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- EMDB-20795: Integrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-20795
TitleIntegrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Primary map: sharpened, focused refinement. Five additional maps.)
Map dataIntegrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Primary map: sharpened, focused refinement, 3.5 A resolution. Five additional maps.)
Sample
  • Complex: Ternary complex of Integrin alpha-v beta-8 with Fab C6D4 and Fab 11D12v2
    • Complex: alpha-v beta-8 integrin
      • Protein or peptide: Integrin alpha-VIntegrin alpha V
      • Protein or peptide: Integrin beta-8
    • Complex: C6D4 Fab
      • Protein or peptide: C6D4 heavy chain Fab
      • Protein or peptide: C6D4 light chain Fab
    • Complex: 11D12v2 Fab
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


ganglioside metabolic process / Langerhans cell differentiation / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding ...ganglioside metabolic process / Langerhans cell differentiation / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / Laminin interactions / placenta blood vessel development / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / regulation of phagocytosis / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / filopodium membrane / positive regulation of small GTPase mediated signal transduction / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of epidermal cells / cartilage development / apoptotic cell clearance / heterotypic cell-cell adhesion / integrin complex / positive regulation of intracellular signal transduction / Molecules associated with elastic fibres / cell adhesion mediated by integrin / microvillus membrane / Syndecan interactions / negative chemotaxis / endodermal cell differentiation / cell-substrate adhesion / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / fibronectin binding / positive regulation of cell adhesion / ECM proteoglycans / voltage-gated calcium channel activity / vasculogenesis / Integrin cell surface interactions / specific granule membrane / coreceptor activity / phagocytic vesicle / extrinsic apoptotic signaling pathway in absence of ligand / ERK1 and ERK2 cascade / cell-matrix adhesion / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / protein kinase C binding / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / calcium ion transmembrane transport / response to virus / cell-cell adhesion / ruffle membrane / VEGFA-VEGFR2 Pathway / positive regulation of angiogenesis / cell migration / integrin binding / virus receptor activity / positive regulation of cytosolic calcium ion concentration / angiogenesis / protease binding / cell adhesion / positive regulation of cell migration / immune response / symbiont entry into host cell / external side of plasma membrane / negative regulation of gene expression / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region ...: / Integrin alpha Ig-like domain 3 / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Integrin alpha-V / Integrin beta-8
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsCampbell MG / Cormier A / Cheng Y / Nishimura SL
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)U54HL119893 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL134183 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL113032 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)S10OD020054 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01GM098672 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P41CA196276 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)S10OD021741 United States
CitationJournal: Cell / Year: 2020
Title: Cryo-EM Reveals Integrin-Mediated TGF-β Activation without Release from Latent TGF-β.
Authors: Melody G Campbell / Anthony Cormier / Saburo Ito / Robert I Seed / Andrew J Bondesson / Jianlong Lou / James D Marks / Jody L Baron / Yifan Cheng / Stephen L Nishimura /
Abstract: Integrin αvβ8 binds with exquisite specificity to latent transforming growth factor-β (L-TGF-β). This binding is essential for activating L-TGF-β presented by a variety of cell types. ...Integrin αvβ8 binds with exquisite specificity to latent transforming growth factor-β (L-TGF-β). This binding is essential for activating L-TGF-β presented by a variety of cell types. Inhibiting αvβ8-mediated TGF-β activation blocks immunosuppressive regulatory T cell differentiation, which is a potential therapeutic strategy in cancer. Using cryo-electron microscopy, structure-guided mutagenesis, and cell-based assays, we reveal the binding interactions between the entire αvβ8 ectodomain and its intact natural ligand, L-TGF-β, as well as two different inhibitory antibody fragments to understand the structural underpinnings of αvβ8 binding specificity and TGF-β activation. Our studies reveal a mechanism of TGF-β activation where mature TGF-β signals within the confines of L-TGF-β and the release and diffusion of TGF-β are not required. The structural details of this mechanism provide a rational basis for therapeutic strategies to inhibit αvβ8-mediated L-TGF-β activation.
History
DepositionOct 2, 2019-
Header (metadata) releaseOct 16, 2019-
Map releaseFeb 5, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.75
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.75
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ujb
  • Surface level: 0.75
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ujb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20795.png

Downloads & links

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Map

FileDownload / File: emd_20795.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIntegrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Primary map: sharpened, focused refinement, 3.5 A resolution. Five additional maps.)
Voxel sizeX=Y=Z: 1.345 Å
Density
Contour LevelBy AUTHOR: 0.75 / Movie #1: 0.75
Minimum - Maximum-2.3280354 - 4.3353744
Average (Standard dev.)0.003037052 (±0.060404006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 403.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3451.3451.345
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z403.500403.500403.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-2.3284.3350.003

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Supplemental data

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Additional map: Integrin alpha-v beta-8 in complex with Fabs C6D4...

Fileemd_20795_additional_1.map
AnnotationIntegrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Additional map: unsharpened, focused refinement.)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Integrin alpha-v beta-8 in complex with Fabs C6D4...

Fileemd_20795_additional_2.map
AnnotationIntegrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Additional map: sharpened, full complex, 3.8 A resolution)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Integrin alpha-v beta-8 in complex with Fabs C6D4...

Fileemd_20795_additional_3.map
AnnotationIntegrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Additional map: unsharpened, full complex.)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Integrin alpha-v beta-8 in complex with Fabs C6D4...

Fileemd_20795_additional_4.map
AnnotationIntegrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Additional map: sharpened, focused refinement ii, 3.3 A resolution)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Integrin alpha-v beta-8 in complex with Fabs C6D4...

Fileemd_20795_additional_5.map
AnnotationIntegrin alpha-v beta-8 in complex with Fabs C6D4 and 11D12v2 (Additional map: unsharpened, focused refinement ii.)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of Integrin alpha-v beta-8 with Fab C6D4 and Fab ...

EntireName: Ternary complex of Integrin alpha-v beta-8 with Fab C6D4 and Fab 11D12v2
Components
  • Complex: Ternary complex of Integrin alpha-v beta-8 with Fab C6D4 and Fab 11D12v2
    • Complex: alpha-v beta-8 integrin
      • Protein or peptide: Integrin alpha-VIntegrin alpha V
      • Protein or peptide: Integrin beta-8
    • Complex: C6D4 Fab
      • Protein or peptide: C6D4 heavy chain Fab
      • Protein or peptide: C6D4 light chain Fab
    • Complex: 11D12v2 Fab
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Ternary complex of Integrin alpha-v beta-8 with Fab C6D4 and Fab ...

SupramoleculeName: Ternary complex of Integrin alpha-v beta-8 with Fab C6D4 and Fab 11D12v2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: alpha-v beta-8 integrin

SupramoleculeName: alpha-v beta-8 integrin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)

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Supramolecule #3: C6D4 Fab

SupramoleculeName: C6D4 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: 11D12v2 Fab

SupramoleculeName: 11D12v2 Fab / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Integrin alpha-V

MacromoleculeName: Integrin alpha-V / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 112.813352 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: FNLDVDSPAE YSGPEGSYFG FAVDFFVPSA SSRMFLLVGA PKANTTQPGI VEGGQVLKCD WSSTRRCQPI EFDATGNRDY AKDDPLEFK SHQWFGASVR SKQDKILACA PLYHWRTEMK QEREPVGTCF LQDGTKTVEY APCRSQDIDA DGQGFCQGGF S IDFTKADR ...String:
FNLDVDSPAE YSGPEGSYFG FAVDFFVPSA SSRMFLLVGA PKANTTQPGI VEGGQVLKCD WSSTRRCQPI EFDATGNRDY AKDDPLEFK SHQWFGASVR SKQDKILACA PLYHWRTEMK QEREPVGTCF LQDGTKTVEY APCRSQDIDA DGQGFCQGGF S IDFTKADR VLLGGPGSFY WQGQLISDQV AEIVSKYDPN VYSIKYNNQL ATRTAQAIFD DSYLGYSVAV GDFNGDGIDD FV SGVPRAA RTLGMVYIYD GKNMSSLYNF TGEQMAAYFG FSVAATDING DDYADVFIGA PLFMDRGSDG KLQEVGQVSV SLQ RASGDF QTTKLNGFEV FARFGSAIAP LGDLDQDGFN DIAIAAPYGG EDKKGIVYIF NGRSTGLNAV PSQILEGQWA ARSM PPSFG YSMKGATDID KNGYPDLIVG AFGVDRAILY RARPVITVNA GLEVYPSILN QDNKTCSLPG TALKVSCFNV RFCLK ADGK GVLPRKLNFQ VELLLDKLKQ KGAIRRALFL YSRSPSHSKN MTISRGGLMQ CEELIAYLRD ESEFRDKLTP ITIFME YRL DYRTAADTTG LQPILNQFTP ANISRQAHIL LDCGEDNVCK PKLEVSVDSD QKKIYIGDDN PLTLIVKAQN QGEGAYE AE LIVSIPLQAD FIGVVRNNEA LARLSCAFKT ENQTRQVVCD LGNPMKAGTQ LLAGLRFSVH QQSEMDTSVK FDLQIQSS N LFDKVSPVVS HKVDLAVLAA VEIRGVSSPD HVFLPIPNWE HKENPETEED VGPVVQHIYE LRNNGPSSFS KAMLHLQWP YKYNNNTLLY ILHYDIDGPM NCTSDMEINP LRIKISSLQT TEKNDTVAGQ GERDHLITKR DLALSEGDIH TLGCGVAQCL KIVCQVGRL DRGKSAILYV KSLLWTETFM NKENQNHSYS LKSSASFNVI EFPYKNLPIE DITNSTLVTT NVTWGIQPAP M PVPVWVII LAVLAGLLLL AVLVFVMYRM GFFKRVRPPQ EEQEREQLQP HENGEGNSET

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Macromolecule #2: Integrin beta-8

MacromoleculeName: Integrin beta-8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.276664 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EDNRCASSNA ASCARCLALG PECGWCVQED FISGGSRSER CDIVSNLISK GCSVDSIEYP SVHVIIPTEN EINTQVTPGE VSIQLRPGA EANFMLKVHP LKKYPVDLYY LVDVSASMHN NIEKLNSVGN DLSRKMAFFS RDFRLGFGSY VDKTVSPYIS I HPERIHNQ ...String:
EDNRCASSNA ASCARCLALG PECGWCVQED FISGGSRSER CDIVSNLISK GCSVDSIEYP SVHVIIPTEN EINTQVTPGE VSIQLRPGA EANFMLKVHP LKKYPVDLYY LVDVSASMHN NIEKLNSVGN DLSRKMAFFS RDFRLGFGSY VDKTVSPYIS I HPERIHNQ CSDYNLDCMP PHGYIHVLSL TENITEFEKA VHRQKISGNI DTPEGGFDAM LQAAVCESHI GWRKEAKRLL LV MTDQTSH LALDSKLAGI VVPNDGNCHL KNNVYVKSTT MEHPSLGQLS EKLIDNNINV IFAVQGKQFH WYKDLLPLLP GTI AGEIES KAANLNNLVV EAYQKLISEV KVQVENQVQG IYFNITAICP DGSRKPGMEG CRNVTSNDEV LFNVTVTMKK CDVT GGKNY AIIKPIGFNE TAKIHIHRNC SCQCEDNRGP KGKCVDETFL DSKCFQCDEN KCHFDEDQFS SESCKSHKDQ PVCSG RGVC VCGKCSCHKI KLGKVYGKYC EKDDFSCPYH HGNLCAGHGE CEAGRCQCFS GWEGDRCQCP SAAAQHCVNS KGQVCS GRG TCVCGRCECT DPRSIGRFCE HCPTCYTACK ENWNCMQCLH PHNLSQAILD QCKTSCALME QQHYVDQTSE CFSSPSY LR IFFIIFIVTF LIGLLKVLII RQVILQWNSN KIKSSSDYRV SASKKDKLIL QSVCTRAVTY RREKPEEIKM DISKLNAH E TFRCNF

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Macromolecule #3: C6D4 heavy chain Fab

MacromoleculeName: C6D4 heavy chain Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.785475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIQLVQSGPE LKKPGETVKI SCKASGYTFT DYSMHWVKQA PGKGLKWVAR INTETGEPTF ADDFRGRFAV SLETSASTAY LQINNLKNE DTATYFCAIF YYGRDSWGQG TTLTVSSAKT TAPSVYPLAP VCGDTTGSSV TLGCLVKGYF PEPVTLTWNS G SLSSGVHT ...String:
QIQLVQSGPE LKKPGETVKI SCKASGYTFT DYSMHWVKQA PGKGLKWVAR INTETGEPTF ADDFRGRFAV SLETSASTAY LQINNLKNE DTATYFCAIF YYGRDSWGQG TTLTVSSAKT TAPSVYPLAP VCGDTTGSSV TLGCLVKGYF PEPVTLTWNS G SLSSGVHT FPAVLQSDLY TLSSSVTVTS STWPSQSITC NVAHPASSTK VDKK

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Macromolecule #4: C6D4 light chain Fab

MacromoleculeName: C6D4 light chain Fab / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.14076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPSS LAVSAGEKVT MSCKSSQSLL NSRTRKNYLA WYQQKPGQSP RLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVQAEDL AVYYCKQSYN LLSFGAGTKL ELKAADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
DIVMTQSPSS LAVSAGEKVT MSCKSSQSLL NSRTRKNYLA WYQQKPGQSP RLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVQAEDL AVYYCKQSYN LLSFGAGTKL ELKAADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRNE C

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84266

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