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- PDB-2mgu: Structure of the complex between calmodulin and the binding domai... -

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Basic information

Entry
Database: PDB / ID: 2mgu
TitleStructure of the complex between calmodulin and the binding domain of HIV-1 matrix protein
Components
  • Calmodulin
  • MA8-43
KeywordsPROTEIN BINDING / calmodulin / HIV-1 matrix
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / : / regulation of high voltage-gated calcium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : ...regulation of store-operated calcium channel activity / : / regulation of high voltage-gated calcium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / viral budding via host ESCRT complex / negative regulation of ryanodine-sensitive calcium-release channel activity / calcineurin-mediated signaling / regulation of synaptic vesicle endocytosis / protein phosphatase activator activity / postsynaptic cytosol / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / calcium channel regulator activity / potassium ion transmembrane transport / sperm midpiece / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / positive regulation of nitric-oxide synthase activity / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / calcium-mediated signaling / Schaffer collateral - CA1 synapse / host multivesicular body / cellular response to type II interferon / ISG15 antiviral mechanism / response to calcium ion / spindle pole / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / myelin sheath / growth cone / viral nucleocapsid / protein autophosphorylation / vesicle / transmembrane transporter binding / host cell cytoplasm / neuron projection / positive regulation of apoptotic process / protein domain specific binding / viral translational frameshifting / centrosome / calcium ion binding / protein kinase binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / protein-containing complex / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / : / EF-hand domain pair / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / EF-hand, calcium binding motif / Matrix protein, lentiviral and alpha-retroviral, N-terminal ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / : / EF-hand domain pair / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / EF-hand, calcium binding motif / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Retrovirus capsid, C-terminal / Retroviral matrix protein / EF-hand calcium-binding domain profile. / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / EF-hand domain / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Gag polyprotein / Calmodulin-1 / Gag polyprotein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Human immunodeficiency virus 1
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsVlach, J. / Samal, A. / Saad, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Solution Structure of Calmodulin Bound to the Binding Domain of the HIV-1 Matrix Protein.
Authors: Vlach, J. / Samal, A.B. / Saad, J.S.
History
DepositionNov 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _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.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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
M: MA8-43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1996
Polymers21,0382
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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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, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Protein/peptide MA8-43


Mass: 4317.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZJG2, UniProt: P12493*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D HNCO
1713D 1H-15N NOESY
1813D 1H-15N TOCSY

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Sample preparation

DetailsContents: 0.1-1.2 mM [U-95% 13C; U-95% 15N] calmodulin, 0.1-1.2 mM MA8-43, 5 mM CALCIUM ION, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMcalmodulin-1[U-95% 13C; U-95% 15N]0.1-1.21
mMMA8-43-20.1-1.21
5 mMCALCIUM ION-31
Sample conditionsIonic strength: 0.015 / pH: 6.3 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2CCPNchemical shift assignment
CcpNmr Analysis2.2CCPNdata analysis
CYANAanyGuntert, Mumenthaler and Wuthrichstructure solution
CYANAanyGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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