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- PDB-2ygg: Complex of CaMBR and CaM -

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Basic information

Entry
Database: PDB / ID: 2ygg
TitleComplex of CaMBR and CaM
Components
  • CALMODULIN
  • SODIUM/HYDROGEN EXCHANGER 1
KeywordsMETAL BINDING PROTEIN/TRANSPORT PROTEIN / METAL BINDING PROTEIN-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / regulation of store-operated calcium channel activity / positive regulation of calcium:sodium antiporter activity / Hyaluronan uptake and degradation / regulation of high voltage-gated calcium channel activity / regulation of cardiac muscle cell membrane potential / potassium:proton antiporter activity ...sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / regulation of store-operated calcium channel activity / positive regulation of calcium:sodium antiporter activity / Hyaluronan uptake and degradation / regulation of high voltage-gated calcium channel activity / regulation of cardiac muscle cell membrane potential / potassium:proton antiporter activity / cellular response to electrical stimulus / sodium:proton antiporter activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / positive regulation of action potential / sodium ion export across plasma membrane / maintenance of cell polarity / : / regulation of pH / cellular response to acidic pH / positive regulation of calcineurin-NFAT signaling cascade / establishment of protein localization to mitochondrial membrane / cardiac muscle cell differentiation / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / type 3 metabotropic glutamate receptor binding / protein phosphatase 2B binding / ion binding / regulation of stress fiber assembly / cardiac muscle cell contraction / response to acidic pH / establishment of protein localization to membrane / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of mitochondrial membrane permeability / cellular response to cold / regulation of synaptic vesicle endocytosis / cellular response to antibiotic / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / regulation of focal adhesion assembly / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle hypertrophy / nitric-oxide synthase binding / protein phosphatase activator activity / positive regulation of the force of heart contraction / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / intercalated disc / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / positive regulation of DNA binding / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / monoatomic ion transport / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / phosphatidylinositol-4,5-bisphosphate binding / T-tubule / cellular response to epinephrine stimulus / calcium channel complex / response to muscle stretch / activation of adenylate cyclase activity / adenylate cyclase activator activity / proton transmembrane transport / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / stem cell differentiation / regulation of intracellular pH / phospholipid binding / positive regulation of receptor signaling pathway via JAK-STAT / spindle pole / cellular response to type II interferon / response to calcium ion / cellular response to mechanical stimulus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2020 / Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2020 / Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / Helix non-globular / EF-hand, calcium binding motif / Special / 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
Calmodulin-1 / Sodium/hydrogen exchanger 1 / Calmodulin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.227 Å
AuthorsKoester, S. / Yildiz, O.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of Human Na+/H+ Exchanger Nhe1 Regulatory Region in Complex with Cam and Ca2+
Authors: Koester, S. / Pavkov-Keller, T. / Kuehlbrandt, W. / Yildiz, O.
History
DepositionApr 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Nov 19, 2014Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SODIUM/HYDROGEN EXCHANGER 1
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,36111
Polymers25,4742
Non-polymers8869
Water2,054114
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-78.2 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.700, 38.350, 34.100
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein SODIUM/HYDROGEN EXCHANGER 1 / APNH / NA(+)/H(+) ANTIPORTER\ / AMILORIDE-SENSITIVE / NA(+)/H(+) EXCHANGER 1 / NHE-1 / SOLUTE ...APNH / NA(+)/H(+) ANTIPORTER\ / AMILORIDE-SENSITIVE / NA(+)/H(+) EXCHANGER 1 / NHE-1 / SOLUTE CARRIER FAMILY 9 MEMBER 1 / NHE1


Mass: 8550.799 Da / Num. of mol.: 1 / Fragment: CAM BINDING REGION, RESIDUES 622-689
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19634
#2: Protein CALMODULIN / / CAM


Mass: 16923.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS

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Non-polymers , 5 types, 123 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.58 Å3/Da / Density % sol: 52.23 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.23→20 Å / Num. obs: 12449 / % possible obs: 96 % / Observed criterion σ(I): 5.9 / Redundancy: 12.6 % / Biso Wilson estimate: 28.84 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.5
Reflection shellResolution: 2.23→2.4 Å / Redundancy: 11 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.9 / % possible all: 83.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.227→37.668 Å / SU ML: 0.27 / σ(F): 2 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 623 5 %
Rwork0.1734 --
obs0.1763 12447 96.01 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.9732 Å20 Å2-1.966 Å2
2--3.836 Å20 Å2
3----0.5549 Å2
Refinement stepCycle: LAST / Resolution: 2.227→37.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 53 114 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011780
X-RAY DIFFRACTIONf_angle_d1.1562383
X-RAY DIFFRACTIONf_dihedral_angle_d20.935700
X-RAY DIFFRACTIONf_chiral_restr0.081257
X-RAY DIFFRACTIONf_plane_restr0.004313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2275-2.45160.24251400.18492639X-RAY DIFFRACTION87
2.4516-2.80620.24841560.17793001X-RAY DIFFRACTION99
2.8062-3.53520.23141620.15663040X-RAY DIFFRACTION99
3.5352-37.67350.22471650.17883144X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 32.9408 Å / Origin y: 5.8417 Å / Origin z: 0.8299 Å
111213212223313233
T0.0829 Å2-0.0327 Å20.0907 Å2-0.1958 Å2-0.0318 Å2---0.042 Å2
L0.444 °20.0813 °20.1013 °2-0.5408 °20.0603 °2--0.7761 °2
S0.1001 Å °-0.2337 Å °-0.3722 Å °0.2345 Å °-0.1414 Å °0.0068 Å °0.1119 Å °-0.5889 Å °-0.0076 Å °
Refinement TLS groupSelection details: ALL

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