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- PDB-4yzf: Crystal structure of the anion exchanger domain of human erythroc... -

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Basic information

Entry
Database: PDB / ID: 4yzf
TitleCrystal structure of the anion exchanger domain of human erythrocyte Band 3
Components
  • (FAB fragment of Immunoglobulin (IgG) molecule) x 2
  • Band 3 anion transport protein
KeywordsIMMUNE SYSTEM / Human membrane protein / anion exchanger / erythrocytes
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
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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-4KU / Band 3 anion transport protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsAlguel, Y. / Arakawa, T. / Yugiri, T.K. / Iwanari, H. / Hatae, H. / Iwata, M. / Abe, Y. / Hino, T. / Suno, C.I. / Kuma, H. ...Alguel, Y. / Arakawa, T. / Yugiri, T.K. / Iwanari, H. / Hatae, H. / Iwata, M. / Abe, Y. / Hino, T. / Suno, C.I. / Kuma, H. / Kang, D. / Murata, T. / Hamakubo, T. / Cameron, A.D. / Kobayashi, T. / Hamasaki, N. / Iwata, S.
CitationJournal: Science / Year: 2015
Title: Crystal structure of the anion exchanger domain of human erythrocyte band 3.
Authors: Arakawa, T. / Kobayashi-Yurugi, T. / Alguel, Y. / Iwanari, H. / Hatae, H. / Iwata, M. / Abe, Y. / Hino, T. / Ikeda-Suno, C. / Kuma, H. / Kang, D. / Murata, T. / Hamakubo, T. / Cameron, A.D. ...Authors: Arakawa, T. / Kobayashi-Yurugi, T. / Alguel, Y. / Iwanari, H. / Hatae, H. / Iwata, M. / Abe, Y. / Hino, T. / Ikeda-Suno, C. / Kuma, H. / Kang, D. / Murata, T. / Hamakubo, T. / Cameron, A.D. / Kobayashi, T. / Hamasaki, N. / Iwata, S.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references

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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
B: Band 3 anion transport protein
C: Band 3 anion transport protein
D: Band 3 anion transport protein
E: FAB fragment of Immunoglobulin (IgG) molecule
F: FAB fragment of Immunoglobulin (IgG) molecule
G: FAB fragment of Immunoglobulin (IgG) molecule
H: FAB fragment of Immunoglobulin (IgG) molecule
I: FAB fragment of Immunoglobulin (IgG) molecule
J: FAB fragment of Immunoglobulin (IgG) molecule
K: FAB fragment of Immunoglobulin (IgG) molecule
L: FAB fragment of Immunoglobulin (IgG) molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)601,71516
Polymers599,85712
Non-polymers1,8584
Water0
1
A: Band 3 anion transport protein
B: Band 3 anion transport protein
E: FAB fragment of Immunoglobulin (IgG) molecule
F: FAB fragment of Immunoglobulin (IgG) molecule
G: FAB fragment of Immunoglobulin (IgG) molecule
H: FAB fragment of Immunoglobulin (IgG) molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,8588
Polymers299,9286
Non-polymers9292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Band 3 anion transport protein
D: Band 3 anion transport protein
I: FAB fragment of Immunoglobulin (IgG) molecule
J: FAB fragment of Immunoglobulin (IgG) molecule
K: FAB fragment of Immunoglobulin (IgG) molecule
L: FAB fragment of Immunoglobulin (IgG) molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,8588
Polymers299,9286
Non-polymers9292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.825, 171.957, 271.700
Angle α, β, γ (deg.)90.00, 101.16, 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 / Anion exchanger 1 / Solute carrier family 4 member 1


Mass: 101883.859 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Outward facing structure of human anion exchanger 1 (Band 3) in co-crystallised with FAB antibody fragments.
Source: (natural) Homo sapiens (human) / References: UniProt: P02730
#2: Antibody
FAB fragment of Immunoglobulin (IgG) molecule


Mass: 23971.762 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody
FAB fragment of Immunoglobulin (IgG) molecule


Mass: 24108.564 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical
ChemComp-4KU / 2,2'-ethane-1,2-diylbis{5-[(sulfanylmethyl)amino]benzenesulfonic acid}


Mass: 464.600 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20N2O6S4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100 mM Tris-HCl (pH 8.0), 22-26 %(v/v) PEG300, 250 mM CH3COOK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.91731
ReflectionResolution: 3.5→50 Å / Num. obs: 84446 / % possible obs: 97.3 % / Redundancy: 5.6 % / Net I/σ(I): 18
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.6 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1951)refinement
xia2data reduction
SHARPphasing
Cootmodel building
Omodel building
xia2data scaling
RefinementResolution: 3.5→37.718 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2901 8122 5.01 %
Rwork0.2744 --
obs0.2752 162116 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→37.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28724 0 0 0 28724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829484
X-RAY DIFFRACTIONf_angle_d1.36940148
X-RAY DIFFRACTIONf_dihedral_angle_d15.23210584
X-RAY DIFFRACTIONf_chiral_restr0.0564656
X-RAY DIFFRACTIONf_plane_restr0.0074936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4969-3.53660.42492370.40444402X-RAY DIFFRACTION83
3.5366-3.57820.36932500.39545024X-RAY DIFFRACTION91
3.5782-3.62180.43452310.38464640X-RAY DIFFRACTION86
3.6218-3.66760.3932370.36814310X-RAY DIFFRACTION80
3.6676-3.71580.38162440.36974899X-RAY DIFFRACTION89
3.7158-3.76670.36622510.35865138X-RAY DIFFRACTION96
3.7667-3.82040.33712690.34415304X-RAY DIFFRACTION96
3.8204-3.87740.33993040.3325112X-RAY DIFFRACTION97
3.8774-3.93790.30882300.32385337X-RAY DIFFRACTION97
3.9379-4.00240.34742790.31565242X-RAY DIFFRACTION97
4.0024-4.07140.32022630.31255291X-RAY DIFFRACTION97
4.0714-4.14530.36772550.30165249X-RAY DIFFRACTION97
4.1453-4.22490.31023100.28995291X-RAY DIFFRACTION97
4.2249-4.31110.29243020.27365237X-RAY DIFFRACTION98
4.3111-4.40470.29022740.2665338X-RAY DIFFRACTION98
4.4047-4.5070.24332480.25115248X-RAY DIFFRACTION97
4.507-4.61950.29882590.24185375X-RAY DIFFRACTION98
4.6195-4.74420.23023170.23125235X-RAY DIFFRACTION98
4.7442-4.88350.22832930.23155263X-RAY DIFFRACTION98
4.8835-5.04070.22152990.23095273X-RAY DIFFRACTION97
5.0407-5.22050.26482770.24585300X-RAY DIFFRACTION96
5.2205-5.42890.24952260.2514718X-RAY DIFFRACTION88
5.4289-5.67520.31892730.26125184X-RAY DIFFRACTION96
5.6752-5.97330.25692920.27075339X-RAY DIFFRACTION99
5.9733-6.34590.34032700.26765383X-RAY DIFFRACTION98
6.3459-6.83320.30693080.28355252X-RAY DIFFRACTION98
6.8332-7.5160.27722770.25065331X-RAY DIFFRACTION98
7.516-8.59230.24143140.20725250X-RAY DIFFRACTION97
8.5923-10.78330.20072360.19025052X-RAY DIFFRACTION92
10.7833-37.72060.31512970.3274977X-RAY DIFFRACTION92
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)
10.8435-0.4289-1.25451.0744-2.00584.77570.0586-0.26620.64420.45850.00130.4752-0.5886-1.0979-0.44150.77430.4852-0.54880.5891-0.04551.46318.361310.218143.366
20.97890.7148-1.43980.9936-1.30113.77380.1151-0.05890.34010.40310.01760.7109-0.1929-1.0741-0.02151.26090.34760.02561.4859-0.19821.5411-13.0546-7.568787.7217
30.45360.7332-2.12570.71-1.29294.4989-0.0742-0.02570.56350.22580.34460.4242-0.7989-0.9909-0.18670.95160.2597-0.50790.8799-0.22671.4403-67.489811.426542.8411
40.93530.6269-1.45771.0105-1.28654.572-0.02050.00460.35340.4238-0.03590.7303-0.3617-1.1155-0.00861.27140.4373-0.04641.8687-0.37741.5243-88.5876-5.646587.6102
52.1738-1.746-0.38892.3816-0.0042.7314-0.32960.3473-0.4740.1037-0.6236-0.12660.52560.1991-2.36150.8910.5741-0.1020.72920.48011.305939.6424-12.38714.722
62.8603-0.3828-1.07474.0110.96312.2176-0.21180.1203-0.921-0.25170.7867-0.30770.4998-0.27451.40851.34570.55020.0551.01650.38051.876470.8062-33.668913.1944
72.27560.3499-0.05170.8284-0.16422.2349-0.3819-0.5729-0.66520.11370.0450.30610.7307-0.1815-0.93260.62231.5553-0.2472-0.27421.25481.152140.0364-22.575734.1242
84.8520.93-0.67383.39191.48473.20970.2867-1.177-0.3564-0.4216-0.036-0.68-0.0521.1207-0.03031.21110.4363-0.10641.36730.39891.473876.0109-28.998627.2185
92.9141-2.20460.33184.0299-1.27621.65990.10740.1488-0.2641-0.0468-0.27560.1985-0.40350.4177-0.17231.85260.1936-0.21411.4825-0.05440.9886.0224-39.9278117.6749
103.13440.6925-1.04342.0323-0.51664.86140.06390.4486-1.28820.76090.102-0.80081.2340.74820.07082.19780.25320.19451.82050.26152.201629.7385-61.7528125.1843
112.1098-0.1083-0.33992.8599-0.88211.83690.52320.8830.4267-0.8737-0.5285-0.7359-0.41530.2252-0.09921.80780.15030.21071.72770.03161.64417.0916-40.578398.9132
120.2819-0.6228-0.02984.6271-1.81720.81610.2499-0.5621-0.06910.33010.1099-0.2614-0.38330.63990.71422.77340.84220.37842.6415-0.20632.236931.1609-72.715114.1155
134.4611-1.7904-0.69023.4706-1.12086.6595-0.29280.2198-0.24760.5857-0.0412-0.12760.2568-0.21180.35230.8404-0.0379-0.18520.6669-0.05821.081-39.1732-12.831112.5171
141.9509-0.189-0.79724.30030.90051.1956-1.1547-0.5815-1.12740.64950.4617-0.97372.47132.51511.349631.22170.78892.86220.21282.8262-10.3713-36.7159.7906
154.37040.1782-0.39522.0044-0.33314.8002-0.1092-0.4756-0.33430.60330.34930.26940.2660.2709-0.20541.2830.24590.04240.7774-0.03821.4663-39.8082-23.723431.4683
163.9783-0.4481-2.08522.75033.23784.52760.396-0.48691.4736-1.8340.6798-1.1602-0.04151.33360.70423.31870.3764-0.69992.02771.02813.0806-4.935-32.743623.9369
172.9773-2.08340.40314.0918-1.69551.3379-0.28650.2497-0.2734-0.0570.08840.48-0.26380.1271-0.16961.71090.0235-0.19461.4958-0.25581.019-71.035-39.6962116.7536
183.21240.5078-0.95271.8827-0.95134.82260.3507-0.3448-0.57160.5252-0.3673-0.67451.94020.69870.09272.35960.14360.10521.55060.06372.1285-48.6915-62.7026123.9679
192.0723-0.3026-0.35892.8223-0.75612.03490.21760.2780.4535-0.4382-0.3729-0.8001-0.1173-0.1999-0.08951.71440.0030.19361.6979-0.06511.5227-60.4141-40.894997.7628
200.1287-0.40030.1774.6883-2.12740.88610.5395-1.15251.05770.8685-0.2637-0.21050.11730.29460.70212.80990.3560.39912.2833-0.62462.0877-47.7799-73.796113.0596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E and resi 1:121
6X-RAY DIFFRACTION6chain E and resi 122:223
7X-RAY DIFFRACTION7chain F and resi 1:111
8X-RAY DIFFRACTION8chain F and resi 112:218
9X-RAY DIFFRACTION9chain G and resi 1:121
10X-RAY DIFFRACTION10chain G and resi 122:223
11X-RAY DIFFRACTION11chain H and resi 1:111
12X-RAY DIFFRACTION12chain H and resi 112:218
13X-RAY DIFFRACTION13chain I and resi 1:121
14X-RAY DIFFRACTION14chain I and resi 122:223
15X-RAY DIFFRACTION15chain J and resi 1:111
16X-RAY DIFFRACTION16chain J and resi 112:218
17X-RAY DIFFRACTION17chain K and resi 1:121
18X-RAY DIFFRACTION18chain K and resi 122:223
19X-RAY DIFFRACTION19chain L and resi 1:111
20X-RAY DIFFRACTION20chain L and resi 112:218

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