[English] 日本語
Yorodumi
- PDB-9ydf: Structure of the cyclic nucleotide binding domain of SLC9C1 -

+
Open data


ID or keywords:

Loading...

-
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 / sodium ion import across plasma membrane / motile cilium / 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 / sodium ion import across plasma membrane / motile cilium / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more