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- PDB-5jho: Crystal structure of the regulatory domain of the sodium driven c... -

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Basic information

Entry
Database: PDB / ID: 5jho
TitleCrystal structure of the regulatory domain of the sodium driven chloride bicarbonate exchanger.
ComponentsElectroneutral sodium bicarbonate exchanger 1
KeywordsTRANSPORT PROTEIN / membrane protein / bicarbonate exchanger / anion transport
Function / homology
Function and homology information


hippocampal mossy fiber / sodium:bicarbonate symporter activity / : / positive regulation of synaptic vesicle exocytosis / sodium ion transmembrane transporter activity / monoatomic ion homeostasis / symmetric synapse / Bicarbonate transporters / solute:inorganic anion antiporter activity / bicarbonate transport ...hippocampal mossy fiber / sodium:bicarbonate symporter activity / : / positive regulation of synaptic vesicle exocytosis / sodium ion transmembrane transporter activity / monoatomic ion homeostasis / symmetric synapse / Bicarbonate transporters / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride transmembrane transporter activity / neuronal cell body membrane / glial cell projection / transmembrane transporter activity / transport across blood-brain barrier / asymmetric synapse / sodium ion transmembrane transport / axon terminus / chloride transmembrane transport / regulation of membrane potential / regulation of intracellular pH / modulation of chemical synaptic transmission / transmembrane transport / terminal bouton / synaptic vesicle / presynapse / presynaptic membrane / membrane => GO:0016020 / neuron projection / glutamatergic synapse / dendrite / membrane / plasma membrane
Similarity search - Function
Sodium bicarbonate cotransporter / Band 3 cytoplasmic domain / Band 3 cytoplasmic domain / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain / Phosphotransferase/anion transporter
Similarity search - Domain/homology
Electroneutral sodium bicarbonate exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.801 Å
AuthorsAlvadia, C. / Sommer, T. / Bjerregaard-Andersen, K. / Morth, J.P.
Funding support Norway, Denmark, 2items
OrganizationGrant numberCountry
Research Council of NorwayES486454 Norway
Lundbeck foundationR34-A3616 Denmark
CitationJournal: Sci Rep / Year: 2017
Title: The crystal structure of the regulatory domain of the human sodium-driven chloride/bicarbonate exchanger.
Authors: Alvadia, C.M. / Sommer, T. / Bjerregaard-Andersen, K. / Damkier, H.H. / Montrasio, M. / Aalkjaer, C. / Morth, J.P.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Electroneutral sodium bicarbonate exchanger 1
B: Electroneutral sodium bicarbonate exchanger 1


Theoretical massNumber of molelcules
Total (without water)77,8122
Polymers77,8122
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-10 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.040, 98.040, 212.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Electroneutral sodium bicarbonate exchanger 1 / Electroneutral Na(+)-driven Cl-HCO3 exchanger / Solute carrier family 4 member 8 / k-NBC3


Mass: 38906.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC4A8, KIAA0739, NBC, NBC3, NDCBE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: Q2Y0W8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.29 Å3/Da / Density % sol: 62.58 % / Description: bipymidal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 40 mg/ml protein, 100 mM Formic Acid , pH 4.4, 9 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.8→69.32 Å / Num. obs: 26378 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 76.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.5
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.801→24.988 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.87
RfactorNum. reflection% reflection
Rfree0.2378 1334 5.08 %
Rwork0.2004 --
obs0.2022 26275 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.801→24.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 0 5 3784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013849
X-RAY DIFFRACTIONf_angle_d1.3945210
X-RAY DIFFRACTIONf_dihedral_angle_d14.1961440
X-RAY DIFFRACTIONf_chiral_restr0.054598
X-RAY DIFFRACTIONf_plane_restr0.007675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8013-2.90130.34861230.29852422X-RAY DIFFRACTION100
2.9013-3.01730.29741110.27342454X-RAY DIFFRACTION100
3.0173-3.15430.30531310.24962474X-RAY DIFFRACTION100
3.1543-3.32030.28261420.24062417X-RAY DIFFRACTION100
3.3203-3.52780.26221350.23622472X-RAY DIFFRACTION100
3.5278-3.79930.26361360.22862476X-RAY DIFFRACTION100
3.7993-4.180.24581430.20432474X-RAY DIFFRACTION100
4.18-4.78120.20411220.16322519X-RAY DIFFRACTION100
4.7812-6.010.20581510.18272538X-RAY DIFFRACTION100
6.01-24.98890.22241400.18172695X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5227-0.19990.19020.02850.30143.633-0.36931.67962.8506-0.7635-0.4553-1.6673-1.41370.5189-0.34141.5951-0.00140.25161.11130.62971.4753-19.377392.422680.3484
26.1123-1.22180.56253.52780.15045.1228-0.3802-1.24110.24980.29520.60620.1378-0.5539-0.4354-0.32560.81120.2893-0.09850.9744-0.0210.6983-28.083480.422998.8393
34.07314.8262-3.57227.1205-6.01275.385-0.6225-0.1928-1.1122-1.12650.99120.74640.8383-1.549-0.31641.14050.2341-0.27671.19440.02871.1105-43.853778.759884.2581
48.94480.9077-1.64358.4322-2.34355.7227-0.4321-1.68691.3053-0.10620.42321.2537-0.5339-0.86640.02330.89910.3793-0.18021.26330.0450.887-39.206482.378697.7807
58.5796-2.78030.43634.4505-0.28824.61160.0396-0.05770.6485-0.37040.0377-0.2537-0.1665-0.1979-0.12620.66470.2186-0.07170.5546-0.03950.4577-27.284681.103990.9981
68.3326-0.87791.46640.46141.46887.6036-0.34060.0965-1.09530.31190.25461.61791.164-0.15090.21070.6738-0.27030.04110.70690.19821.3566-9.533847.29594.3655
74.9949-0.4812-1.32312.944-0.18367.99780.2824-0.03270.1075-0.6269-0.0223-0.4147-0.81250.418-0.22860.64480.07110.1440.49-0.01410.63636.934665.569890.1674
88.46574.1967-5.59526.7529-1.68573.9494-0.72041.03-0.7208-1.510.66530.05080.564-0.53380.12981.35270.22980.11390.9386-0.20510.75948.297753.239673.4833
96.13130.9162-4.89167.16852.76565.6334-0.1515-0.0703-0.1444-0.6779-0.3642-1.18470.24742.5642-0.25470.87280.21220.31460.99620.0261.044618.432961.479386.2317
106.1683-1.4737-0.614.8185-0.1236.8885-0.02790.2315-0.1772-0.3015-0.0246-0.06810.082-0.17120.05440.55160.04820.0290.4038-0.05420.44242.044859.837389.7119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 43 through 62 )
2X-RAY DIFFRACTION2chain 'B' and (resid 63 through 133 )
3X-RAY DIFFRACTION3chain 'B' and (resid 134 through 152 )
4X-RAY DIFFRACTION4chain 'B' and (resid 153 through 254 )
5X-RAY DIFFRACTION5chain 'B' and (resid 255 through 344 )
6X-RAY DIFFRACTION6chain 'A' and (resid 42 through 62 )
7X-RAY DIFFRACTION7chain 'A' and (resid 63 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 152 )
9X-RAY DIFFRACTION9chain 'A' and (resid 153 through 236 )
10X-RAY DIFFRACTION10chain 'A' and (resid 237 through 344 )

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