[English] 日本語
Yorodumi
- PDB-2hqw: Crystal Structure of Ca2+/Calmodulin bound to NMDA Receptor NR1C1... -

+
Open data


ID or keywords:

Loading...

-
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 high voltage-gated calcium channel activity / excitatory chemical synaptic transmission / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / pons maturation / Synaptic adhesion-like molecules / regulation of cell communication ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / excitatory chemical synaptic transmission / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / pons maturation / Synaptic adhesion-like molecules / regulation of cell communication / positive regulation of Schwann cell migration / : / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / establishment of protein localization to mitochondrial membrane / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / type 3 metabotropic glutamate receptor binding / voltage-gated monoatomic cation channel activity / response to morphine / glutamate-gated calcium ion channel activity / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / establishment of protein localization to membrane / Neurexins and neuroligins / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / regulation of synaptic vesicle endocytosis / regulation of synapse assembly / negative regulation of high voltage-gated calcium channel activity / glycine binding / regulation of synaptic vesicle exocytosis / positive regulation of calcium ion transport into cytosol / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / male mating behavior / regulation of neuronal synaptic plasticity / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / regulation of dendrite morphogenesis / autophagosome membrane docking / regulation of axonogenesis / suckling behavior / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / startle response / Unblocking of NMDA receptors, glutamate binding and activation / response to amine / protein phosphatase activator activity / monoatomic cation transmembrane transport / social behavior / positive regulation of excitatory postsynaptic potential / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / ligand-gated monoatomic ion channel activity / associative learning / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / monoatomic cation transport / excitatory synapse / positive regulation of dendritic spine maintenance / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / glutamate receptor binding / cellular response to interferon-beta / regulation of cardiac muscle contraction / phosphatase binding / calcium channel inhibitor activity / calcium ion homeostasis / positive regulation of DNA binding / synaptic cleft / cellular response to manganese ion / enzyme regulator activity / prepulse inhibition / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of neuron apoptotic process / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / monoatomic cation channel activity
Similarity search - Function
EF-hand / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 / Recoverin; domain 1 ...EF-hand / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 / Recoverin; domain 1 / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / EF-hand domain pair / Periplasmic binding protein-like I / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more