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- EMDB-1645: Structure of human erythrocyte anion exchanger 1 revealed by elec... -

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Basic information

Entry
Database: EMDB / ID: EMD-1645
TitleStructure of human erythrocyte anion exchanger 1 revealed by electron crystallography.
Map data3D map of AE1 solved by electron crystallography.
Sample
  • Sample: Membrane domain of anion exchanger 1
  • Protein or peptide: Anion Exchanger 1
KeywordsAE1 / anion exchanger 1 / band 3 / SLC4A1
Biological speciesHomo sapiens (human)
Methodelectron crystallography / cryo EM / Resolution: 7.5 Å
AuthorsYamaguchi T / Ikeda Y / Abe Y / Kuma H / Kang D / Hamasaki N / Hirai T
CitationJournal: J Mol Biol / Year: 2010
Title: Structure of the membrane domain of human erythrocyte anion exchanger 1 revealed by electron crystallography.
Authors: Tomohiro Yamaguchi / Yohei Ikeda / Yoshito Abe / Hiroyuki Kuma / Dongchon Kang / Naotaka Hamasaki / Teruhisa Hirai /
Abstract: The membrane domain of human erythrocyte anion exchanger 1 (AE1) works as a Cl(-)/HCO(3)(-) antiporter. This exchange is a key step for CO(2)/O(2) circulation in the blood. In spite of their ...The membrane domain of human erythrocyte anion exchanger 1 (AE1) works as a Cl(-)/HCO(3)(-) antiporter. This exchange is a key step for CO(2)/O(2) circulation in the blood. In spite of their importance, structural information about AE1 and the AE (anion exchanger) family are still very limited. We used electron microscopy to solve the three-dimensional structure of the AE1 membrane domain, fixed in an outward-open conformation by cross-linking, at 7.5-A resolution. A dimer of AE1 membrane domains packed in two-dimensional array showed a projection map similar to that of the prokaryotic homolog of the ClC chloride channel, a Cl(-)/H(+) antiporter. In a three-dimensional map, there are V-shaped densities near the center of the dimer and slightly narrower V-shaped clusters at a greater distance from the center of the dimer. These appear to be inserted into the membrane from opposite sides. The structural motifs, two homologous pairs of helices in internal repeats of the ClC transporter (helices B+C and J+K), are well fitted to those AE1 densities after simple domain movement.
History
DepositionAug 21, 2009-
Header (metadata) releaseMar 3, 2010-
Map releaseMar 3, 2010-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012294
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.012294
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1645.png

Downloads & links

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Map

FileDownload / File: emd_1645.map.gz / Format: CCP4 / Size: 13.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of AE1 solved by electron crystallography.
Voxel sizeX: 1.21562 Å / Y: 1.26389 Å / Z: 1.23457 Å
Density
Contour LevelBy AUTHOR: 0.012294 / Movie #1: 0.012294
Minimum - Maximum-0.04286516 - 0.04364112
Average (Standard dev.)0.0 (±0.00682935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144160162
Spacing144160162
CellA: 194.4992 Å / B: 182.00017 Å / C: 200.00035 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.215618751.26388888888891.2345679012346
M x/y/z160144162
origin x/y/z0.0000.0000.000
length x/y/z194.499182.000200.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160144162
D min/max/mean-0.0430.044-0.000

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Supplemental data

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Sample components

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Entire : Membrane domain of anion exchanger 1

EntireName: Membrane domain of anion exchanger 1
Components
  • Sample: Membrane domain of anion exchanger 1
  • Protein or peptide: Anion Exchanger 1

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Supramolecule #1000: Membrane domain of anion exchanger 1

SupramoleculeName: Membrane domain of anion exchanger 1 / type: sample / ID: 1000
Details: The sample is cross-linked by H2DIDS. N-terminal cytoplasmic domain is cleaved off by trypsin digestion. Glycosylation is removed by glycosidase.
Oligomeric state: Dimer / Number unique components: 1
Molecular weightExperimental: 55 KDa / Theoretical: 55 KDa / Method: SDS-PAGE

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Macromolecule #1: Anion Exchanger 1

MacromoleculeName: Anion Exchanger 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Band 3 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Erythrocyte / Location in cell: Membrane
Molecular weightExperimental: 55 KDa / Theoretical: 55 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration2.5 mg/mL
GridDetails: Mo grid
VitrificationCryogen name: NITROGEN / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Manual. Excess buffer was removed by pipetting and blotting with filter paper, and then the grid was manually plunged into liquid nitrogen. These operations were ...Details: Vitrification instrument: Manual. Excess buffer was removed by pipetting and blotting with filter paper, and then the grid was manually plunged into liquid nitrogen. These operations were carried out at 4 degrees celsius.
Method: Carbon sandwich method

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Electron microscopy

MicroscopeJEOL 3000SFF
TemperatureAverage: 4 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 31 / Bits/pixel: 12
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Top entry / Specimen holder model: JEOL / Tilt angle min: -60 / Tilt angle max: 60 / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: OTHER / Software - Name: MRC
Crystal parametersUnit cell - A: 194.5 Å / Unit cell - B: 182.0 Å / Unit cell - C: 200 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Plane group: P 2 21 21
CTF correctionDetails: Each film

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Atomic model buiding 1

Initial modelPDB ID:

1ots

SoftwareName: CNS
DetailsProtocol: Rigid Body
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: Free R

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