFRACTIONr_mcangle_it2.3121226
X-RAY DIFFRACTIONr_scbond_it3.3843468
X-RAY DIFFRACTIONr_scangle_it5.4974.5433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 44
Rwork0.238 809
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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