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- EMDB-7939: Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68 -

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Basic information

Entry
Database: EMDB / ID: EMD-7939
TitleIntegrin alpha-v beta-8 in complex with the Fabs 8B8 and 68
Map dataHeadpiece map, 4.8 A resolution, sharpened with a B-factor of -144
Sample
  • Complex: Alpha-v Beta-8 Integrin in complex with the Fabs 68 and 8B8
    • Protein or peptide: Integrin alpha-v
    • Protein or peptide: Integrin beta-8
    • Protein or peptide: 8B8 heavy chain Fab
    • Protein or peptide: 8B8 light chain Fab
    • Protein or peptide: 68 heavy chain Fab
    • Protein or peptide: 68 light chain Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGLYCOPROTEIN / MEMBRANE PROTEIN / ADHESION / FAB
Function / homology
Function and homology information


ganglioside metabolic process / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 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 ...ganglioside metabolic process / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 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 / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / negative regulation of low-density lipoprotein receptor activity / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / regulation of phagocytosis / negative regulation of lipid transport / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / entry into host cell by a symbiont-containing vacuole / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / cartilage development / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / positive regulation of intracellular signal transduction / Molecules associated with elastic fibres / cell adhesion mediated by integrin / microvillus membrane / negative chemotaxis / Syndecan interactions / cell-substrate adhesion / endodermal cell differentiation / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / vasculogenesis / voltage-gated calcium channel activity / coreceptor activity / specific granule membrane / phagocytic vesicle / extrinsic apoptotic signaling pathway in absence of ligand / ERK1 and ERK2 cascade / positive regulation of cell adhesion / cell-matrix adhesion / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / protein kinase C binding / calcium ion transmembrane transport / response to virus / VEGFA-VEGFR2 Pathway / cell-cell adhesion / ruffle membrane / positive regulation of angiogenesis / integrin binding / cell migration / virus receptor activity / positive regulation of cytosolic calcium ion concentration / protease binding / angiogenesis / 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 chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / 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: 4.8 Å
AuthorsCormier A / Campbell MG
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54HL119893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01HL113032 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01HL134183 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098672 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41CA196276 United States
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Cryo-EM structure of the αvβ8 integrin reveals a mechanism for stabilizing integrin extension.
Authors: Anthony Cormier / Melody G Campbell / Saburo Ito / Shenping Wu / Jianlong Lou / James Marks / Jody L Baron / Stephen L Nishimura / Yifan Cheng /
Abstract: Integrins are conformationally flexible cell surface receptors that survey the extracellular environment for their cognate ligands. Interactions with ligands are thought to be linked to global ...Integrins are conformationally flexible cell surface receptors that survey the extracellular environment for their cognate ligands. Interactions with ligands are thought to be linked to global structural rearrangements involving transitions between bent, extended-closed and extended-open forms. Thus far, structural details are lacking for integrins in the extended conformations due to extensive flexibility between the headpiece and legs in this conformation. Here we present single-particle electron cryomicroscopy structures of human αvβ8 integrin in the extended-closed conformation, which has been considered to be a low-affinity intermediate. Our structures show the headpiece rotating about a flexible αv knee, suggesting a ligand surveillance mechanism for integrins in their extended-closed form. Our model predicts that the extended conformation is mainly stabilized by an interface formed between flexible loops in the upper and lower domains of the αv leg. Confirming these findings with the αvβ3 integrin suggests that our model of stabilizing the extended-closed conformation is generalizable to other integrins.
History
DepositionMay 25, 2018-
Header (metadata) releaseJul 25, 2018-
Map releaseJul 25, 2018-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6djp
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7939.png

Downloads & links

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Map

FileDownload / File: emd_7939.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHeadpiece map, 4.8 A resolution, sharpened with a B-factor of -144
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 256 pix.
= 427.52 Å		1.67 Å/pix.
x 256 pix.
= 427.52 Å		1.67 Å/pix.
x 256 pix.
= 427.52 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.59391224 - 1.0694352
Average (Standard dev.)0.0007614384 (±0.016480777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 427.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.671.671.67
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z427.520427.520427.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5941.0690.001

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Supplemental data

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Additional map: Conformation V, sharpened with a B-factor of -300

Fileemd_7939_additional_1.map
AnnotationConformation V, sharpened with a B-factor of -300
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Half-map 01 for headpiece map

Fileemd_7939_additional_10.map
AnnotationHalf-map 01 for headpiece map
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Additional map: Half-map 02 for headpiece map

Fileemd_7939_additional_11.map
AnnotationHalf-map 02 for headpiece map
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Additional map: Conformation I, sharpened with a B-factor of -300

Fileemd_7939_additional_2.map
AnnotationConformation I, sharpened with a B-factor of -300
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Additional map: Conformation II, sharpened with a B-factor of -300

Fileemd_7939_additional_3.map
AnnotationConformation II, sharpened with a B-factor of -300
Projections & Slices
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Additional map: Conformation III, sharpened with a B-factor of -300

Fileemd_7939_additional_4.map
AnnotationConformation III, sharpened with a B-factor of -300
Projections & Slices
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Additional map: Conformation IV, sharpened with a B-factor of -300

Fileemd_7939_additional_5.map
AnnotationConformation IV, sharpened with a B-factor of -300
Projections & Slices
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Additional map: Conformation VI, sharpened with a B-factor of -300

Fileemd_7939_additional_6.map
AnnotationConformation VI, sharpened with a B-factor of -300
Projections & Slices
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Additional map: Full map, 6.4 A resolution, sharpened with a B-factor of -146

Fileemd_7939_additional_7.map
AnnotationFull map, 6.4 A resolution, sharpened with a B-factor of -146
Projections & Slices
AxesZYX

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Additional map: Half-map 01 for full map

Fileemd_7939_additional_8.map
AnnotationHalf-map 01 for full map
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Additional map: Half-map 02 for full map

Fileemd_7939_additional_9.map
AnnotationHalf-map 02 for full map
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Sample components

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Entire : Alpha-v Beta-8 Integrin in complex with the Fabs 68 and 8B8

EntireName: Alpha-v Beta-8 Integrin in complex with the Fabs 68 and 8B8
Components
  • Complex: Alpha-v Beta-8 Integrin in complex with the Fabs 68 and 8B8
    • Protein or peptide: Integrin alpha-v
    • Protein or peptide: Integrin beta-8
    • Protein or peptide: 8B8 heavy chain Fab
    • Protein or peptide: 8B8 light chain Fab
    • Protein or peptide: 68 heavy chain Fab
    • Protein or peptide: 68 light chain Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Alpha-v Beta-8 Integrin in complex with the Fabs 68 and 8B8

SupramoleculeName: Alpha-v Beta-8 Integrin in complex with the Fabs 68 and 8B8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 312 KDa

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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: 106.758266 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 PVPVW

UniProtKB: Integrin alpha-V

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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: 70.837234 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 CFSSPS

UniProtKB: Integrin beta-8

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Macromolecule #3: 8B8 heavy chain Fab

MacromoleculeName: 8B8 heavy chain Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.314826 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVQLVESGPG LVKPSQSLSL TCSVTGYYIT SSYYWNWIRQ FPGNELEWMG YISYDGSNSY NPSLKNRISI TRDTSKNQFF LKLNSVTTE DIATYFCVRE DYDSFDYWGQ GTTLTVSSAK TTAPSVYPLA PVCGDTTGSS VTLGCLVKGY FPEPVTLTWN S GSLSSGVH ...String:
EVQLVESGPG LVKPSQSLSL TCSVTGYYIT SSYYWNWIRQ FPGNELEWMG YISYDGSNSY NPSLKNRISI TRDTSKNQFF LKLNSVTTE DIATYFCVRE DYDSFDYWGQ GTTLTVSSAK TTAPSVYPLA PVCGDTTGSS VTLGCLVKGY FPEPVTLTWN S GSLSSGVH TFPAVLQSDL YTLSSSVTVT SSTWPSQSIT CNVAHPASST KVDKK

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Macromolecule #4: 8B8 light chain Fab

MacromoleculeName: 8B8 light chain Fab / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.241596 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EIVLTQSPAI MSAFPGEKVT MTCSASSSVS YIHWYQQKSG TSPKRWIYDT SKLASGVPAR FSGSGSGTSY SLTISSMEAE DAATYYCHQ WTSNPATFGG GTKLEIKAAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
EIVLTQSPAI MSAFPGEKVT MTCSASSSVS YIHWYQQKSG TSPKRWIYDT SKLASGVPAR FSGSGSGTSY SLTISSMEAE DAATYYCHQ WTSNPATFGG GTKLEIKAAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #5: 68 heavy chain Fab

MacromoleculeName: 68 heavy chain Fab / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.680303 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLQQSGAE LMKPGASVKI SCKATGYTFS TYWIEWIKQR PGHGLEWIGD ILPGSGTTNY NEKFKGRATV TADRSSNTAY MQLSSLTSE DSAVYYCARW GWDSYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG A LTSGVHTF ...String:
EVQLQQSGAE LMKPGASVKI SCKATGYTFS TYWIEWIKQR PGHGLEWIGD ILPGSGTTNY NEKFKGRATV TADRSSNTAY MQLSSLTSE DSAVYYCARW GWDSYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG A LTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKK

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Macromolecule #6: 68 light chain Fab

MacromoleculeName: 68 light chain Fab / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.420795 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIEMTQSPSS LSASLGDRVT ISCSASQGIS NYLNWYQQKP DGTVKLLIYY TSSLHSGVPS RFSGSGSGTD YSLTISNLEP EDIATYYCQ QYSELPYTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIEMTQSPSS LSASLGDRVT ISCSASQGIS NYLNWYQQKP DGTVKLLIYY TSSLHSGVPS RFSGSGSGTD YSLTISNLEP EDIATYYCQ QYSELPYTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration6.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 713 / Average exposure time: 6.0 sec. / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Cryosparc Ab Initio Model used as Initial Model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 17442
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.11)
Final 3D classificationSoftware - Name: RELION

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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