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- PDB-1hyn: CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF HUMAN ERYTHROCYTE ... -

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Basic information

Entry
Database: PDB / ID: 1hyn
TitleCRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF HUMAN ERYTHROCYTE BAND-3 PROTEIN
ComponentsBAND 3 ANION TRANSPORT PROTEIN
KeywordsMEMBRANE PROTEIN
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 / plasma membrane phospholipid scrambling / monoatomic anion transmembrane transporter activity / 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 / plasma membrane phospholipid scrambling / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / bicarbonate transport / monoatomic anion transport / chloride transport / chloride transmembrane transporter activity / erythrocyte development / negative regulation of glycolytic process through fructose-6-phosphate / ankyrin binding / hemoglobin binding / cortical cytoskeleton / protein-membrane adaptor activity / chloride transmembrane transport / protein localization to plasma membrane / regulation of intracellular pH / transmembrane transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / cytoplasmic side of plasma membrane / Z disc / blood coagulation / basolateral plasma membrane / blood microparticle / 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 / Bicarbonate transporter, eukaryotic ...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 / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter family / Phosphotransferase/anion transporter / 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 / MAD / Resolution: 2.6 Å
AuthorsZhang, D. / Kiyatkin, A. / Bolin, J.T. / Low, P.S.
Citation
Journal: Blood / Year: 2000
Title: Crystallographic structure and functional interpretation of the cytoplasmic domain of erythrocyte membrane band 3.
Authors: Zhang, D. / Kiyatkin, A. / Bolin, J.T. / Low, P.S.
#1: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary X-ray Analysis of the Cytoplasmic Domain of Human Erythrocyte Band 3
Authors: Kiyatkin, A. / Natarajan, P. / Munshi, S. / Minor, W. / Johnson, J.E. / Low, P.S.
History
DepositionJan 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 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
P: BAND 3 ANION TRANSPORT PROTEIN
Q: BAND 3 ANION TRANSPORT PROTEIN
R: BAND 3 ANION TRANSPORT PROTEIN
S: BAND 3 ANION TRANSPORT PROTEIN


Theoretical massNumber of molelcules
Total (without water)170,3064
Polymers170,3064
Non-polymers00
Water5,657314
1
P: BAND 3 ANION TRANSPORT PROTEIN
Q: BAND 3 ANION TRANSPORT PROTEIN


Theoretical massNumber of molelcules
Total (without water)85,1532
Polymers85,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-38 kcal/mol
Surface area24500 Å2
MethodPISA
2
R: BAND 3 ANION TRANSPORT PROTEIN
S: BAND 3 ANION TRANSPORT PROTEIN


Theoretical massNumber of molelcules
Total (without water)85,1532
Polymers85,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-36 kcal/mol
Surface area24720 Å2
MethodPISA
3
P: BAND 3 ANION TRANSPORT PROTEIN
Q: BAND 3 ANION TRANSPORT PROTEIN
R: BAND 3 ANION TRANSPORT PROTEIN
S: BAND 3 ANION TRANSPORT PROTEIN

P: BAND 3 ANION TRANSPORT PROTEIN
Q: BAND 3 ANION TRANSPORT PROTEIN
R: BAND 3 ANION TRANSPORT PROTEIN
S: BAND 3 ANION TRANSPORT PROTEIN


Theoretical massNumber of molelcules
Total (without water)340,6128
Polymers340,6128
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area27300 Å2
ΔGint-194 kcal/mol
Surface area91310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.590, 92.580, 123.330
Angle α, β, γ (deg.)90.00, 131.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
BAND 3 ANION TRANSPORT PROTEIN / / ANION EXCHANGE PROTEIN 1 / AE1


Mass: 42576.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02730
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 4.8
Details: METHOD: SITTING DROP VAPOR DIFFUSION WITH SEEDING. TEMPERATURE: 293 K. RESERVOIR: 50-53% SATURATED AMMONIUM SULFATE, 150mM SODIUM CITRATE PH 4.8. PROTEIN: 7 mg/ml PROTEIN IN 5mM SODIUM ...Details: METHOD: SITTING DROP VAPOR DIFFUSION WITH SEEDING. TEMPERATURE: 293 K. RESERVOIR: 50-53% SATURATED AMMONIUM SULFATE, 150mM SODIUM CITRATE PH 4.8. PROTEIN: 7 mg/ml PROTEIN IN 5mM SODIUM PHOSPHATE PH 6.8, 10 mM SODIUM CHLORIDE.
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, sitting drop
Details: Kiyatkin, A., (1995) Proteins: Struct., Funct., Genet., 22, 293.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2-2 mg/mlprotein1drop
25 mMsodium phosphate1drop
3150 mM1dropNaCl
41 mMEDTA1drop
51 mMsodium azide1drop
61 mMdithiothreitol1drop
730 %(v/v)glycerol1drop
865-68 %satammonium sulfate1reservoir
9150 mMsodium citrate1reservoir
101 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9789, 0.9796, 0.9537
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Sep 23, 1998 / Details: RH-coated toroidal mirror
RadiationMonochromator: double crystal SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97961
30.95371
ReflectionResolution: 2.59→50 Å / Num. obs: 46609 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 46.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 37.16
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 18.7 / Rsym value: 0.175 / % possible all: 48.7
Reflection
*PLUS
Lowest resolution: 35 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.208

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Processing

Software
NameClassification
SOLVEphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→8 Å / Data cutoff high absF: 0.1 / Data cutoff low absF: 100000 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3612 8.1 %random
Rwork0.216 ---
obs-44748 99 %-
Displacement parametersBiso mean: 31.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9384 0 0 314 9698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.08
X-RAY DIFFRACTIONx_angle_deg1.67
X-RAY DIFFRACTIONx_dihedral_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d1.209
X-RAY DIFFRACTIONx_mcbond_it3.52.88
X-RAY DIFFRACTIONx_mcangle_it5.54.74
X-RAY DIFFRACTIONx_scbond_it55.84
X-RAY DIFFRACTIONx_scangle_it89.1
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.323 429 7.9 %
Rwork0.29 4986 -
obs--98 %
Xplor fileSerial no: 1 / Param file: parhcsdx.pro
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 8.1 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.209
X-RAY DIFFRACTIONx_mcbond_it3.52.88
X-RAY DIFFRACTIONx_scbond_it55.84
X-RAY DIFFRACTIONx_mcangle_it5.54.74
X-RAY DIFFRACTIONx_scangle_it89.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.323 / % reflection Rfree: 7.9 % / Rfactor Rwork: 0.29

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