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- PDB-6hcs: Crystal structure of CaM-peptide complex containing AzF at positi... -

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Basic information

Entry
Database: PDB / ID: 6hcs
TitleCrystal structure of CaM-peptide complex containing AzF at position 108
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit beta
  • Calmodulin-1
KeywordsPROTEIN BINDING / calmodulin / unnatural amino acid / AzF
Function / homology
Function and homology information


regulation of synaptic transmission, cholinergic / activation of meiosis involved in egg activation / HSF1-dependent transactivation / cell projection morphogenesis / RAF activation / Ion transport by P-type ATPases / hippocampal neuron apoptotic process / calcium- and calmodulin-dependent protein kinase complex / cellular response to homocysteine / positive regulation of synapse maturation ...regulation of synaptic transmission, cholinergic / activation of meiosis involved in egg activation / HSF1-dependent transactivation / cell projection morphogenesis / RAF activation / Ion transport by P-type ATPases / hippocampal neuron apoptotic process / calcium- and calmodulin-dependent protein kinase complex / cellular response to homocysteine / positive regulation of synapse maturation / Interferon gamma signaling / Ca2+/calmodulin-dependent protein kinase / regulation of neuron migration / positive regulation of dendritic spine morphogenesis / structural constituent of postsynaptic actin cytoskeleton / Trafficking of AMPA receptors / regulation of synapse maturation / calcium/calmodulin-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / RAF/MAP kinase cascade / 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 / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / Ion homeostasis / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / response to psychosocial stress / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / calcineurin-mediated signaling / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / phospholipase binding / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of neuronal synaptic plasticity / neuromuscular process controlling balance / Long-term potentiation / protein phosphatase activator activity / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / Unblocking of NMDA receptors, glutamate binding and activation / detection of calcium ion / regulation of cardiac muscle contraction / spindle midzone / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of protein localization to plasma membrane / Protein methylation / response to cadmium ion / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / voltage-gated potassium channel complex / sarcoplasmic reticulum membrane / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / positive regulation of apoptotic signaling pathway
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / : / 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 ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / : / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Calcium/calmodulin-dependent protein kinase type II subunit beta / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCreon, A. / Josts, I. / Tidow, H.
CitationJournal: Struct Dyn / Year: 2018
Title: Conformation-specific detection of calmodulin binding using the unnatural amino acid p-azido-phenylalanine (AzF) as an IR-sensor.
Authors: Creon, A. / Josts, I. / Niebling, S. / Huse, N. / Tidow, H.
History
DepositionAug 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 17, 2024Group: 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
C: Calmodulin-1
D: Calcium/calmodulin-dependent protein kinase type II subunit beta
E: Calmodulin-1
F: Calcium/calmodulin-dependent protein kinase type II subunit beta
G: Calmodulin-1
H: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,24724
Polymers87,6068
Non-polymers64116
Water4,378243
1
A: Calmodulin-1
B: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0626
Polymers21,9012
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-75 kcal/mol
Surface area8300 Å2
MethodPISA
2
C: Calmodulin-1
D: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0626
Polymers21,9012
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-81 kcal/mol
Surface area8540 Å2
MethodPISA
3
E: Calmodulin-1
F: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0626
Polymers21,9012
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-54 kcal/mol
Surface area8600 Å2
MethodPISA
4
G: Calmodulin-1
H: Calcium/calmodulin-dependent protein kinase type II subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0626
Polymers21,9012
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-66 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.263, 37.214, 121.193
Angle α, β, γ (deg.)90.00, 100.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Calmodulin-1


Mass: 19014.879 Da / Num. of mol.: 4
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: Protein/peptide
Calcium/calmodulin-dependent protein kinase type II subunit beta / CaMK-II subunit beta


Mass: 2886.528 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
References: UniProt: P08413, Ca2+/calmodulin-dependent protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 % sol: 36.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 6000, lithium chloride, sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.917143 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917143 Å / Relative weight: 1
ReflectionResolution: 2→43.12 Å / Num. obs: 45156 / % possible obs: 97.59 % / Redundancy: 3.3 % / Net I/σ(I): 13.62
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CDM

1cdm


Resolution: 2→43.119 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.59
RfactorNum. reflection% reflection
Rfree0.2944 2256 5.01 %
Rwork0.2602 --
obs0.2619 45027 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 16 243 5239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075031
X-RAY DIFFRACTIONf_angle_d0.8596711
X-RAY DIFFRACTIONf_dihedral_angle_d35.1481892
X-RAY DIFFRACTIONf_chiral_restr0.046744
X-RAY DIFFRACTIONf_plane_restr0.004893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.34881530.31732680X-RAY DIFFRACTION99
2.0435-2.0910.34281400.30472707X-RAY DIFFRACTION99
2.091-2.14330.30661380.29662654X-RAY DIFFRACTION99
2.1433-2.20130.28951210.27932725X-RAY DIFFRACTION99
2.2013-2.2660.31051480.27512638X-RAY DIFFRACTION98
2.266-2.33920.31591430.2692670X-RAY DIFFRACTION98
2.3392-2.42280.33521340.27022667X-RAY DIFFRACTION98
2.4228-2.51980.3041480.26652647X-RAY DIFFRACTION97
2.5198-2.63440.2851470.26072645X-RAY DIFFRACTION97
2.6344-2.77330.30431340.26152667X-RAY DIFFRACTION99
2.7733-2.9470.31261410.27922716X-RAY DIFFRACTION99
2.947-3.17450.32731470.27082673X-RAY DIFFRACTION98
3.1745-3.49380.30921480.2542599X-RAY DIFFRACTION95
3.4938-3.99910.25031250.24472640X-RAY DIFFRACTION95
3.9991-5.03720.26391600.23542672X-RAY DIFFRACTION96
5.0372-43.12890.28491290.24972771X-RAY DIFFRACTION95

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