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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24848 | |||||||||
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Title | Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer | |||||||||
![]() | Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.12 Å | |||||||||
![]() | Arimura Y / Funabiki H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Mechanics of the Alpha-2-Macroglobulin Transformation. Authors: Yasuhiro Arimura / Hironori Funabiki / ![]() Abstract: Alpha-2-Macroglobulin (A2M) is the critical pan-protease inhibitor of the innate immune system. When proteases cleave the A2M bait region, global structural transformation of the A2M tetramer is ...Alpha-2-Macroglobulin (A2M) is the critical pan-protease inhibitor of the innate immune system. When proteases cleave the A2M bait region, global structural transformation of the A2M tetramer is triggered to entrap the protease. The structural basis behind the cleavage-induced transformation and the protease entrapment remains unclear. Here, we report cryo-EM structures of native- and intermediate-forms of the Xenopus laevis egg A2M homolog (A2Moo or ovomacroglobulin) tetramer at 3.7-4.1 Å and 6.4 Å resolution, respectively. In the native A2Moo tetramer, two pairs of dimers arrange into a cross-like configuration with four 60 Å-wide bait-exposing grooves. Each bait in the native form threads into an aperture formed by three macroglobulin domains (MG2, MG3, MG6). The bait is released from the narrowed aperture in the induced protomer of the intermediate form. We propose that the intact bait region works as a "latch-lock" to block futile A2M transformation until its protease-mediated cleavage. | |||||||||
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 | ![]() | 56.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.1 KB 21.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 154.8 KB | ||
Others | ![]() ![]() ![]() | 59.4 MB 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7s63MC ![]() 7s62C ![]() 7s64C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer
File | emd_24848_additional_1.map | ||||||||||||
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Annotation | Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer
File | emd_24848_half_map_1.map | ||||||||||||
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Annotation | Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer
File | emd_24848_half_map_2.map | ||||||||||||
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Annotation | Native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer
Entire | Name: native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer |
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Components |
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-Supramolecule #1: native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer
Supramolecule | Name: native-form oocyte/egg Alpha-2-Macroglobulin (A2Moo) tetramer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Alpha 2-Macroglobulin
Macromolecule | Name: Alpha 2-Macroglobulin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 159.480812 KDa |
Sequence | String: MSPNRFLLCV CILGLIAGGA AKVQYALTIP ALLKSGETQR ACVNLIGYHQ PLALSVVLEH QRVNISIFSE KVQPPHYFKC NKFMVPTVI TNAPDFVTLS VSGGGEDIKD RKAVVIAPLN TICLIQMDKP VYKPGCKVRF RLISLNTMLL PISEKYTAVY L EDPSGSRI ...String: MSPNRFLLCV CILGLIAGGA AKVQYALTIP ALLKSGETQR ACVNLIGYHQ PLALSVVLEH QRVNISIFSE KVQPPHYFKC NKFMVPTVI TNAPDFVTLS VSGGGEDIKD RKAVVIAPLN TICLIQMDKP VYKPGCKVRF RLISLNTMLL PISEKYTAVY L EDPSGSRI AQWQNQESVG GVVQLEFPLI SDAAPGSYTI TAEGESCESA RQGFTVDEYI LPRFSVIVDP PNTISILDDI LT LNVSAIY TYGQPVPGSV TIKCCREASS YYGRKGNCFK GNRGICTNIT GELGPDGAFY GVVSLLPFQM GQSGFQMSLG VAL TVTEEG TGIQVTHQFF IMITSQLATL IFDYDALKEF YKRGIPYLVK VILTDANDNP MANEQVEVEL AGKTIGAVLT DKEG RAEYA IDTSSFVQEN FTVVVSYENP HQCYYTEWEG PDFPTAQHFV MRFYSETGSF LDIQGSSVEL NCGQVHNISV RYILS LDGM GEGATTATFY YLAMSRAKIV QHGQRDVHLN QSKSGLFNIG LNVTSDLAPG AELIVYCILD LELIADTISL DIEKCF QNQ VSLSFSDDLG PTASNVSLNL SAAPGSLCGV KVIDSSLLLI NPYESLSASG VYYSIPYLSL FGYNYGGFNL EEPEPPC ED PNTVIFCKGR YYLPVSSSTE GDTYQNLRRV GLVLGTSSKI RKPVVCGMEA KFSVPRKSSG ESDFGSSLSN GHVETLRK N FSETFLWRLV SVDSEGQNTI TETVPDTITK WQGSMFCVSE KEGFGITKYS ANFTSFLPFF VELSLPYSLT REEILVMKA FVSNYLEECI KIIVTLQPSA DFEVIPQDVK QDQCICSGGR SSYSWNIIAS SLGRISFIVS AETTHIGASC DGPSDQSQST RKDTVIQTI LVQPEGIRKE ETSSNLVCVE DSNVEMPINL TLPENIVQGS ASAFVTFVGD VLGLPLSNLQ NLLQMPYGCG E QNLARMAP IPYVLEYLNN TNQLTDELLQ TAVQFLNEGY YRQLRYKLPS GAYDAFWSSP SDGSSWLSAY TFKTFEKAKK YI YVDGKIQ QQTLLYLQTS QKLDNGCFKA EGNLFMRQCG QERDLCFTAY LAIALLESNY SSGMTLLDDA LGCLEAAMSS AST LYFKSY TVYVFTLVQN WEIRNTLLNE LKSKVVSERG TLHWEREDKL GQEGIPLYYP NYSPAEVEIT AYMLLSIAKG SDPT HDDLT YMAQISVWLI QQQNSYGGFR STQDTVVALQ ALAFYAQLLF KSNAHHNVFL RSEYGDVGQL NLSEHNRLVV QRLQL PEVS GNYSISINGT GCCLVQSTIR YNIPVPKENS AFYVAADSVS KNCLNGVAYT ITITVSVSYR GLRNETNMVI IDIQML SGY QADYPSLRQL ENSQQVSKTE EQDNHVFLYL NAVPLKTIQL SFKVLIGSRV LNVKSASVYV YDYYETGENG FASYSQP C |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 68 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 33.11 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Average electron dose: 38.34 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #2 - Detector mode: SUPER-RESOLUTION / #2 - Average electron dose: 35.27 e/Å2 / #3 - Image recording ID: 4 / #3 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #3 - Detector mode: SUPER-RESOLUTION / #3 - Average electron dose: 34.2 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |