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- EMDB-12634: Cryo-EM structure of human integrin alpha5beta1 (open form) in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-12634
TitleCryo-EM structure of human integrin alpha5beta1 (open form) in complex with fibronectin and TS2/16 Fv-clasp
Map data
Sample
  • Complex: Ternary complex of integrin a5b1, fibronectin and TS2/16 Fv-clasp
    • Protein or peptide: Integrin alpha-5
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: Isoform 1 of Fibronectin
    • Protein or peptide: TS2/16 VH(S112C)-SARAH Chimera
    • Protein or peptide: TS2/16 VL-SARAH(S37C) Chimera
  • Ligand: MANGANESE (II) ION
Keywordsintegrin / fibronectin / TS2/16 / cell adhesion / plasma membrane protein / a5b1 / alpha5beta1 / focal adhesion / open conformation
Function / homology
Function and homology information


integrin alpha8-beta1 complex / : / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification ...integrin alpha8-beta1 complex / : / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / negative regulation of monocyte activation / Formation of the ureteric bud / negative regulation of transforming growth factor beta production / positive regulation of fibroblast growth factor receptor signaling pathway / CD40 signaling pathway / Extracellular matrix organization / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / positive regulation of substrate-dependent cell migration, cell attachment to substrate / basement membrane organization / regulation of synapse pruning / integrin alphav-beta1 complex / neural crest cell migration involved in autonomic nervous system development / myelin sheath abaxonal region / peptidase activator activity / CHL1 interactions / fibrinogen complex / RUNX2 regulates genes involved in cell migration / cardiac muscle cell myoblast differentiation / alphav-beta3 integrin-vitronectin complex / MET interacts with TNS proteins / Laminin interactions / peptide cross-linking / leukocyte tethering or rolling / cardiac muscle cell differentiation / germ cell migration / cell projection organization / Platelet Adhesion to exposed collagen / integrin activation / vascular endothelial growth factor receptor 2 binding / ALK mutants bind TKIs / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / axon extension / myoblast differentiation / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / proteoglycan binding / wound healing, spreading of epidermal cells / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / epidermal growth factor receptor binding / lamellipodium assembly / biological process involved in interaction with symbiont / extracellular matrix structural constituent / dendrite morphogenesis / sarcomere organization / Molecules associated with elastic fibres / MET activates PTK2 signaling / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / positive regulation of wound healing / muscle organ development / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / positive regulation of neuroblast proliferation / maintenance of blood-brain barrier / negative regulation of Rho protein signal transduction / positive regulation of sprouting angiogenesis / cell-substrate adhesion / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / homophilic cell adhesion via plasma membrane adhesion molecules
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / 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 / Kringle-like fold / von Willebrand factor A-like domain superfamily / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Fibronectin / Integrin beta-1 / Integrin alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSchumacher S / Dedden D
Funding support Germany, European Union, United States, 6 items
OrganizationGrant numberCountry
Max Planck Society Germany
Other privateBoehringer Ingelheim Foundation Plus 3 Program Germany
European Research Council (ERC)ERC-CoG 724209European Union
European Molecular Biology Organization (EMBO)Young Investigator ProgramEuropean Union
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS) United States
CitationJournal: Sci Adv / Year: 2021
Title: Structural insights into integrin αβ opening by fibronectin ligand.
Authors: Stephanie Schumacher / Dirk Dedden / Roberto Vazquez Nunez / Kyoko Matoba / Junichi Takagi / Christian Biertümpfel / Naoko Mizuno /
Abstract: Integrin αβ is a major fibronectin receptor critical for cell migration. Upon complex formation, fibronectin and αβ undergo conformational changes. While this is key for cell-tissue connections, ...Integrin αβ is a major fibronectin receptor critical for cell migration. Upon complex formation, fibronectin and αβ undergo conformational changes. While this is key for cell-tissue connections, its mechanism is unknown. Here, we report cryo-electron microscopy structures of native human αβ with fibronectin to 3.1-angstrom resolution, and in its resting state to 4.6-angstrom resolution. The αβ-fibronectin complex revealed simultaneous interactions at the arginine-glycine-aspartate loop, the synergy site, and a newly identified binding site proximal to adjacent to metal ion-dependent adhesion site, inducing the translocation of helix α1 to secure integrin opening. Resting αβ adopts an incompletely bent conformation, challenging the model of integrin sharp bending inhibiting ligand binding. Our biochemical and structural analyses showed that affinity of αβ for fibronectin is increased with manganese ions (Mn) while adopting the half-bent conformation, indicating that ligand-binding affinity does not depend on conformation, and αβ opening is induced by ligand-binding.
History
DepositionMar 17, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0292
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0292
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nwl
  • Surface level: 0.0292
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12634.png

Downloads & links

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Map

FileDownload / File: emd_12634.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 360 pix.
= 498.24 Å		1.38 Å/pix.
x 360 pix.
= 498.24 Å		1.38 Å/pix.
x 360 pix.
= 498.24 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.384 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0292 / Movie #1: 0.0292
Minimum - Maximum-0.07339407 - 0.15871869
Average (Standard dev.)0.00011240059 (±0.0019957777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 498.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3841.3841.384
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z498.240498.240498.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0730.1590.000

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Supplemental data

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Mask #1

Fileemd_12634_msk_1.map
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Additional map: focused map around the high resolution parts

Fileemd_12634_additional_1.map
Annotationfocused map around the high resolution parts
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Additional map: working map including also low resolution parts

Fileemd_12634_additional_2.map
Annotationworking map including also low resolution parts
Projections & Slices
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Half map: #2

Fileemd_12634_half_map_1.map
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Half map: #1

Fileemd_12634_half_map_2.map
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Sample components

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Entire : Ternary complex of integrin a5b1, fibronectin and TS2/16 Fv-clasp

EntireName: Ternary complex of integrin a5b1, fibronectin and TS2/16 Fv-clasp
Components
  • Complex: Ternary complex of integrin a5b1, fibronectin and TS2/16 Fv-clasp
    • Protein or peptide: Integrin alpha-5
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: Isoform 1 of Fibronectin
    • Protein or peptide: TS2/16 VH(S112C)-SARAH Chimera
    • Protein or peptide: TS2/16 VL-SARAH(S37C) Chimera
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Ternary complex of integrin a5b1, fibronectin and TS2/16 Fv-clasp

SupramoleculeName: Ternary complex of integrin a5b1, fibronectin and TS2/16 Fv-clasp
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Integrin alpha-5

MacromoleculeName: Integrin alpha-5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: placenta
Molecular weightTheoretical: 110.111555 KDa
SequenceString: FNLDAEAPAV LSGPPGSFFG FSVEFYRPGT DGVSVLVGAP KANTSQPGVL QGGAVYLCPW GASPTQCTPI EFDSKGSRLL ESSLSSSEG EEPVEYKSLQ WFGATVRAHG SSILACAPLY SWRTEKEPLS DPVGTCYLST DNFTRILEYA PCRSDFSWAA G QGYCQGGF ...String:
FNLDAEAPAV LSGPPGSFFG FSVEFYRPGT DGVSVLVGAP KANTSQPGVL QGGAVYLCPW GASPTQCTPI EFDSKGSRLL ESSLSSSEG EEPVEYKSLQ WFGATVRAHG SSILACAPLY SWRTEKEPLS DPVGTCYLST DNFTRILEYA PCRSDFSWAA G QGYCQGGF SAEFTKTGRV VLGGPGSYFW QGQILSATQE QIAESYYPEY LINLVQGQLQ TRQASSIYDD SYLGYSVAVG EF SGDDTED FVAGVPKGNL TYGYVTILNG SDIRSLYNFS GEQMASYFGY AVAATDVNGD GLDDLLVGAP LLMDRTPDGR PQE VGRVYV YLQHPAGIEP TPTLTLTGHD EFGRFGSSLT PLGDLDQDGY NDVAIGAPFG GETQQGVVFV FPGGPGGLGS KPSQ VLQPL WAASHTPDFF GSALRGGRDL DGNGYPDLIV GSFGVDKAVV YRGRPIVSAS ASLTIFPAMF NPEERSCSLE GNPVA CINL SFCLNASGKH VADSIGFTVE LQLDWQKQKG GVRRALFLAS RQATLTQTLL IQNGAREDCR EMKIYLRNES EFRDKL SPI HIALNFSLDP QAPVDSHGLR PALHYQSKSR IEDKAQILLD CGEDNICVPD LQLEVFGEQN HVYLGDKNAL NLTFHAQ NV GEGGAYEAEL RVTAPPEAEY SGLVRHPGNF SSLSCDYFAV NQSRLLVCDL GNPMKAGASL WGGLRFTVPH LRDTKKTI Q FDFQILSKNL NNSQSDVVSF RLSVEAQAQV TLNGVSKPEA VLFPVSDWHP RDQPQKEEDL GPAVHHVYEL INQGPSSIS QGVLELSCPQ ALEGQQLLYV TRVTGLNCTT NHPINPKGLE LDPEGSLHHQ QKREAPSRSS ASSGPQILKC PEAECFRLRC ELGPLHQQE SQSLQLHFRV WAKTFLQREH QPFSLQCEAV YKALKMPYRI LPRQLPQKER QVATAVQWTK AEGSYGVPLW I IILAILFG LLLLGLLIYI LYKLGFFKRS LPYGTAMEKA QLKPPATSDA

UniProtKB: Integrin alpha-5

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Macromolecule #2: Integrin beta-1

MacromoleculeName: Integrin beta-1 / type: protein_or_peptide / ID: 2 / Details: Sequenced used from GenBank entry CAA30790 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: placenta
Molecular weightTheoretical: 86.338594 KDa
SequenceString: QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDIK KNKNVTNRSK GTAEKLKPE DIHQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL ENVKSLGTDL MNEMRRITSD F RIGFGSFV ...String:
QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDIK KNKNVTNRSK GTAEKLKPE DIHQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL ENVKSLGTDL MNEMRRITSD F RIGFGSFV EKTVMPYIST TPAKLRNPCT SEQNCTTPFS YKNVLSLTNK GEVFNELVGK QRISGNLDSP EGGFDAIMQV AV CGSLIGW RNVTRLLVFS TDAGFHFAGD GKLGGIVLPN DGQCHLENNM YTMSHYYDYP SIAHLVQKLS ENNIQTIFAV TEE FQPVYK ELKNLIPKSA VGTLSANSSN VIQLIIDAYN SLSSEVILEN GKLSEGVTIS YKSYCKNGVN GTGENGRKCS NISI GDEVQ FEISITSNKC PKKDSDSFKI RPLGFTEEVE VILQYICECE CQSEGIPESP KCHEGNGTFE CGACRCNEGR VGRHC ECST DEVNSEDMDA YCRKENSSEI CSNNGECVCG QCVCRKRDNT NEIYSGKFCE CDNFNCDRSN GLICGGNGVC KCRVCE CNP NYTGSACDCS LDTSTCEASN GQICNGRGIC ECGVCKCTDP KFQGQTCEMC QTCLGVCAEH KECVQCRAFN KGEKKDT CT QECSYFNITK VESRDKLPQP VQPDPVSHCK EKDVDDCWFY FTYSVNGNNE VMVHVVENPE CPTGPDIIPI VAGVVAGI V LIGLALLLIW KLLMIIHDRR EFAKFEKEKM NAKWDTGENP IYKSAVTTVV NPKYEGK

UniProtKB: Integrin beta-1

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Macromolecule #3: Isoform 1 of Fibronectin

MacromoleculeName: Isoform 1 of Fibronectin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.98116 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PLSPPTNLHL EANPDTGVLT VSWERSTTPD ITGYRITTTP TNGQQGNSLE EVVHADQSSC TFDNLSPGLE YNVSVYTVKD DKESVPISD TIIPAVPPPT DLRFTNIGPD TMRVTWAPPP SIDLTNFLVR YSPVKNEEDV AELSISPSDN AVVLTNLLPG T EYVVSVSS ...String:
PLSPPTNLHL EANPDTGVLT VSWERSTTPD ITGYRITTTP TNGQQGNSLE EVVHADQSSC TFDNLSPGLE YNVSVYTVKD DKESVPISD TIIPAVPPPT DLRFTNIGPD TMRVTWAPPP SIDLTNFLVR YSPVKNEEDV AELSISPSDN AVVLTNLLPG T EYVVSVSS VYEQHESTPL RGRQKTGLDS PTGIDFSDIT ANSFTVHWIA PRATITGYRI RHHPEHFSGR PREDRVPHSR NS ITLTNLT PGTEYVVSIV ALNGREESPL LIGQQSTVSD VPRDLEVVAA TPTSLLISWD APAVTVRYYR ITYGETGGNS PVQ EFTVPG SKSTATISGL KPGVDYTITV YAVTGRGDSP ASSKPISINY RT

UniProtKB: Fibronectin

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Macromolecule #4: TS2/16 VH(S112C)-SARAH Chimera

MacromoleculeName: TS2/16 VH(S112C)-SARAH Chimera / type: protein_or_peptide / ID: 4 / Details: Chimera: Mus musculus, Homo sapiens; 10090, 9660; / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 19.463992 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDVKLVESGG GLVKPGGSLK LSCAASGFTF SSYTMSWVRQ TPEKRLEWVA TISSGGSYTY YPDSVKGRFT ISRDKAKNTL YLQMGSLKS EDTAMYYCTR IGYDEDYAMD HWGQGTSVTV CSGSDYEFLK SWTVEDLQKR LLALDPMMEQ EIEEIRQKYQ S KRQPILDA IEAK

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Macromolecule #5: TS2/16 VL-SARAH(S37C) Chimera

MacromoleculeName: TS2/16 VL-SARAH(S37C) Chimera / type: protein_or_peptide / ID: 5 / Details: Chimera: Mus musculus, Homo sapiens; 10090, 9660; / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.270742 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSHMQIVVTQ RPTTMAASPG DKIIITCSVS SIISSNYLHW YSQKPGFSPK LLIYRTSNLA SGVPPRFSGS GSGTSYSLTI GTMEAEDVA TYYCQQGSDI PLTFGDGTKL DLKRGSDYEF LKSWTVEDLQ KRLLALDPMM EQEIEEIRQK YQCKRQPILD A IEAK

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Macromolecule #11: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 11 / Number of copies: 7 / Formula: MN
Molecular weightTheoretical: 54.938 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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTristris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
1.0 mMMnCl2manganese chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: GloQube at 20 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsIntegrin a5b1 was assembled into MSPE3D1 nanodiscs containing lipids Folch fraction I lipids from bovine brain at a ratio of 1:29:3460, respectively. The assembly mix was incubated with SM-2 BioBeads to remove DDM detergent from solubilized lipids and then purified by size-exclusion chromatography using a Superose 6 3.2/300 column and mixed with FN7-10 and TS/2/16 at stoichiometric ratios.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 6144 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9431 / Average exposure time: 7.39 sec. / Average electron dose: 59.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.62 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsinitial image processing automatically by FOCUS pipeline: gain normalization, motion correction and dose-weighting in MotionCor2 CTF estimation by GCTF
Particle selectionNumber selected: 4218951
Startup modelType of model: OTHER
Details: 30 A-low pass filtered model from previous data analysis was used: 3754 particles were manually picked and used for 2D classification to generate a template for gautomatch, which picked ...Details: 30 A-low pass filtered model from previous data analysis was used: 3754 particles were manually picked and used for 2D classification to generate a template for gautomatch, which picked 105351 particles. Further 2D classification of 10949 classes, initial model generation and 3D in Relion yielded a prominent model from 16765 particles.
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 680610
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 6 / Avg.num./class: 25000 / Software - Name: RELION (ver. 3.0) / Details: 1492856 particles in total
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4wk0

chain_id: A, source_name: PDB, initial_model_type: experimental model

4wk0

chain_id: B, source_name: PDB, initial_model_type: experimental model

3vi3

chain_id: A, source_name: PDB, initial_model_type: experimental model

3vi3

chain_id: B, source_name: PDB, initial_model_type: experimental model

1fnf

chain_id: A, source_name: PDB, initial_model_type: experimental model

5xcx

chain_id: A, source_name: PDB, initial_model_type: experimental model

5xcx

chain_id: B, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7nwl:
Cryo-EM structure of human integrin alpha5beta1 (open form) in complex with fibronectin and TS2/16 Fv-clasp

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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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