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- PDB-7nqc: Calmodulin extracts the Ras family protein RalA from lipid bilaye... -

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Basic information

Entry
Database: PDB / ID: 7nqc
TitleCalmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane targeting motifs
Components
  • Calmodulin-1
  • PRO-ASN-GLY-LYS-LYS-LYS-ARG-LYS-SER-LEU-ALA-LYS-ARG-ILE-ARG-GLU-ARG-CMF
KeywordsSIGNALING PROTEIN / farnesylation / calcium binding
Function / homology
Function and homology information


establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding ...establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / protein phosphatase activator activity / calcium channel regulator activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / sperm midpiece / response to amphetamine / calcium channel complex / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / calcium-mediated signaling / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / spindle pole / cellular response to type II interferon / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / transmembrane transporter binding / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-ULW / Calmodulin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChamberlain, S.G. / Owen, D. / Mott, H.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P504853/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane-targeting motifs.
Authors: Chamberlain, S.G. / Gohlke, A. / Shafiq, A. / Squires, I.J. / Owen, D. / Mott, H.R.
History
DepositionMar 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-1
B: PRO-ASN-GLY-LYS-LYS-LYS-ARG-LYS-SER-LEU-ALA-LYS-ARG-ILE-ARG-GLU-ARG-CMF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2887
Polymers20,7502
Non-polymers5385
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, R-Max value halved when RalA-HVR is unmodified due to only C-lobe of Calmodulin being available for binding. Amine coupling to chip results in 50% occlusion of C- ...Evidence: surface plasmon resonance, R-Max value halved when RalA-HVR is unmodified due to only C-lobe of Calmodulin being available for binding. Amine coupling to chip results in 50% occlusion of C-lobe., NMR titration experiments show that the N-lobe of CaM bind to the lipid moiety while the C-lobe binds to the HVR.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2020 Å2
ΔGint-15 kcal/mol
Surface area10520 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Calmodulin-1 /


Mass: 18572.418 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, CaMI / Plasmid: pQE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DP29
#2: Protein/peptide PRO-ASN-GLY-LYS-LYS-LYS-ARG-LYS-SER-LEU-ALA-LYS-ARG-ILE-ARG-GLU-ARG-CMF


Mass: 2177.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RalA / Production host: Escherichia coli BL21 (bacteria) / References: small monomeric GTPase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ULW / [(2~{Z},6~{Z})-3,7,11-trimethyldodeca-2,6-dienyl] 3-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]propanoate


Mass: 377.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H35NO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
122isotropic13D HNCA
132isotropic13D HN(CA)CB
1112isotropic13D HN(CO)CA
1122isotropic13D HN(COCA)CB
142isotropic13D 1H-13C NOESY
152isotropic13D (H)CCH-TOCSY
162isotropic12D 1H-13C HSQC
172isotropic13D 13C Filtered, 13C Edited NOESY
183isotropic13D 1H-13C NOESY
193isotropic12D 1H-13C HSQC
1103isotropic13D 13C Filtered, 13C Edited NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-15N] Calmodulin, 0.8 mM NA RalA HVR, 90% H2O/10% D2O15N CaM, UL peptide90% H2O/10% D2O
solution21.1 mM U-15N, 13C Calmodulin, 1.1 mM NA RalA HVR, 90% H2O/10% D2O15N,13C CaM, UL peptide90% H2O/10% D2O
solution31.0 mM Calmodulin, 1.0 mM 15N,13C RalA HVR, 90% H2O/10% D2O15N,13C peptide UL CaM90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMCalmodulin[U-15N]1
0.8 mMRalA HVRNA1
1.1 mMCalmodulinU-15N, 13C2
1.1 mMRalA HVRNA2
1.0 mMCalmodulinnatural abundance3
1.0 mMRalA HVR15N,13C3
Sample conditionsIonic strength: 109 mM / Label: 1 / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE9502

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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