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- PDB-3ead: Crystal structure of CALX-CBD1 -

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Basic information

Entry
Database: PDB / ID: 3ead
TitleCrystal structure of CALX-CBD1
ComponentsNa/Ca exchange protein
KeywordsMEMBRANE PROTEIN / cbd1 / calcium regulation / Membrane / Transmembrane
Function / homology
Function and homology information


rhabdomere membrane / calcium:sodium antiporter activity / neuromuscular process controlling posture / calcium ion import across plasma membrane / phototransduction / sodium ion transmembrane transport / response to endoplasmic reticulum stress / sarcolemma / calmodulin binding / postsynapse ...rhabdomere membrane / calcium:sodium antiporter activity / neuromuscular process controlling posture / calcium ion import across plasma membrane / phototransduction / sodium ion transmembrane transport / response to endoplasmic reticulum stress / sarcolemma / calmodulin binding / postsynapse / axon / calcium ion binding
Similarity search - Function
CalX-beta domain / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / : / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Sodium/calcium exchanger membrane region ...CalX-beta domain / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / : / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sodium/calcium exchanger Calx / Sodium/calcium exchanger Calx
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZheng, L. / Wang, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of progressive Ca2+ binding states of the Ca2+ sensor Ca2+ binding domain 1 (CBD1) from the CALX Na+/Ca2+ exchanger reveal incremental conformational transitions.
Authors: Wu, M. / Le, H.D. / Wang, M. / Yurkov, V. / Omelchenko, A. / Hnatowich, M. / Nix, J. / Hryshko, L.V. / Zheng, L.
History
DepositionAug 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 5, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_asym_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_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Na/Ca exchange protein
B: Na/Ca exchange protein
C: Na/Ca exchange protein
D: Na/Ca exchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,66221
Polymers61,9294
Non-polymers73317
Water1,71195
1
A: Na/Ca exchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7356
Polymers15,4821
Non-polymers2525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Na/Ca exchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6425
Polymers15,4821
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Na/Ca exchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6425
Polymers15,4821
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Na/Ca exchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6425
Polymers15,4821
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.372, 73.722, 129.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114D372 - 382
2114B372 - 382
1211D383 - 389
2211B383 - 389
1314D390 - 442
2314B390 - 442
1411D443 - 453
2411B443 - 453
1514D454 - 477
2514B454 - 477
1611D478 - 483
2611B478 - 483

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Components

#1: Protein
Na/Ca exchange protein


Mass: 15482.130 Da / Num. of mol.: 4 / Fragment: CALX-CBD1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Calx, NCX, CG5685 / Plasmid: pET28a-Calx-cbd1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q24413, UniProt: Q9VDG5*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 50 mM MES, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.90682 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2005
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.90682 Å / Relative weight: 1
ReflectionResolution: 2.25→19.6 Å / Num. obs: 26203 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1259 / % possible all: 71.8

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2DPK

2dpk


Resolution: 2.25→19.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 19.385 / SU ML: 0.233 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26933 1341 5.1 %RANDOM
Rwork0.20973 ---
obs0.21279 24832 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.676 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20 Å2
2--4.62 Å20 Å2
3----3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.242 Å0.297 Å
Luzzati sigma a-0.233 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 22 95 3693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.964945
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1715444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98423.838198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.99215594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0831532
X-RAY DIFFRACTIONr_chiral_restr0.1390.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.21667
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22451
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2143
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1570.227
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.721.52277
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21723605
X-RAY DIFFRACTIONr_scbond_it2.18231539
X-RAY DIFFRACTIONr_scangle_it3.0474.51340
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: D / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
147tight positional0.190.05
198medium positional0.390.5
147tight thermal0.150.5
198medium thermal0.82
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 74 -
Rwork0.285 1389 -
obs--73.15 %

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