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- PDB-2hqw: Crystal Structure of Ca2+/Calmodulin bound to NMDA Receptor NR1C1... -

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Basic information

Entry
Database: PDB / ID: 2hqw
TitleCrystal Structure of Ca2+/Calmodulin bound to NMDA Receptor NR1C1 peptide
Components
  • Calmodulin
  • Glutamate NMDA receptor subunit zeta 1
KeywordsMETAL BINDING PROTEIN / Calmodulin / EF hand motif / globular complex / ion channel / NR1 / C1 casette / N-methyl-D-aspartate receptor / glutamate / central nervous system / neuronal channel / calcium channel / ER retention signal
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / : / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / glycine-gated cation channel activity / : / : / : ...regulation of store-operated calcium channel activity / : / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / glycine-gated cation channel activity / : / : / : / : / : / excitatory chemical synaptic transmission / transporter inhibitor activity / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / positive regulation of Schwann cell migration / regulation of cell communication / Synaptic adhesion-like molecules / : / olfactory learning / type 3 metabotropic glutamate receptor binding / dendritic branch / conditioned taste aversion / protein localization to postsynaptic membrane / establishment of protein localization to membrane / transmitter-gated monoatomic ion channel activity / suckling behavior / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / Assembly and cell surface presentation of NMDA receptors / RAF/MAP kinase cascade / response to amine / neurotransmitter receptor complex / Synaptic adhesion-like molecules / response to glycoside / positive regulation of DNA binding / Neurexins and neuroligins / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / ligand-gated sodium channel activity / negative regulation of high voltage-gated calcium channel activity / neuromuscular process / regulation of axonogenesis / calcium ion transmembrane import into cytosol / response to corticosterone / regulation of dendrite morphogenesis / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / male mating behavior / regulation of synapse assembly / protein heterotetramerization / : / response to morphine / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / glycine binding / startle response / positive regulation of reactive oxygen species biosynthetic process / Negative regulation of NMDA receptor-mediated neuronal transmission / parallel fiber to Purkinje cell synapse / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / monoatomic ion channel complex / adenylate cyclase binding / protein phosphatase activator activity / Long-term potentiation / positive regulation of calcium ion transport into cytosol / monoatomic cation transmembrane transport / cellular response to glycine / associative learning / positive regulation of dendritic spine maintenance / Unblocking of NMDA receptors, glutamate binding and activation / regulation of synaptic vesicle endocytosis / regulation of neuronal synaptic plasticity / monoatomic cation transport / glutamate receptor binding / detection of calcium ion / social behavior / ligand-gated monoatomic ion channel activity / postsynaptic cytosol / regulation of cardiac muscle contraction / cell surface receptor signaling pathway via JAK-STAT / catalytic complex / prepulse inhibition / phosphatase binding / long-term memory / phosphatidylinositol 3-kinase binding / positive regulation of nitric-oxide synthase activity
Similarity search - Function
: / : / EF-hand / Recoverin; domain 1 / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site ...: / : / EF-hand / Recoverin; domain 1 / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / EF-hand domain pair / Receptor, ligand binding region / Receptor family ligand binding region / EF-hand, calcium binding motif / Periplasmic binding protein-like I / 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 / Glutamate receptor ionotropic, NMDA 1 / Calmodulin-1 / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAkyol, Z. / Gakhar, L. / Sorensen, B.R. / Hell, J.H. / Shea, M.A.
CitationJournal: Structure / Year: 2007
Title: The NMDA Receptor NR1 C1 Region Bound to Calmodulin: Structural Insights into Functional Differences between Homologous Domains.
Authors: Ataman, Z.A. / Gakhar, L. / Sorensen, B.R. / Hell, J.W. / Shea, M.A.
History
DepositionJul 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 14, 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_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_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

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Assembly

Deposited unit
A: Calmodulin
B: Glutamate NMDA receptor subunit zeta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6476
Polymers19,4872
Non-polymers1604
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-78 kcal/mol
Surface area8530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.371, 40.371, 175.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): Lys-S / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Protein/peptide Glutamate NMDA receptor subunit zeta 1 / N-methyl-D-aspartate receptor subunit NR1 / NR1C1 peptide


Mass: 2765.287 Da / Num. of mol.: 1 / Fragment: C-TERMINAL TAIL, C1 REGION / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q05586, UniProt: P35439*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.: 66 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 7% PEG 6000, 5mM CaCl2, 100 mM sodium acetate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00808 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 13, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00808 Å / Relative weight: 1
ReflectionResolution: 1.9→19.69 Å / Num. obs: 13652 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.01 % / Biso Wilson estimate: 38.32 Å2 / Rsym value: 0.034 / Net I/σ(I): 17.36
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.56 % / Mean I/σ(I) obs: 3.92 / Num. unique all: 3353 / Rsym value: 0.255 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8.57 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.206 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24789 273 2 %RANDOM
Rwork0.20614 ---
all0.20695 13379 --
obs0.20695 13379 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.361 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 4 66 1337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221279
X-RAY DIFFRACTIONr_bond_other_d0.0050.02881
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9611711
X-RAY DIFFRACTIONr_angle_other_deg1.05832143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3525.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33315244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4641510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021431
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_nbd_refined0.2430.2374
X-RAY DIFFRACTIONr_nbd_other0.1860.2932
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2633
X-RAY DIFFRACTIONr_nbtor_other0.0910.2677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.216
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9721.5817
X-RAY DIFFRACTIONr_mcbond_other0.2471.5327
X-RAY DIFFRACTIONr_mcangle_it1.53621262
X-RAY DIFFRACTIONr_scbond_it2.3343514
X-RAY DIFFRACTIONr_scangle_it3.6024.5449
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 18 -
Rwork0.262 870 -
obs-870 100 %

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