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- EMDB-32051: native alpha-2-macroglobulin monomer -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-32051
Titlenative alpha-2-macroglobulin monomer
Map data
Sample
  • Tissue: native alpha-2-macroglobulin
    • Protein or peptide: Alpha-2-macroglobulin
Keywordsprotease inhibitor / BLOOD CLOTTING
Function / homology
Function and homology information


negative regulation of complement activation, lectin pathway / interleukin-1 binding / brain-derived neurotrophic factor binding / interleukin-8 binding / response to prostaglandin E / embryonic liver development / acute inflammatory response to antigenic stimulus / luteinization / tumor necrosis factor binding / HDL assembly ...negative regulation of complement activation, lectin pathway / interleukin-1 binding / brain-derived neurotrophic factor binding / interleukin-8 binding / response to prostaglandin E / embryonic liver development / acute inflammatory response to antigenic stimulus / luteinization / tumor necrosis factor binding / HDL assembly / response to carbon dioxide / nerve growth factor binding / endopeptidase inhibitor activity / growth factor binding / response to glucocorticoid / Intrinsic Pathway of Fibrin Clot Formation / Degradation of the extracellular matrix / response to nutrient / platelet alpha granule lumen / acute-phase response / stem cell differentiation / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding / Platelet degranulation / protease binding / collagen-containing extracellular matrix / blood microparticle / signaling receptor binding / enzyme binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Alpha-2-macroglobulin, TED domain / TonB box, conserved site / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 ...Alpha-2-macroglobulin, TED domain / TonB box, conserved site / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Alpha-2-macroglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsHuang X / Wang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Sci China Life Sci / Year: 2022
Title: Cryo-EM structures reveal the dynamic transformation of human alpha-2-macroglobulin working as a protease inhibitor.
Authors: Xiaoxing Huang / Youwang Wang / Cong Yu / Hui Zhang / Qiang Ru / Xinxin Li / Kai Song / Min Zhou / Ping Zhu /
Abstract: Human alpha-2-macroglobulin is a well-known inhibitor of a broad spectrum of proteases and plays important roles in immunity, inflammation, and infections. Here, we report the cryo-EM structures of ...Human alpha-2-macroglobulin is a well-known inhibitor of a broad spectrum of proteases and plays important roles in immunity, inflammation, and infections. Here, we report the cryo-EM structures of human alpha-2-macroglobulin in its native state, induced state transformed by its authentic substrate, human trypsin, and serial intermediate states between the native and fully induced states. These structures exhibit distinct conformations, which reveal the dynamic transformation of alpha-2-macro-globulin that acts as a protease inhibitor. The results shed light on the molecular mechanism of alpha-2-macroglobulin in entrapping substrates.
History
DepositionOct 14, 2021-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32051.png

Downloads & links

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Map

FileDownload / File: emd_32051.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-53.006476999999997 - 62.883270000000003
Average (Standard dev.)-0.000000000000611 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : native alpha-2-macroglobulin

EntireName: native alpha-2-macroglobulin
Components
  • Tissue: native alpha-2-macroglobulin
    • Protein or peptide: Alpha-2-macroglobulin

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Supramolecule #1: native alpha-2-macroglobulin

SupramoleculeName: native alpha-2-macroglobulin / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Alpha-2-macroglobulin

MacromoleculeName: Alpha-2-macroglobulin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 160.108031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GKPQYMVLVP SLLHTETTEK GCVLLSYLNE TVTVSASLES VRGNRSLFTD LEAENDVLHC VAFAVPKSSS NEEVMFLTVQ VKGPTQEFK KRTTVMVKNE DSLVFVQTDK SIYKPGQTVK FRVVSMDENF HPLNELIPLV YIQDPKGNRI AQWQSFQLEG G LKQFSFPL ...String:
GKPQYMVLVP SLLHTETTEK GCVLLSYLNE TVTVSASLES VRGNRSLFTD LEAENDVLHC VAFAVPKSSS NEEVMFLTVQ VKGPTQEFK KRTTVMVKNE DSLVFVQTDK SIYKPGQTVK FRVVSMDENF HPLNELIPLV YIQDPKGNRI AQWQSFQLEG G LKQFSFPL SSEPFQGSYK VVVQKKSGGR TEHPFTVEEF VLPKFEVQVT VPKIITILEE EMNVSVCGLY TYGKPVPGHV TV SICRKYS DASDCHGEDS QAFCEKFSGQ LNSHGCFYQQ VKTKVFQLKR KEYEMKLHTE AQIQEEGTVV ELTGRQSSEI TRT ITKLSF VKVDSHFRQG IPFFGQVRLV DGKGVPIPNK VIFIRGNEAN YYSNATTDEH GLVQFSINTT NVMGTSLTVR VNYK DRSPC YGYQWVSEEH EEAHHTAYLV FSPSKSFVHL EPMSHELPCG HTQTVQAHYI LNGGTLLGLK KLSFYYLIMA KGGIV RTGT HGLLVKQEDM KGHFSISIPV KSDIAPVARL LIYAVLPTGD VIGDSAKYDV ENCLANKVDL SFSPSQSLPA SHAHLR VTA APQSVCALRA VDQSVLLMKP DAELSASSVY NLLPEKDLTG FPGPLNDQDN EDCINRHNVY INGITYTPVS STNEKDM YS FLEDMGLKAF TNSKIRKPKM CPQLQQYEMH GPEGLRVGFY ESDVMGRGHA RLVHVEEPHT ETVRKYFPET WIWDLVVV N SAGVAEVGVT VPDTITEWKA GAFCLSEDAG LGISSTASLR AFQPFFVELT MPYSVIRGEA FTLKATVLNY LPKCIRVSV QLEASPAFLA VPVEKEQAPH CICANGRQTV SWAVTPKSLG NVNFTVSAEA LESQELCGTE VPSVPEHGRK DTVIKPLLVE PEGLEKETT FNSLLCPSGG EVSEELSLKL PPNVVEESAR ASVSVLGDIL GSAMQNTQNL LQMPYGCGEQ NMVLFAPNIY V LDYLNETQ QLTPEIKSKA IGYLNTGYQR QLNYKHYDGS YSTFGERYGR NQGNTWLTAF VLKTFAQARA YIFIDEAHIT QA LIWLSQR QKDNGCFRSS GSLLNNAIKG GVEDEVTLSA YITIALLEIP LTVTHPVVRN ALFCLESAWK TAQEGDHGSH VYT KALLAY AFALAGNQDK RKEVLKSLNE EAVKKDNSVH WERPQKPKAP VGHFYEPQAP SAEVEMTSYV LLAYLTAQPA PTSE DLTSA TNIVKWITKQ QNAQGGFSST QDTVVALHAL SKYGAATFTR TGKAAQVTIQ SSGTFSSKFQ VDNNNRLLLQ QVSLP ELPG EYSMKVTGEG CVYLQTSLKY NILPEKEEFP FALGVQTLPQ TCDEPKAHTS FQISLSVSYT GSRSASNMAI VDVKMV SGF IPLKPTVKML ERSNHVSRTE VSSNHVLIYL DKVSNQTLSL FFTVLQDVPV RDLKPAIVKV YDYYETDEFA IAEYNAP CS

UniProtKB: Alpha-2-macroglobulin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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