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- EMDB-4620: A dimer component of alpha-1 antitrypsin heat-induced polymers ge... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4620 | ||||||||||||
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Title | A dimer component of alpha-1 antitrypsin heat-induced polymers generated from wild-type M plasma protein and decorated with Fab 4B12 | ||||||||||||
![]() | Unmasked dimer component of alpha-1 antitrypsin heat-induced polymers generated from purified plasma wild-type M variant; subunits rotated ~60 degrees around dimer axis. | ||||||||||||
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Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.4 Å | ||||||||||||
![]() | Elliston ELK / Redzej A / Orlova EV / Lomas DA / Irving JA | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The structural basis for Z α-antitrypsin polymerization in the liver. Authors: Sarah V Faull / Emma L K Elliston / Bibek Gooptu / Alistair M Jagger / Ibrahim Aldobiyan / Adam Redzej / Magd Badaoui / Nina Heyer-Chauhan / S Tamir Rashid / Gary M Reynolds / David H Adams ...Authors: Sarah V Faull / Emma L K Elliston / Bibek Gooptu / Alistair M Jagger / Ibrahim Aldobiyan / Adam Redzej / Magd Badaoui / Nina Heyer-Chauhan / S Tamir Rashid / Gary M Reynolds / David H Adams / Elena Miranda / Elena V Orlova / James A Irving / David A Lomas / ![]() ![]() Abstract: The serpinopathies are among a diverse set of conformational diseases that involve the aberrant self-association of proteins into ordered aggregates. α-Antitrypsin deficiency is the archetypal ...The serpinopathies are among a diverse set of conformational diseases that involve the aberrant self-association of proteins into ordered aggregates. α-Antitrypsin deficiency is the archetypal serpinopathy and results from the formation and deposition of mutant forms of α-antitrypsin as "polymer" chains in liver tissue. No detailed structural analysis has been performed of this material. Moreover, there is little information on the relevance of well-studied artificially induced polymers to these disease-associated molecules. We have isolated polymers from the liver tissue of Z α-antitrypsin homozygotes (E342K) who have undergone transplantation, labeled them using a Fab fragment, and performed single-particle analysis of negative-stain electron micrographs. The data show structural equivalence between heat-induced and ex vivo polymers and that the intersubunit linkage is best explained by a carboxyl-terminal domain swap between molecules of α-antitrypsin. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.1 KB 22.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.4 KB | Display | ![]() |
Images | ![]() | 33.4 KB | ||
Masks | ![]() | 12.9 MB | ![]() | |
Others | ![]() ![]() | 1.5 MB 1.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Unmasked dimer component of alpha-1 antitrypsin heat-induced polymers generated from purified plasma wild-type M variant; subunits rotated ~60 degrees around dimer axis. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Tightly masked dimer component of alpha-1 antitrypsin heat-induced...
File | emd_4620_additional.map | ||||||||||||
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Annotation | Tightly masked dimer component of alpha-1 antitrypsin heat-induced polymers generated from purified plasma wild-type M variant; subunits rotated ~60 degrees around dimer axis. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Tightly masked dimer component of alpha-1 antitrypsin heat-induced...
File | emd_4620_additional_1.map | ||||||||||||
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Annotation | Tightly masked dimer component of alpha-1 antitrypsin heat-induced polymers generated from purified plasma wild-type M variant; subunits rotated ~60 degrees around dimer axis. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Polymers induced by heating monomeric wild-type alpha-1 antitryps...
Entire | Name: Polymers induced by heating monomeric wild-type alpha-1 antitrypsin and labelled with 4B12 Fab fragments |
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Components |
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-Supramolecule #1: Polymers induced by heating monomeric wild-type alpha-1 antitryps...
Supramolecule | Name: Polymers induced by heating monomeric wild-type alpha-1 antitrypsin and labelled with 4B12 Fab fragments type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all Details: Polymers of alpha-1 antitrypsin were prepared from purified plasma protein by heating at 55 degrees C for 48 hours and purified by chromatography. These were labelled with the Fab fragment ...Details: Polymers of alpha-1 antitrypsin were prepared from purified plasma protein by heating at 55 degrees C for 48 hours and purified by chromatography. These were labelled with the Fab fragment of a non-conformationally selective monoclonal antibody (4B12). |
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Source (natural) | Organism: ![]() |
-Supramolecule #2: Complex between two 4B12 Fab fragments and a dimer component of p...
Supramolecule | Name: Complex between two 4B12 Fab fragments and a dimer component of polymers induced by heating of the wild-type M alpha-1 antitrypsin variant type: complex / ID: 2 / Parent: 1 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 200 KDa |
-Macromolecule #1: Alpha-1 antitrypsin
Macromolecule | Name: Alpha-1 antitrypsin / type: protein_or_peptide / ID: 1 / Details: Wild-type M variant of alpha-1 antitrypsin / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: EDPQGDAAQK TDTSHHDQDH PTFNKITPNL AEFAFS LYR QLAHQSNSTN IFFSPVSIAT AFAMLSLGTK ADTHDEILEG LNFNLTEIPE AQIHEGF QE LLRTLNQPDS QLQLTTGNGL FLSEGLKLVD KFLEDVKKLY HSEAFTVNFG DTEEAKKQ I NDYVEKGTQG ...String: EDPQGDAAQK TDTSHHDQDH PTFNKITPNL AEFAFS LYR QLAHQSNSTN IFFSPVSIAT AFAMLSLGTK ADTHDEILEG LNFNLTEIPE AQIHEGF QE LLRTLNQPDS QLQLTTGNGL FLSEGLKLVD KFLEDVKKLY HSEAFTVNFG DTEEAKKQ I NDYVEKGTQG KIVDLVKELD RDTVFALVNY IFFKGKWERP FEVKDTEEED FHVDQVTTV KVPMMKRLGM FNIQHCKKLS SWVLLMKYLG NATAIFFLPD EGKLQHLENE LTHDIITKFL ENEDRRSAS LHLPKLSITG TYDLKSVLGQ LGITKVFSNG ADLSGVTEEA PLKLSKAVHK A VLTIDEKG TEAAGAMFLE AIPMSIPPEV KFNKPFVFLM IEQNTKSPLF MGKVVNPTQK |
-Macromolecule #2: 4B12 Fab heavy chain
Macromolecule | Name: 4B12 Fab heavy chain / type: protein_or_peptide / ID: 2 Details: Heavy chain of the Fab fragment of a non-conformationally-selective antibody (4B12) that binds to alpha-1-antitrypsin Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: QVKLEESGPE LVKPGASVKI SCKASGYSFI GYYMHWVKQS HVKSLEWIGR INPYNGATRY NQNFQDRATL TVDKSSSTAY MDFHSLTSED SAVYYCVRWP GDYWGQGTSV TVSSAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP VTVTWNSGSL SSGVHTFPAV ...String: QVKLEESGPE LVKPGASVKI SCKASGYSFI GYYMHWVKQS HVKSLEWIGR INPYNGATRY NQNFQDRATL TVDKSSSTAY MDFHSLTSED SAVYYCVRWP GDYWGQGTSV TVSSAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP VTVTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK IVPRDCTS |
-Macromolecule #3: 4B12 Fab light chain
Macromolecule | Name: 4B12 Fab light chain / type: protein_or_peptide / ID: 3 Details: Light chain of the Fab fragment of a non-conformationally-selective antibody (4B12) that binds to alpha-1-antitrypsin Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: DIVMTQTPSS LSASLGGKVT ITCKASQDIN NYIAWYQLKP GKGPRQLIHY TSKLQPGIPS RFSGSGSGSD YSFSISNLEP EDIGTYYCLR YEDLWTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS ...String: DIVMTQTPSS LSASLGGKVT ITCKASQDIN NYIAWYQLKP GKGPRQLIHY TSKLQPGIPS RFSGSGSGSD YSFSISNLEP EDIGTYYCLR YEDLWTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS TYSMSSTLTL TKDEYERHNS YTCEATHKTS TSPIVKSFN |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.04 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Staining | Type: NEGATIVE / Material: Uranyl acetate Details: 3 microlitres of prepared sample was applied to glow-discharged carbon film on 400 mesh copper (CF400-Cu) grids. Sample was bound to the grid for 1 minute before blotting excess solution ...Details: 3 microlitres of prepared sample was applied to glow-discharged carbon film on 400 mesh copper (CF400-Cu) grids. Sample was bound to the grid for 1 minute before blotting excess solution with filter paper, rinsing with water twice. 4 microlitres of 2% w/v uranyl acetate was applied for 1 minute before blotting; this was repeated once. | ||||||||||||
Grid | Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Details | The sample comprises a mixed population of unbranched polymers of varying lengths, labelled with the Fab fragment of the 4B12 antibody. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Digitization - Dimensions - Width: 5120 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Sampling interval: 6.4 µm / Digitization - Frames/image: 1-18 / Number grids imaged: 1 / Number real images: 169 / Average exposure time: 1.8 sec. / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 1.15 µm / Calibrated defocus min: 0.233 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 41470 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |