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- EMDB-43152: Cryogenic electron microscopy model of full-length talin lacking ... -

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Basic information

Entry
Database: EMDB / ID: EMD-43152
TitleCryogenic electron microscopy model of full-length talin lacking F2, R12 and FABD.
Map dataModel of full-length talin lacking F2, R12 and FABD.
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 / bioluminescence / integrin-mediated signaling pathway / generation of precursor metabolites and energy / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Green fluorescent protein / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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
DepositionDec 16, 2023-
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_43152.png

Downloads & links

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Map

FileDownload / File: emd_43152.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationModel of full-length talin lacking F2, R12 and FABD.
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-2.422805 - 3.1166198
Average (Standard dev.)-0.0002573 (±0.039921544)
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_43152_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_43152_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_43152_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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 299.867344 KDa
Recombinant expressionOrganism: Mammalian expression vector HA-MCS-pcDNA3.1 (others)
SequenceString: MHHHHHHHHH HMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNYNS H NVYIMADK ...String:
MHHHHHHHHH HMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNYNS H NVYIMADK QKNGIKVNFK IRHNIEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSA LSKDPNEKRD HMVLLEFVTA AG ITLGMDE LYKGSLEVLF QGPAAAMVAL SLKISIGNVV KTMQFEPSTM VYDACRMIRE RIPEALAGPP NDFGLFLSDD DPK KGIWLE AGKALDYYML RNGDTMEYRK KQRPLKIRML DGTVKTIMVD DSKTVTDMLM TICARIGITN HDEYSLVREL MEEK KDEGT GTLRKDKTLL RDEKKMEKLK QKLHTDDELN WLDHGRTLRE QGVEEHETLL LRRKFFYSDQ NVDSRDPVQL NLLYV QARD DILNGSHPVS FDKACEFAGF QCQIQFGPHN EQKHKAGFLD LKDFLPKEYV KQKGERKIFQ AHKNCGQMSE IEAKVR YVK LARSLKTYGV SFFLVKEKMK GKNKLVPRLL GITKECVMRV DEKTKEVIQE WSLTNIKRWA ASPKSFTLDF GDYQDGY YS VQTTEGEQIA QLIAGYIDII LKKKKSKDHF GLEGDEESTM LEDSVSPKKS TVLQQQYNRV GKVEHGSVAL PAIMRSGA S GPENFQVGSM PPAQQQITSG QMHRGHMPPL TSAQQALTGT INSSMQAVQA AQATLDDFET LPPLGQDAAS KAWRKNKMD ESKHEIHSQV DAITAGTASV VNLTAGDPAE TDYTAVGCAV TTISSNLTEM SRGVKLLAAL LEDEGGNGRP LLQAAKGLAG AVSELLRSA QPASAEPRQN LLLAAGNVGQ ASGELLQQIG ESDTDPHFQD VLMQLANAVA SAAAALVLKA KSVAQRTEDS G LQTQVIAA ATQCALSTSQ LVACTKVVAP TISSPVCQEQ LVEAGRLVAK AVEGCVSASQ AATEDGQLLR GVGAAATAVT QA LNELLQH VKAHATGAGP AGRYDQATDT ILTVTENIFS SMGDAGEMVR QARILAQATS DLVNAIKADA EGESDLENSR KLL SAAKIL ADATAKMVEA AKGAAAHPDS EEQQQRLREA AEGLRMATNA AAQNAIKKKL VQRLEHAAKQ AAASATQTIA AAQH AASAP KASAGPQPLL VQSCKAVAEQ IPLLVQGVRG SQAQPDSPSA QLALIAASQS FLQPGGKMVA AAKASVPTIQ DQASA MQLS QCAKNLGTAL AELRTAAQKA QEACGPLEMD SALSVVQNLE KDLQEIKAAA RDGKLKPLPG ETMEKCTQDL GNSTKA VSS AIAKLLGEIA QGNENYAGIA ARDVAGGLRS LAQAARGVAA LTSDPAVQAI VLDTASDVLD KASSLIEEAK KASGHPG DP ESQQRLAQVA KAVTQALNRC VSCLPGQRDV DNALRAVGDA SKRLLSDLLP PSTGTFQEAQ SRLNEAAAGL NQAATELV Q ASRGTPQDLA RASGRFGQDF STFLEAGVEM AGQAPSQEDR AQVVSNLKGI SMSSSKLLLA AKALSTDPAS PNLKSQLAA AARAVTDSIN QLITMCTQQA PGQKECDNAL RQLETVRELL ENPVQPINDM SYFGCLDSVM ENSKVLGEAM TGISQNAKNG NLPEFGDAI ATASKALCGF TEAAAQAAYL VGVSDPNSQA GQQGLVEPTQ FARANQAIQM ACQSLGEPGC TQAQVLSAAT I VAKHTSAL CNSCRLASAR TANPTAKRQF VQSAKEVANS TANLVKTIKA LDGDFTEENR AQCRAATAPL LEAVDNLSAF AS NPEFSSV PAQISPEGRA AMEPIVISAK TMLESAGGLI QTARALAVNP RDPPRWSVLA GHSRTVSDSI KKLITSMRDK APG QLECET AIAALNSCLR DLDQASLAAV SQQLAPREGI SQEALHTQML TAVQEISHLI EPLASAARAE ASQLGHKVSQ MAQY FEPLT LAAVGAASKT LSHPQQMALL DQTKTLAESA LQLLYTAKEA GGNPKQAAHT QEALEEAVQM MTEAVEDLTT TLNEA ASAA GVVGGMVDSI TQAINQLDEG PMGDPEGSFV DYQTTMVRTA KAIAVTVQEM VTKSNTSPEE LGPLANQLTS DYGRLA SQA KPAAVAAENE EIGAHIKHRV QELGHGCSAL VTKAGALQCS PSDVYTKKEL IECARRVSEK VSHVLAALQA GNRGTQA CI TAASAVSGII ADLDTTIMFA TAGTLNREGA ETFADHREGI LKTAKVLVED TKVLVQNAAG SQEKLAQAAQ SSVATITR L ADVVKLGAAS LGAEDPETQV VLINAVKDVA KALGDLISAT KAAAGKVGDD PAVWQLKNSA KVMVTNVTSL LKTVKAVED EATKGTRALE ATTEHIRQEL AVFCSPEPPA KTSTPEDFIR MTKGITMATA KAVAAGNSCR QEDVIATANL SRRAIADMLR ACKEAAFHP EVAPDVRLRA LHYGRECANG YLELLDHVLL TLQKPNPDLK QQLTGHSKRV AGSVTELIQA AEAMKGTEWV D PEDPTVIA ENELLGAAAA IEAAAKKLEQ LKPRAKPKEA DESLNFEEQI LEAVKSIAAA TSALVKAASA AQRELVAQGK VG AIPANAL DDGQWSQGLI SAARMVAAAT NNLCEAANAA VQGHASQEKL ISSAKQVAAS TAQLLVACKV KADQDSEAMK RLQ AAGNAV KRASDNLVKA AQKAAAFEDQ ENETVVVKEK MVGGIAQIIA AQEEMLRKER ELEEARKKLA QIRQQQYKFL PSEL RDEH

UniProtKB: Green fluorescent protein, 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 / Mesh: 300 / 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
SoftwareName: SerialEM / Details: Data collection
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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 439156
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6r9t


Chain - Chain ID: A / Chain - Residue range: 208-2479 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8vdo:
Cryogenic electron microscopy model of full-length talin lacking F2, R12 and FABD.

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