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- PDB-2bec: Crystal structure of CHP2 in complex with its binding region in N... -

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Basic information

Entry
Database: PDB / ID: 2bec
TitleCrystal structure of CHP2 in complex with its binding region in NHE1 and insights into the mechanism of pH regulation
Components
  • Calcineurin B homologous protein 2
  • Sodium/hydrogen exchanger 1
KeywordsMETAL BINDING PROTEIN/TRANSPORT PROTEIN / Calcineurin-homologous protein / Calcium-binding protein / NHE1 regulating protein / METAL BINDING PROTEIN-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of phosphatase activity / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / cation-transporting ATPase complex / Hyaluronan degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / positive regulation of action potential / sodium:proton antiporter activity ...positive regulation of phosphatase activity / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / cation-transporting ATPase complex / Hyaluronan degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / positive regulation of action potential / sodium:proton antiporter activity / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / cardiac muscle cell differentiation / sodium ion export across plasma membrane / protein phosphatase 2B binding / intracellular sodium ion homeostasis / regulation of stress fiber assembly / cardiac muscle cell contraction / sodium ion import across plasma membrane / positive regulation of mitochondrial membrane permeability / response to acidic pH / regulation of cardiac muscle contraction by calcium ion signaling / cellular response to acidic pH / regulation of focal adhesion assembly / positive regulation of cardiac muscle hypertrophy / cellular response to cold / cellular response to antibiotic / positive regulation of the force of heart contraction / protein complex oligomerization / intercalated disc / response to muscle stretch / monoatomic ion transport / phosphatidylinositol-4,5-bisphosphate binding / potassium ion transmembrane transport / cellular response to epinephrine stimulus / T-tubule / proton transmembrane transport / cellular response to calcium ion / stem cell differentiation / regulation of intracellular pH / cellular response to mechanical stimulus / positive regulation of protein import into nucleus / phospholipid binding / cellular response to insulin stimulus / calcium-dependent protein binding / cell migration / lamellipodium / protein transport / positive regulation of cell growth / cellular response to hypoxia / basolateral plasma membrane / protein-macromolecule adaptor activity / molecular adaptor activity / calmodulin binding / apical plasma membrane / positive regulation of apoptotic process / membrane raft / focal adhesion / positive regulation of cell population proliferation / calcium ion binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / 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, transmembrane / EF hand / EF hand domain ...: / 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, transmembrane / EF hand / EF hand domain / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
YTTRIUM (III) ION / Calcineurin B homologous protein 2 / Sodium/hydrogen exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsBen Ammar, Y. / Takeda, S. / Hisamitsu, T. / Mori, H. / Wakabayashi, S.
Citation
Journal: Embo J. / Year: 2006
Title: Crystal structure of CHP2 complexed with NHE1-cytosolic region and an implication for pH regulation
Authors: Ben Ammar, Y. / Takeda, S. / Hisamitsu, T. / Mori, H. / Wakabayashi, S.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005
Title: Crystallization and preliminary crystallographic analysis of the human calcineurin homologous protein CHP2 bound to the cytoplasmic region of the Na+/H+ exchanger NHE1
Authors: Ben Ammar, Y. / Takeda, S. / Sugawara, M. / Miyano, M. / Mori, H. / Wakabayashi, S.
History
DepositionOct 24, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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_ref_seq_dif / 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.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_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_ref_seq_dif.details / _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: Calcineurin B homologous protein 2
B: Sodium/hydrogen exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5104
Polymers28,3322
Non-polymers1782
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-40 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.262, 49.262, 102.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsAsymmetric unit contains one physiological unit

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Components

#1: Protein Calcineurin B homologous protein 2 / Hepatocellular carcinoma-associated antigen 520 / Human Calcineurin Homologous Protein CHP2


Mass: 23316.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star / References: UniProt: O43745
#2: Protein/peptide Sodium/hydrogen exchanger 1 / Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1 / Na(+)/H(+) antiporter / ...Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1 / Na(+)/H(+) antiporter / amiloride-sensitive / APNH


Mass: 5015.683 Da / Num. of mol.: 1 / Fragment: residues 503-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star / References: UniProt: P19634
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Y

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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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M ammonium acetate, 0.1M Bis-Tris, 0.01M yttrium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL44B220.7270, 0.7266, 1.0000
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 11, 2005
ADSC QUANTUM 2102CCDDec 20, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1rotated-inclined double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.7271
30.72661
ReflectionResolution: 2.7→50 Å / Num. all: 6996 / Num. obs: 6807 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / % possible all: 83.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.7→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.287 350 random
Rwork0.218 --
all0.22 6746 -
obs0.22 6653 -
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 2 0 1674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004751
X-RAY DIFFRACTIONc_angle_deg1.00095
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree: 0.514 / Rfactor Rwork: 0.385

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