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- PDB-9ydf: Structure of the cyclic nucleotide binding domain of SLC9C1 -

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Basic information

Entry
Database: PDB / ID: 9ydf
TitleStructure of the cyclic nucleotide binding domain of SLC9C1
ComponentsSolute carrier family 9 member C1
KeywordsTRANSPORT PROTEIN / Transporter / cyclic nucleotide binding domain / sperm-specific protein / SGC / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium:proton antiporter activity / flagellated sperm motility / motile cilium / sodium ion import across plasma membrane / monoatomic ion channel activity / potassium ion transmembrane transport / regulation of intracellular pH / Stimuli-sensing channels / spermatogenesis ...potassium:proton antiporter activity / sodium:proton antiporter activity / flagellated sperm motility / motile cilium / sodium ion import across plasma membrane / monoatomic ion channel activity / potassium ion transmembrane transport / regulation of intracellular pH / Stimuli-sensing channels / spermatogenesis / cell differentiation / plasma membrane
Similarity search - Function
Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Voltage-dependent channel domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Solute carrier family 9 member C1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLyu, C. / Dong, A. / Chandrasekaran, R. / Mamai, A. / Arrowsmith, C.H. / Edwards, A.M. / Burgess-Brown, N. / Tredup, C. / Harding, R.J. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To be published
Title: Structure of the cyclic nucleotide binding domain of SLC9C1
Authors: Lyu, C. / Dong, A. / Chandrasekaran, R. / Mamai, A. / Arrowsmith, C.H. / Edwards, A.M. / Burgess-Brown, N. / Tredup, C. / Harding, R.J. / Structural Genomics Consortium (SGC)
History
DepositionSep 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 9 member C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1103
Polymers19,9861
Non-polymers1242
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.788, 45.788, 276.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Solute carrier family 9 member C1 / Na(+)/H(+) exchanger 10 / NHE-10 / Sodium/hydrogen exchanger 10 / Solute carrier family 9 member 10 ...Na(+)/H(+) exchanger 10 / NHE-10 / Sodium/hydrogen exchanger 10 / Solute carrier family 9 member 10 / Sperm-specific Na(+)/H(+) exchanger / sNHE


Mass: 19986.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9C1, SLC9A10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4G0N8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) polyethylene glycol (PEG) 3350, 0.2 M Calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 9891 / % possible obs: 99.4 % / Redundancy: 29 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.016 / Rrim(I) all: 0.087 / Χ2: 0.81 / Net I/σ(I): 6.3 / Num. measured all: 286680
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.18-2.2224.80.9744310.8920.9710.1940.9940.69595.1
2.22-2.2629.20.8624700.9310.9820.1570.8760.72396.5
2.26-2.329.10.6874670.9630.990.1260.6990.7197.5
2.3-2.3530.40.6024560.9780.9940.1080.6120.70798.3
2.35-2.431.30.4574930.980.9950.0810.4640.71599.4
2.4-2.4630.60.3784570.9950.9990.0680.3840.73799.8
2.46-2.52310.3744900.9890.9970.0670.380.71100
2.52-2.5830.90.3054700.9920.9980.0550.310.728100
2.58-2.6630.20.2344910.9950.9990.0430.2380.733100
2.66-2.7528.60.2064820.9950.9990.0380.2090.728100
2.75-2.8426.20.1614930.9970.9990.0320.1640.744100
2.84-2.9631.70.1434760.99810.0250.1460.754100
2.96-3.0931.30.1124940.99910.020.1140.777100
3.09-3.2630.90.0895060.99910.0160.090.885100
3.26-3.4630.30.0694900.99910.0120.070.907100
3.46-3.7329.20.0624990.99910.0110.0630.926100
3.73-4.126.10.051518110.010.0520.923100
4.1-4.728.50.048526110.0090.0481.03100
4.7-5.9127.90.047544110.0090.0480.91100
5.91-5023.30.0536380.99910.0110.0541.09799.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→46.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.157 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23745 465 4.7 %RANDOM
Rwork0.20263 ---
obs0.20423 9336 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.945 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.18→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 0 19 1036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121043
X-RAY DIFFRACTIONr_bond_other_d0.0010.016983
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.8091413
X-RAY DIFFRACTIONr_angle_other_deg0.4731.7372270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06410170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3273.065527
X-RAY DIFFRACTIONr_mcbond_other2.3273.065527
X-RAY DIFFRACTIONr_mcangle_it3.395.47657
X-RAY DIFFRACTIONr_mcangle_other3.3885.473658
X-RAY DIFFRACTIONr_scbond_it3.4613.48516
X-RAY DIFFRACTIONr_scbond_other3.4583.482517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4296.232757
X-RAY DIFFRACTIONr_long_range_B_refined6.69229.411131
X-RAY DIFFRACTIONr_long_range_B_other6.6929.411130
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.184→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 33 -
Rwork0.22 623 -
obs--95.91 %
Refinement TLS params.Method: refined / Origin x: 9.1133 Å / Origin y: -16.1938 Å / Origin z: -9.0915 Å
111213212223313233
T0.0559 Å20.0105 Å20.0168 Å2-0.0122 Å20.0021 Å2--0.0114 Å2
L3.481 °21.8646 °21.2411 °2-3.3493 °20.8568 °2--1.5702 °2
S-0.1034 Å °0.0643 Å °-0.0057 Å °-0.0244 Å °0.058 Å °0.1167 Å °0.0694 Å °-0.0067 Å °0.0454 Å °

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