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- EMDB-4772: Cryo-EM structure of autoinhibited human talin-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-4772
TitleCryo-EM structure of autoinhibited human talin-1
Map databest map
Sample
  • Complex: Talin-1
    • Protein or peptide: Talin-1
Function / homology
Function and homology information


LIM domain binding / vinculin binding / XBP1(S) activates chaperone genes / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / integrin activation / cell-substrate junction assembly / cell-cell junction assembly / cortical actin cytoskeleton organization / regulation of focal adhesion assembly / phosphatidylserine binding ...LIM domain binding / vinculin binding / XBP1(S) activates chaperone genes / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / integrin activation / cell-substrate junction assembly / cell-cell junction assembly / cortical actin cytoskeleton organization / regulation of focal adhesion assembly / phosphatidylserine binding / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / Smooth Muscle Contraction / ruffle / phosphatidylinositol binding / Integrin signaling / integrin-mediated signaling pathway / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / structural constituent of cytoskeleton / cell-cell adhesion / platelet aggregation / ruffle membrane / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin filament binding / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / cytoskeleton / cadherin binding / focal adhesion / cell surface / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
: / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM ...: / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsDedden D / Schumacher S / Zacharias M / Biertumpfel C / Mizuno N
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research CouncilERC-CoG, 724209 Germany
Other privateBoehringer Ingelheim Stiftung Plus3 Germany
CitationJournal: Cell / Year: 2019
Title: The Architecture of Talin1 Reveals an Autoinhibition Mechanism.
Authors: Dirk Dedden / Stephanie Schumacher / Charlotte F Kelley / Martin Zacharias / Christian Biertümpfel / Reinhard Fässler / Naoko Mizuno /
Abstract: Focal adhesions (FAs) are protein machineries essential for cell adhesion, migration, and differentiation. Talin is an integrin-activating and tension-sensing FA component directly connecting ...Focal adhesions (FAs) are protein machineries essential for cell adhesion, migration, and differentiation. Talin is an integrin-activating and tension-sensing FA component directly connecting integrins in the plasma membrane with the actomyosin cytoskeleton. To understand how talin function is regulated, we determined a cryoelectron microscopy (cryo-EM) structure of full-length talin1 revealing a two-way mode of autoinhibition. The actin-binding rod domains fold into a 15-nm globular arrangement that is interlocked by the integrin-binding FERM head. In turn, the rod domains R9 and R12 shield access of the FERM domain to integrin and the phospholipid PIP at the membrane. This mechanism likely ensures synchronous inhibition of integrin, membrane, and cytoskeleton binding. We also demonstrate that compacted talin1 reversibly unfolds to an ∼60-nm string-like conformation, revealing interaction sites for vinculin and actin. Our data explain how fast switching between active and inactive conformations of talin could regulate FA turnover, a process critical for cell adhesion and signaling.
History
DepositionApr 4, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseOct 16, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r9t
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4772.png

Downloads & links

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Map

FileDownload / File: emd_4772.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbest map
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0232 / Movie #1: 0.0232
Minimum - Maximum-0.029035201 - 0.08947763
Average (Standard dev.)0.00060505804 (±0.0037976513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 237.43999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z237.440237.440237.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0290.0890.001

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Supplemental data

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Additional map: map with additional density

Fileemd_4772_additional.map
Annotationmap with additional density
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-1

EntireName: Talin-1
Components
  • Complex: Talin-1
    • Protein or peptide: Talin-1

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Supramolecule #1: Talin-1

SupramoleculeName: Talin-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: autoinhibited
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Talin-1

MacromoleculeName: Talin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 270.773719 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVALSLKISI GNVVKTMQFE PSTMVYDACR IIRERIPEAP AGPPSDFGLF LSDDDPKKGI WLEAGKALDY YMLRNGDTME YRKKQRPLK IRMLDGTVKT IMVDDSKTVT DMLMTICARI GITNHDEYSL VRELMEEKKE EITGTLRKDK TLLRDEKKME K LKQKLHTD ...String:
MVALSLKISI GNVVKTMQFE PSTMVYDACR IIRERIPEAP AGPPSDFGLF LSDDDPKKGI WLEAGKALDY YMLRNGDTME YRKKQRPLK IRMLDGTVKT IMVDDSKTVT DMLMTICARI GITNHDEYSL VRELMEEKKE EITGTLRKDK TLLRDEKKME K LKQKLHTD DELNWLDHGR TLREQGVEEH ETLLLRRKFF YSDQNVDSRD PVQLNLLYVQ ARDDILNGSH PVSFDKACEF AG FQCQIQF GPHNEQKHKA GFLDLKDFLP KEYVKQKGER KIFQAHKNCG QMSEIEAKVR YVKLARSLKT YGVSFFLVKE KMK GKNKLV PRLLGITKEC VMRVDEKTKE VIQEWNLTNI KRWAASPKSF TLDFGDYQDG YYSVQTTEGE QIAQLIAGYI DIIL KKKKS KDHFGLEGDE ESTMLEDSVS PKKSTVLQQQ YNRVGKVEHG SVALPAIMRS GASGPENFQV GSMPPAQQQI TSGQM HRGH MPPLTSAQQA LTGTINSSMQ AVQAAQATLD DFDTLPPLGQ DAASKAWRKN KMDESKHEIH SQVDAITAGT ASVVNL TAG DPAETDYTAV GCAVTTISSN LTEMSRGVKL LAALLEDEGG SGRPLLQAAK GLAGAVSELL RSAQPASAEP RQNLLQA AG NVGQASGELL QQIGESDTDP HFQDALMQLA KAVASAAAAL VLKAKSVAQR TEDSGLQTQV IAAATQCALS TSQLVACT K VVAPTISSPV CQEQLVEAGR LVAKAVEGCV SASQAATEDG QLLRGVGAAA TAVTQALNEL LQHVKAHATG AGPAGRYDQ ATDTILTVTE NIFSSMGDAG EMVRQARILA QATSDLVNAI KADAEGESDL ENSRKLLSAA KILADATAKM VEAAKGAAAH PDSEEQQQR LREAAEGLRM ATNAAAQNAI KKKLVQRLEH AAKQAAASAT QTIAAAQHAA STPKASAGPQ PLLVQSCKAV A EQIPLLVQ GVRGSQAQPD SPSAQLALIA ASQSFLQPGG KMVAAAKASV PTIQDQASAM QLSQCAKNLG TALAELRTAA QK AQEACGP LEMDSALSVV QNLEKDLQEV KAAARDGKLK PLPGETMEKC TQDLGNSTKA VSSAIAQLLG EVAQGNENYA GIA ARDVAG GLRSLAQAAR GVAALTSDPA VQAIVLDTAS DVLDKASSLI EEAKKAAGHP GDPESQQRLA QVAKAVTQAL NRCV SCLPG QRDVDNALRA VGDASKRLLS DSLPPSTGTF QEAQSRLNEA AAGLNQAATE LVQASRGTPQ DLARASGRFG QDFST FLEA GVEMAGQAPS QEDRAQVVSN LKGISMSSSK LLLAAKALST DPAAPNLKSQ LAAAARAVTD SINQLITMCT QQAPGQ KEC DNALRELETV RELLENPVQP INDMSYFGCL DSVMENSKVL GEAMTGISQN AKNGNLPEFG DAISTASKAL CGFTEAA AQ AAYLVGVSDP NSQAGQQGLV EPTQFARANQ AIQMACQSLG EPGCTQAQVL SAATIVAKHT SALCNSCRLA SARTTNPT A KRQFVQSAKE VANSTANLVK TIKALDGAFT EENRAQCRAA TAPLLEAVDN LSAFASNPEF SSIPAQISPE GRAAMEPIV ISAKTMLESA GGLIQTARAL AVNPRDPPSW SVLAGHSRTV SDSIKKLITS MRDKAPGQLE CETAIAALNS CLRDLDQASL AAVSQQLAP REGISQEALH TQMLTAVQEI SHLIEPLANA ARAEASQLGH KVSQMAQYFE PLTLAAVGAA SKTLSHPQQM A LLDQTKTL AESALQLLYT AKEAGGNPKQ AAHTQEALEE AVQMMTEAVE DLTTTLNEAA SAAGVVGGMV DSITQAINQL DE GPMGEPE GSFVDYQTTM VRTAKAIAVT VQEMVTKSNT SPEELGPLAN QLTSDYGRLA SEAKPAAVAA ENEEIGSHIK HRV QELGHG CAALVTKAGA LQCSPSDAYT KKELIECARR VSEKVSHVLA ALQAGNRGTQ ACITAASAVS GIIADLDTTI MFAT AGTLN REGTETFADH REGILKTAKV LVEDTKVLVQ NAAGSQEKLA QAAQSSVATI TRLADVVKLG AASLGAEDPE TQVVL INAV KDVAKALGDL ISATKAAAGK VGDDPAVWQL KNSAKVMVTN VTSLLKTVKA VEDEATKGTR ALEATTEHIR QELAVF CSP EPPAKTSTPE DFIRMTKGIT MATAKAVAAG NSCRQEDVIA TANLSRRAIA DMLRACKEAA YHPEVAPDVR LRALHYG RE CANGYLELLD HVLLTLQKPS PELKQQLTGH SKRVAGSVTE LIQAAEAMKG TEWVDPEDPT VIAENELLGA AAAIEAAA K KLEQLKPRAK PKEADESLNF EEQILEAAKS IAAATSALVK AASAAQRELV AQGKVGAIPA NALDDGQWSQ GLISAARMV AAATNNLCEA ANAAVQGHAS QEKLISSAKQ VAASTAQLLV ACKVKADQDS EAMKRLQAAG NAVKRASDNL VKAAQKAAAF EEQENETVV VKEKMVGGIA QIIAAQEEML RKERELEEAR KKLAQIRQQQ YKFLPSELRD EHLVVLFQ

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
75.0 mMKClKCl
0.5 mM(HO2CCH2)2NCH2CH2N(CH2CO2H)2EDTAEthylenediaminetetraacetic acid
0.5 mMHSCH2CH2OHb-mercaptoethanol2-Mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotted 4 seconds before plunging, blot force 4.
DetailsGraFix

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.62 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 11007 / Average exposure time: 10.0 sec. / Average electron dose: 76.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1873975
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 50000 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 30438

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Atomic model buiding 1

Initial model
PDB IDChain

3ivf

chain_id: a, residue_range: 210-398

1sj8

chain_id: a, residue_range: 486-785

2l7a

chain_id: a, residue_range: 786-910

2lqg

chain_id: a, residue_range: 911-1046

2l7n

chain_id: a, residue_range: 1047-1205

2l10

chain_id: a, residue_range: 1206-1355

5ic1

chain_id: a, residue_range: 1356-1822

2kvp

chain_id: a, residue_range: 1823-1971

3dyj

chain_id: a, residue_range: 1972-2297

2jsw

chain_id: a, residue_range: 2298-2479
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 377
Output model

PDB-6r9t:
Cryo-EM structure of autoinhibited human talin-1

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