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- EMDB-44931: Cryogenic electron microscopy model of talin with alternate FABD ... -

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Basic information

Entry
Database: EMDB / ID: EMD-44931
TitleCryogenic electron microscopy model of talin with alternate FABD conformation
Map dataFInal volume
Sample
  • Organelle or cellular component: Talin monomer
    • Protein or peptide: Green fluorescent protein, Talin-1
KeywordsTalin / focal adhesion / f-actin binding / CELL ADHESION
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Smooth Muscle Contraction / Platelet degranulation / cortical microtubule organization / vinculin binding ...GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Smooth Muscle Contraction / Platelet degranulation / cortical microtubule organization / vinculin binding / integrin activation / cell-substrate junction assembly / cortical actin cytoskeleton organization / phosphatidylserine binding / ruffle / phosphatidylinositol binding / integrin-mediated signaling pathway / adherens junction / structural constituent of cytoskeleton / ruffle membrane / actin filament binding / integrin binding / cytoskeleton / cell adhesion / focal adhesion / cell surface / cytosol
Similarity search - Function
Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain ...Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsIzard T / Rangarajan ES
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To be published
Title: High-resolution snapshots of talin auto-inhibitory states
Authors: Izard T / Rangarajan ES
History
DepositionMay 19, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44931.png

Downloads & links

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Map

FileDownload / File: emd_44931.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFInal volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 368.64 Å		1.15 Å/pix.
x 320 pix.
= 368.64 Å		1.15 Å/pix.
x 320 pix.
= 368.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.152 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.218
Minimum - Maximum-0.6793137 - 1.1524068
Average (Standard dev.)-0.00031288285 (±0.022471208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44931_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_44931_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_44931_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Talin monomer

EntireName: Talin monomer
Components
  • Organelle or cellular component: Talin monomer
    • Protein or peptide: Green fluorescent protein, Talin-1

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Supramolecule #1: Talin monomer

SupramoleculeName: Talin monomer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Green fluorescent protein, Talin-1

MacromoleculeName: Green fluorescent protein, Talin-1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others)
SequenceString: MHHHHHHHHH HMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCFSRYPDHM KQHDFFKSAM PEGYVQERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK ...String:
MHHHHHHHHH HMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCFSRYPDHM KQHDFFKSAM PEGYVQERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK NGIKVNFKIR HNIEDGSVQL ADHYQQNTPI GDGPVLLPDN HYLSTQSALS KDPNEKRDHM VLLEFVTAAG ITLGMDELYK GSLEVLFQGP AAAMVALSLK ISIGNVVKTM QFEPSTMVYD ACRMIRERIP EALAGPPNDF GLFLSDDDPK KGIWLEAGKA LDYYMLRNGD TMEYRKKQRP LKIRMLDGTV KTIMVDDSKT VTDMLMTICA RIGITNHDEY SLVRELMEEK KDEGTGTLRK DKTLLRDEKK MEKLKQKLHT DDELNWLDHG RTLREQGVEE HETLLLRRKF FYSDQNVDSR DPVQLNLLYV QARDDILNGS HPVSFDKACE FAGFQCQIQF GPHNEQKHKA GFLDLKDFLP KEYVKQKGER KIFQAHKNCG QMSEIEAKVR YVKLARSLKT YGVSFFLVKE KMKGKNKLVP RLLGITKECV MRVDEKTKEV IQEWSLTNIK RWAASPKSFT LDFGDYQDGY YSVQTTEGEQ IAQLIAGYID IILKKKKSKD HFGLEGDEES TMLEDSVSPK KSTVLQQQYN RVGKVEHGSV ALPAIMRSGA SGPENFQVGS MPPAQQQITS GQMHRGHMPP LTSAQQALTG TINSSMQAVQ AAQATLDDFE TLPPLGQDAA SKAWRKNKMD ESKHEIHSQV DAITAGTASV VNLTAGDPAE TDYTAVGCAV TTISSNLTEM SRGVKLLAAL LEDEGGNGRP LLQAAKGLAG AVSELLRSAQ PASAEPRQNL LLAAGNVGQA SGELLQQIGE SDTDPHFQDV LMQLANAVAS AAAALVLKAK SVAQRTEDSG LQTQVIAAAT QCALSTSQLV ACTKVVAPTI SSPVCQEQLV EAGRLVAKAV EGCVSASQAA TEDGQLLRGV GAAATAVTQA LNELLQHVKA HATGAGPAGR YDQATDTILT VTENIFSSMG DAGEMVRQAR ILAQATSDLV NAIKADAEGE SDLENSRKLL SAAKILADAT AKMVEAAKGA AAHPDSEEQQ QRLREAAEGL RMATNAAAQN AIKKKLVQRL EHAAKQAAAS ATQTIAAAQH AASAPKASAG PQPLLVQSCK AVAEQIPLLV QGVRGSQAQP DSPSAQLALI AASQSFLQPG GKMVAAAKAS VPTIQDQASA MQLSQCAKNL GTALAELRTA AQKAQEACGP LEMDSALSVV QNLEKDLQEI KAAARDGKLK PLPGETMEKC TQDLGNSTKA VSSAIAKLLG EIAQGNENYA GIAARDVAGG LRSLAQAARG VAALTSDPAV QAIVLDTASD VLDKASSLIE EAKKASGHPG DPESQQRLAQ VAKAVTQALN RCVSCLPGQR DVDNALRAVG DASKRLLSDL LPPSTGTFQE AQSRLNEAAA GLNQAATELV QASRGTPQDL ARASGRFGQD FSTFLEAGVE MAGQAPSQED RAQVVSNLKG ISMSSSKLLL AAKALSTDPA SPNLKSQLAA AARAVTDSIN QLITMCTQQA PGQKECDNAL RQLETVRELL ENPVQPINDM SYFGCLDSVM ENSKVLGEAM TGISQNAKNG NLPEFGDAIA TASKALCGFT EAAAQAAYLV GVSDPNSQAG QQGLVEPTQF ARANQAIQMA CQSLGEPGCT QAQVLSAATI VAKHTSALCN SCRLASARTA NPTAKRQFVQ SAKEVANSTA NLVKTIKALD GDFTEENRAQ CRAATAPLLE AVDNLSAFAS NPEFSSVPAQ ISPEGRAAME PIVISAKTML ESAGGLIQTA RALAVNPRDP PRWSVLAGHS RTVSDSIKKL ITSMRDKAPG QLECETAIAA LNSCLRDLDQ ASLAAVSQQL APREGISQEA LHTQMLTAVQ EISHLIEPLA SAARAEASQL GHKVSQMAQY FEPLTLAAVG AASKTLSHPQ QMALLDQTKT LAESALQLLY TAKEAGGNPK QAAHTQEALE EAVQMMTEAV EDLTTTLNEA ASAAGVVGGM VDSITQAINQ LDEGPMGDPE GSFVDYQTTM VRTAKAIAVT VQEMVTKSNT SPEELGPLAN QLTSDYGRLA SQAKPAAVAA ENEEIGAHIK HRVQELGHGC SALVTKAGAL QCSPSDVYTK KELIECARRV SEKVSHVLAA LQAGNRGTQA CITAASAVSG IIADLDTTIM FATAGTLNRE GAETFADHRE GILKTAKVLV EDTKVLVQNA AGSQEKLAQA AQSSVATITR LADVVKLGAA SLGAEDPETQ VVLINAVKDV AKALGDLISA TKAAAGKVGD DPAVWQLKNS AKVMVTNVTS LLKTVKAVED EATKGTRALE ATTEHIRQEL AVFCSPEPPA KTSTPEDFIR MTKGITMATA KAVAAGNSCR QEDVIATANL SRRAIADMLR ACKEAAFHPE VAPDVRLRAL HYGRECANGY LELLDHVLLT LQKPNPDLKQ QLTGHSKRVA GSVTELIQAA EAMKGTEWVD PEDPTVIAEN ELLGAAAAIE AAAKKLEQLK PRAKPKEADE SLNFEEQILE AVKSIAAATS ALVKAASAAQ RELVAQGKVG AIPANALDDG QWSQGLISAA RMVAAATNNL CEAANAAVQG HASQEKLISS AKQVAASTAQ LLVACKVKAD QDSEAMKRLQ AAGNAVKRAS DNLVKAAQKA AAFEDQENET VVVKEKMVGG IAQIIAAQEE MLRKERELEE ARKKLAQIRQ QQYKFLPSEL RDEH

UniProtKB: Talin-1

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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

Concentration0.5 mg/mL
BufferpH: 8
GridModel: Au-flat 1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6r9t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 61926
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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