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- PDB-4ky9: Structural and Functional Analysis of a Putative Substrate Access... -

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Basic information

Entry
Database: PDB / ID: 4ky9
TitleStructural and Functional Analysis of a Putative Substrate Access Tunnel in the Cytosolic Domain of Human Anion Exchanger 1
ComponentsBand 3 anion transport protein
KeywordsMEMBRANE PROTEIN / cytosolic domain
Function / homology
Function and homology information


pH elevation / Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) / negative regulation of urine volume / Bicarbonate transporters / intracellular monoatomic ion homeostasis / ankyrin-1 complex / monoatomic anion transmembrane transporter activity / plasma membrane phospholipid scrambling / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity ...pH elevation / Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) / negative regulation of urine volume / Bicarbonate transporters / intracellular monoatomic ion homeostasis / ankyrin-1 complex / monoatomic anion transmembrane transporter activity / plasma membrane phospholipid scrambling / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride transmembrane transporter activity / ankyrin binding / hemoglobin binding / negative regulation of glycolytic process through fructose-6-phosphate / erythrocyte development / cortical cytoskeleton / protein-membrane adaptor activity / chloride transmembrane transport / regulation of intracellular pH / protein localization to plasma membrane / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / transmembrane transport / cytoplasmic side of plasma membrane / Z disc / blood coagulation / blood microparticle / basolateral plasma membrane / protein homodimerization activity / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Anion exchange protein 1 / Anion exchange protein / Anion exchange, conserved site / Anion exchangers family signature 1. / Anion exchangers family signature 2. / Band 3 cytoplasmic domain / Band 3 cytoplasmic domain / Phosphotransferase/anion transporter ...Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Anion exchange protein 1 / Anion exchange protein / Anion exchange, conserved site / Anion exchangers family signature 1. / Anion exchangers family signature 2. / Band 3 cytoplasmic domain / Band 3 cytoplasmic domain / Phosphotransferase/anion transporter / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Band 3 anion transport protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsShnitsar, V. / Calmettes, C. / Reithmeier, R.A.F. / Moraes, T.F.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A substrate access tunnel in the cytosolic domain is not an essential feature of the solute carrier 4 (SLC4) family of bicarbonate transporters.
Authors: Shnitsar, V. / Li, J. / Li, X. / Calmettes, C. / Basu, A. / Casey, J.R. / Moraes, T.F. / Reithmeier, R.A.
History
DepositionMay 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Feb 28, 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: Band 3 anion transport protein
P: Band 3 anion transport protein


Theoretical massNumber of molelcules
Total (without water)68,4302
Polymers68,4302
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-41 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.905, 80.700, 104.278
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Band 3 anion transport protein / Anion exchange protein 1 / AE 1 / Anion exchanger 1 / Solute carrier family 4 member 1


Mass: 34214.859 Da / Num. of mol.: 2 / Fragment: UNP residues 51-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC4A1, AE1, DI, EPB3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02730
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM BisTris pH 6.5, 18% PEG 3350, with 0.5% (w/v) octylglucoside, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.23→43.79 Å / Num. obs: 32556 / Biso Wilson estimate: 49.34 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→43.79 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.25 / σ(F): 1.35 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1429 4.98 %
Rwork0.1853 --
obs0.1871 28717 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.6 Å2 / Biso mean: 62.9477 Å2 / Biso min: 20.88 Å2
Refinement stepCycle: LAST / Resolution: 2.23→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 0 150 4550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084501
X-RAY DIFFRACTIONf_angle_d1.2596110
X-RAY DIFFRACTIONf_chiral_restr0.064697
X-RAY DIFFRACTIONf_plane_restr0.006798
X-RAY DIFFRACTIONf_dihedral_angle_d14.7641706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.30970.31541430.253227502893100
2.3097-2.40220.27691680.230627142882100
2.4022-2.51150.28351570.213327342891100
2.5115-2.64390.26441590.211627232882100
2.6439-2.80950.23651390.20122771291099
2.8095-3.02640.23141340.19792718285299
3.0264-3.33090.26661460.19922744289098
3.3309-3.81260.21751380.17642728286697
3.8126-4.80250.17411360.14952740287696
4.8025-43.80220.21021090.18842666277589
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)
10.70910.19940.48720.0978-0.04870.9577-0.30350.4331-0.2084-0.21490.01580.59310.6409-1.176-0.19260.4878-0.19450.0880.7092-0.1390.4588-21.977-8.5684-49.3385
20.2312-0.20120.19760.1959-0.14550.1208-0.19720.0747-0.30120.3756-0.11730.40720.3836-0.4665-0.0370.2894-0.06220.07640.5132-0.10880.4098-16.8739-3.9838-36.676
30.59350.67080.29811.8635-0.16670.55270.04680.5465-0.125-0.4695-0.0591-0.67140.0927-0.2788-0.11920.34380.0470.14180.52570.0261-0.0497-7.3934-3.6522-60.2753
40.6610.86490.52191.33760.97180.7765-0.1006-0.2406-0.51850.10690.2618-0.52610.8893-0.10110.15960.6706-0.17070.17770.8051-0.00930.7457-19.1217-15.1933-45.3581
50.0616-0.02850.01310.02970.01860.02260.11360.0275-0.24310.0212-0.08940.0476-0.1006-0.099800.73880.13490.13870.72230.05170.9167-25.14078.9392-43.8446
60.55610.5564-0.25120.59010.07581.81910.02020.19810.23860.0218-0.08030.011-0.1356-0.3578-00.27180.02810.02970.25580.03040.2996-10.18411.0123-50.5046
70.60660.17580.2720.33880.1480.1387-0.3014-0.34410.29270.2950.19990.5286-0.1196-0.1845-0.00840.40320.11280.00770.3881-0.06970.3936-3.15.5837-28.2197
80.1948-0.28130.08110.4401-0.1630.0461-0.2074-0.40980.48940.40830.178-0.1114-0.47530.081-0.02340.44860.0075-0.08330.3962-0.09290.350122.08534.0906-18.7296
90.99450.15220.24770.3654-0.21560.3161-0.1436-0.16440.22290.17740.0435-0.1667-0.1064-0.025900.34170.0522-0.05130.2795-0.05330.348711.9422-3.8502-23.6848
100.46870.17160.36690.507-0.11880.7811-0.14850.05120.2851-0.00720.3411-0.54-0.04650.5827-0.07970.2792-0.0402-0.0250.3554-0.12320.422528.1775-2.8378-26.6533
110.0055-0.0027-0.00220.0163-0.01410.0084-0.2717-0.3043-0.184-0.3196-0.3070.071-0.4657-0.6617-01.30390.0588-0.28171.0312-0.10921.423625.367310.337-30.9714
121.64710.44381.77510.11870.47741.9469-0.7823-0.34950.06950.1445-0.21130.09180.1194-0.3787-1.37720.590.14210.28670.61880.00010.59527.93982.9749-15.9406
130.39950.18070.05670.64560.07220.1815-0.0182-0.2974-0.12180.0678-0.0028-0.20780.17190.3677-00.29160.0226-0.01390.32130.00170.236720.7411-8.1113-22.9983
141.27390.3140.47640.72540.24110.7391-0.1037-0.1596-0.07320.27030.16090.197-0.1144-0.0677-0.00010.30470.0015-0.00890.20620.03980.30194.7995-7.4013-28.2744
150.0990.1034-0.02470.1078-0.06420.16620.0413-0.3931-0.11771.081-0.2966-0.218-0.69720.4142-00.85960.02160.14340.70420.04921.0645-8.8059-10.2923-24.6931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 57:82)A57 - 82
2X-RAY DIFFRACTION2(chain A and resid 83:107)A83 - 107
3X-RAY DIFFRACTION3(chain A and resid 108:160)A108 - 160
4X-RAY DIFFRACTION4(chain A and resid 161:201)A161 - 201
5X-RAY DIFFRACTION5(chain A and resid 202:225)A202 - 225
6X-RAY DIFFRACTION6(chain A and resid 226:310)A226 - 310
7X-RAY DIFFRACTION7(chain A and resid 311:350)A311 - 350
8X-RAY DIFFRACTION8(chain P and resid 56:77)P56 - 77
9X-RAY DIFFRACTION9(chain P and resid 78:128)P78 - 128
10X-RAY DIFFRACTION10(chain P and resid 129:179)P129 - 179
11X-RAY DIFFRACTION11(chain P and resid 180:192)P180 - 192
12X-RAY DIFFRACTION12(chain P and resid 193:224)P193 - 224
13X-RAY DIFFRACTION13(chain P and resid 225:271)P225 - 271
14X-RAY DIFFRACTION14(chain P and resid 272:330)P272 - 330
15X-RAY DIFFRACTION15(chain P and resid 331:348)P331 - 348

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