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- EMDB-39872: Cryo-EM Structure of the Arabidopsis thaliana TIC Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39872
TitleCryo-EM Structure of the Arabidopsis thaliana TIC Complex
Map data
Sample
  • Complex: Arabidopsis thaliana TIC Complex
    • Protein or peptide: Protein TIC 214
    • Protein or peptide: Protein TIC 20-I, chloroplastic
    • Protein or peptide: Actin T1-like protein
    • Protein or peptide: Protein TIC 100
    • Protein or peptide: Protein TIC 56, chloroplastic
    • Protein or peptide: Nucleusenvelope protein
KeywordsComplex / Translocase / Channel / Membrane protein.
Function / homology
Function and homology information


protein import into chloroplast stroma / chloroplast inner membrane / chloroplast organization / embryo development ending in seed dormancy / chloroplast envelope / plastid / chloroplast thylakoid membrane / protein transmembrane transporter activity / chloroplast / nucleus ...protein import into chloroplast stroma / chloroplast inner membrane / chloroplast organization / embryo development ending in seed dormancy / chloroplast envelope / plastid / chloroplast thylakoid membrane / protein transmembrane transporter activity / chloroplast / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein TIC214 / Ycf1 / Chloroplast protein import component Tic20 / Protein TIC56 / Chloroplast import apparatus Tic20-like / GYF domain 2 / GYF domain 2 / MORN motif / MORN repeat
Similarity search - Domain/homology
Protein TIC 214 / Actin T1-like protein / Protein TIC 56, chloroplastic / Protein TIC 20-I, chloroplastic / Protein TIC 100 / Nucleusenvelope protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWu J / Yan Z / Jin Z / Xu Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2024
Title: Structural insights into the chloroplast protein import in land plants.
Authors: Ke Liang / Zeyu Jin / Xiechao Zhan / Yuxin Li / Qikui Xu / Yanqiu Xie / Yi Yang / Shaojie Wang / Jianping Wu / Zhen Yan /
Abstract: Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi ...Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi complex has been identified as the chloroplast import motor. However, its assembly and cooperation with the TIC complex during preprotein translocation remain unclear. Here, we present the structures of the Ycf2-FtsHi and TIC complexes from Arabidopsis and an ultracomplex formed between them from Pisum. The Ycf2-FtsHi structure reveals a heterohexameric AAA+ ATPase motor module with characteristic features. Four previously uncharacterized components of Ycf2-FtsHi were identified, which aid in complex assembly and anchoring of the motor module at a tilted angle relative to the membrane. When considering the structures of the TIC complex and the TIC-Ycf2-FtsHi ultracomplex together, it becomes evident that the tilted motor module of Ycf2-FtsHi enables its close contact with the TIC complex, thereby facilitating efficient preprotein translocation. Our study provides valuable structural insights into the chloroplast protein import process in land plants.
History
DepositionApr 23, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39872.png

Downloads & links

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Map

FileDownload / File: emd_39872.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 376 pix.
= 408.712 Å		1.09 Å/pix.
x 376 pix.
= 408.712 Å		1.09 Å/pix.
x 376 pix.
= 408.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.772
Minimum - Maximum-3.5341883 - 5.8860593
Average (Standard dev.)0.00006304538 (±0.10018925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 408.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39872_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39872_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana TIC Complex

EntireName: Arabidopsis thaliana TIC Complex
Components
  • Complex: Arabidopsis thaliana TIC Complex
    • Protein or peptide: Protein TIC 214
    • Protein or peptide: Protein TIC 20-I, chloroplastic
    • Protein or peptide: Actin T1-like protein
    • Protein or peptide: Protein TIC 100
    • Protein or peptide: Protein TIC 56, chloroplastic
    • Protein or peptide: Nucleusenvelope protein

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Supramolecule #1: Arabidopsis thaliana TIC Complex

SupramoleculeName: Arabidopsis thaliana TIC Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Protein TIC 214

MacromoleculeName: Protein TIC 214 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 214.072812 KDa
SequenceString: MMVFQSFILG NLVSLCMKII NSVVVVGLYY GFLTTFSIGP SYLFLLRARV MDEGEEGTEK KVSATTGFIA GQLMMFISIY YAPLHLALG RPHTITVLAL PYLLFHFFWN NHKHFFDYGS TTRNEMRNLR IQCVFLNNLI FQLFNHFILP SSMLARLVNI Y MFRCNNKM ...String:
MMVFQSFILG NLVSLCMKII NSVVVVGLYY GFLTTFSIGP SYLFLLRARV MDEGEEGTEK KVSATTGFIA GQLMMFISIY YAPLHLALG RPHTITVLAL PYLLFHFFWN NHKHFFDYGS TTRNEMRNLR IQCVFLNNLI FQLFNHFILP SSMLARLVNI Y MFRCNNKM LFVTSSFVGW LIGHILFMKW VGLVLVWIQQ NNSIRSNVVI RSNKYKFLVS ELRNSMARIF SILLFITCVY YL GRIPSPI FTKKLKGTSE TGGTKQDQEV STEEAPFPSL FSEEGEDLDK IDEMEEIRVN GKDKINKDDE FHVRTYYNYK TVS ENLYGN KENSNLEFFK IKKKEDHFLW FEKPFVTLVF DYKRWNRPNR YIKNDKIENI VRNEMSQYFF YTCQSDGKER ISFT YPPNL STFFEMIQKR IPSFTKEKKT FDQVSTYWSL IHEEKRENLK KEFLNRIEAL DKEWSVENIL EKTTRFCYNE AKKEY LPKI YDPFLHGISR GRIKKLPPFQ IITETYRKNN LGGSWINKIH GLLLKINYKK FEQTIEKFNR KSLSIEKKLS FFSEPQ QEE KINSEEEIKT FKFLFDIVRT DSNDQTLIKN FMDFPEINKK VPRWSYKLIS ELEELEGENE ENVPMEPGIR SRKAKRV VV FTDKEPHGEI YTNLKDNQNS DQNDEMALIR YSQQSDFRRE IIKGSMRSQR RKTVIWEFFQ AKVHSPLFFD RIDKLFFF S FDIWGLKKKI IKNFIWKKKI DKKEEEQSKR EETRRIEIAE TWDSFLFAQI IRGSLLVTQS ILRKYIILPL LIIIKNSVR MLLFQFPEWS QDLKDWKREM HVKCTYNGVQ LSETEFPRNW LTDGIQIKIL FPFYLKPWHK SKFQASQKAR LKKTKDKGEK NDFCFLTVW GMETELPFGS AQRKPSFFEP ISKELKKRIK KLKKKSFVVL KIFKERAPIF LKVAKETKNW ILKNFIFIKG I SKRNLIPL FGPREIYELN EPKKDSIISN QMIHELSVQN KSLEWTNSSL SEKKIKNLID RKKTIRNQIE EISKEKQNLT NS CTKLRYD SKIIESSKKI WQTFKRKNTR LIRKSIFFFK FCIEQMSIAI FLGIINIPRI TTQLFFESTK KILDKYIYKN EEN GEKKKN TLYFISTIKN LISNKKKMSY DLCSLSQAYV FYKLSQIKVS NFCKLKAVLE YNICITSFFV KNKIKVFFQE HGIF HYELK NKTFLNSEVN QWKNWLRSQY QYNLPQISWA RLVTQNWKNK INKDSLVLNP SLTKEDSYEK KKFDNYKKQK FFEAD SLLN PKHNVKKDSI YNLFCYKSIH STEKNFDMSI GIALDNCLVS SFLEKYNIRG MGEIRHRKYL DWRILNFWFT KKVTIE PWV DTKSKKKYIN TKVQNYQKID KITQTDLANK KRNFFDWMGM NEEILNQRIT NFEFFFFPEF FLFSSTYKMK PWVIPIK LL LLNFNENINV NKKIIRKKKG FIPSNEKESL RFYNLNKEEK ESAGQVELES DKETKRNPEA ARLNQEKNIE ENFAESTI K KRKNKKQYKS NTEAELDLFL TRYSRFQLRW NCFFNQKILN NVKVYCLLVR LNNPNEIAVS SIERGEMSLD ILMIEKNFT FAKLMKKGIL IIEPVRLSVQ NDGQLIIYRT IGISLVHKNK HKISKRYKKK SYINKKFFEK SITKYQNKTV NKKKNNYDFF VPEKILSPK RRREFRILIC FNLKKKNARD TNSRFDKNIQ NLTTVLHKKK DLDLDKDKNN LINLKSFLWP NFKLEDLACM N RYWFNTTN GNHFSMIRIR MYTRFPIP

UniProtKB: Protein TIC 214

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Macromolecule #2: Protein TIC 20-I, chloroplastic

MacromoleculeName: Protein TIC 20-I, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 31.235424 KDa
SequenceString: MITGYSTPSA HVLMSSRAFK SSSYRAAAGQ TQHYLARSSL PVVKNSWGSP PSPFNELPRV SRGVPLSYLS ASSSLLLNGE QGSLSGTLP VLPVRRKTLL TPRASKDVPS SFRFPPMTKK PQWWWRTLAC LPYLMPLHET WMYAETAYHL HPFLEDFEFL T YPFLGAIG ...String:
MITGYSTPSA HVLMSSRAFK SSSYRAAAGQ TQHYLARSSL PVVKNSWGSP PSPFNELPRV SRGVPLSYLS ASSSLLLNGE QGSLSGTLP VLPVRRKTLL TPRASKDVPS SFRFPPMTKK PQWWWRTLAC LPYLMPLHET WMYAETAYHL HPFLEDFEFL T YPFLGAIG RLPSWFLMAY FFVAYLGIVR RKEWPHFFRF HVVMGMLLEI ALQVIGTVSK WMPLGVYWGK FGMHFWTAVA FA YLFTVLE SIRCALAGMY ADIPFVCDAA YIQIPYD

UniProtKB: Protein TIC 20-I, chloroplastic

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Macromolecule #3: Actin T1-like protein

MacromoleculeName: Actin T1-like protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 12.114693 KDa
SequenceString:
MEKYFGNAYR GDPGVPHADA DRFVNIWIGS AAFSVLTWVN PYMWQLSNQF NYHDKWMLFE QYHWKKARAK KQPYEFKWNK IPKEVRDSY YYNWPVYFP

UniProtKB: Actin T1-like protein

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Macromolecule #4: Protein TIC 100

MacromoleculeName: Protein TIC 100 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 100.060797 KDa
SequenceString: MANEELTESQ QQEDPSQQLP NADEEKGSDS DSNSDSDASS QSSGDDFYIS ESENEAEGDN TIFNYVRPSD IPPDPNANPE TNIRRFNRV LDGKRVKRMQ EEEEDKYTFY EDLFDFPRDP ERWKEQDLRE IWADGPLEMT KPGWDPAWAD EDDWDVVNDE I QEGRDPGI ...String:
MANEELTESQ QQEDPSQQLP NADEEKGSDS DSNSDSDASS QSSGDDFYIS ESENEAEGDN TIFNYVRPSD IPPDPNANPE TNIRRFNRV LDGKRVKRMQ EEEEDKYTFY EDLFDFPRDP ERWKEQDLRE IWADGPLEMT KPGWDPAWAD EDDWDVVNDE I QEGRDPGI QPFYVPYRKP YPAIPDNHYD IENAKGVVEE LDRIEEFLQW VSYIFPDGSS YEGTVWDDLA QGKGVYIAEN GL VRYEGEW LQNDMEGHGV IDVDIPDIEP IPGSKLEAKM RAEGRIIKRD YMTPEDRKWL EMDVEDSVAL TDGNFQVPFY ENE EWVTQF GEKPEKGRYR YAGQWKHSRM HGCGVYEVNE RILYGRFYFG ELLEEEHGCT VDICALHSGL AEVAAAKARM FVNK PDGMI REERGPYGDP QHPYFYEEDD VWMAPGFINQ FYEVPEYWET YVGEVDQERE MWLNSFYKAP LRLPMPAELE HWWEN VEVT PEFVLLNKEP EPDPNDPSKL VQKEDPVILH TPTGRIINYV EDEKHGIRLF WQPPLEEGEE VDPSKVEFLP LGFDEF YGK EVVVKKEHPI KSFVLGIEKS VKPMLDGLEK WTEEKKKAYE ERKEMIQQEL ELVEAEICLE EAIEDMDEEL KKKEQEE EK KTEMGLTEED EDVLVPVYKE EKVVTAKEKI QENKQEEKYK DDDDEDDDDG DDDDDDDDDD DLGPSSFGSA DKGRRNSP F SSSSLSFASC TLFPAVQSRL ESSFLAWKQH RAEPSKVNTG IIKGADTASA SIHFPPLSSN NARLKMGKVA NRGCVQRSY GSSRSQSQLM SLSRLLSCNA SSSSSPPDSS SSEYLKDSGL WETPVGDMSV VLSLQIQTKC SDLFAETPAV S

UniProtKB: Protein TIC 100

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Macromolecule #5: Protein TIC 56, chloroplastic

MacromoleculeName: Protein TIC 56, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 61.710707 KDa
SequenceString: MSSMNFNPFQ NWFEKPPNPV PSINFVSLAD SFFPKSQSPN FASIGLPKFS KKSPKPETAG TDEPGPYKQI AEQFLWECEN IPDYRHTPE VDKLLNEDPV FEKKENPSTE EIEAEQKWWE SFRASPVVQF MTRAEEIADD MNKMELEDND TPYRKEDKDY W RAIPHVPG ...String:
MSSMNFNPFQ NWFEKPPNPV PSINFVSLAD SFFPKSQSPN FASIGLPKFS KKSPKPETAG TDEPGPYKQI AEQFLWECEN IPDYRHTPE VDKLLNEDPV FEKKENPSTE EIEAEQKWWE SFRASPVVQF MTRAEEIADD MNKMELEDND TPYRKEDKDY W RAIPHVPG FDGRPMPRKA IKSKEESDDK FWDFMKQFLF GLWGFRQRPY PPGRPIDVAQ AIGYKRLEKR YYDFIMKTGG WW YKDRLGR SRGPCEIITL KTAYGAGIID RDTFIWGEDM DEWAPIHMVY GLEPAIATWE VRLGAAATAF LHKLQKGIPP WVP LKGREP KTYKQLQKEA IESKKRDMAV LEANGGVWPG VRTPSHALFL WASGSELTTV LESDHMPNKF IPKQLRLELA KVIP GLRPW EVISIEQAMD QISYGGEWYR EPLGTYTTGP PYIREWNRSV MRLFRIFYNL SVRVGQKLER TVPGFDTIMD KVQKD YDKR IARRMKRREE ELREEDLKHY SGRTDEDEEE EEEEDDDSNS KKD

UniProtKB: Protein TIC 56, chloroplastic

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Macromolecule #6: Nucleusenvelope protein

MacromoleculeName: Nucleusenvelope protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 30.739518 KDa
SequenceString: MSFTQANCFR PSYYPARITR PNCISSVPIR SSVRFDHFPR TSFTLRATAA VSTQFSPLLD HRRRLPTGKS KQSSAVCLFG GKDKPDGSD EISPWKAIEK AMGKKSVEDM LREQIQKKDF YDTDSGGNMP PRGGGSGGGG GNGEERPEGS GGEDGGLAGI A DETLQVVL ...String:
MSFTQANCFR PSYYPARITR PNCISSVPIR SSVRFDHFPR TSFTLRATAA VSTQFSPLLD HRRRLPTGKS KQSSAVCLFG GKDKPDGSD EISPWKAIEK AMGKKSVEDM LREQIQKKDF YDTDSGGNMP PRGGGSGGGG GNGEERPEGS GGEDGGLAGI A DETLQVVL ATLGFIFLYT YIITGEELVK LARDYIRFLM GRPKTVRLTR AMDSWNGFLE KMSRQRVYDE YWLEKAIINT PT WYDSPEK YRRVIKAYVD SNSDEAYVES NSDEVSY

UniProtKB: Nucleusenvelope protein

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 316225
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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