[English] 日本語
Yorodumi
- EMDB-31890: Cryo-EM structure of Chlamydomonas TOC-TIC supercomplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31890
TitleCryo-EM structure of Chlamydomonas TOC-TIC supercomplex
Map dataComposite map
Sample
  • Complex: TOC-TIC supercomplex
    • Protein or peptide: x 15 types
  • Ligand: x 4 types
Function / homology
Function and homology information


protein import into chloroplast stroma / chloroplast inner membrane / chloroplast outer membrane / chloroplast membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein transport / membrane => GO:0016020 / hydrolase activity / GTP binding / membrane / metal ion binding
Similarity search - Function
CCB3/YggT / Chloroplast protein import component Tic20 / Protein TIC56 / YGGT family / Chloroplast import apparatus Tic20-like / GYF domain 2 / GYF domain 2 / GTPase GIMA/IAN/Toc / AIG1-type guanine nucleotide-binding (G) domain / AIG1 family ...CCB3/YggT / Chloroplast protein import component Tic20 / Protein TIC56 / YGGT family / Chloroplast import apparatus Tic20-like / GYF domain 2 / GYF domain 2 / GTPase GIMA/IAN/Toc / AIG1-type guanine nucleotide-binding (G) domain / AIG1 family / AIG1-type G domain profile. / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AIG1-type G domain-containing protein / Flagellar associated protein / Uncharacterized protein / J domain-containing protein / YggT family protein / YtxH domain-containing protein / Translocase of chloroplast 34 homolog, chloroplastic / Bacterial surface antigen (D15) domain-containing protein / Protein TIC 20 / Uncharacterized protein ...AIG1-type G domain-containing protein / Flagellar associated protein / Uncharacterized protein / J domain-containing protein / YggT family protein / YtxH domain-containing protein / Translocase of chloroplast 34 homolog, chloroplastic / Bacterial surface antigen (D15) domain-containing protein / Protein TIC 20 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized membrane protein ycf78
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWu J / Yan Z / Jin Z / Zhang Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2022
Title: Structure of a TOC-TIC supercomplex spanning two chloroplast envelope membranes.
Authors: Zeyu Jin / Li Wan / Yuqi Zhang / Xuecheng Li / Yong Cao / Haobin Liu / Shengyao Fan / Du Cao / Zhengmao Wang / Xiaobo Li / Junmin Pan / Meng-Qiu Dong / Jianping Wu / Zhen Yan /
Abstract: The TOC and TIC complexes are essential translocons that facilitate the import of the nuclear genome-encoded preproteins across the two envelope membranes of chloroplast, but their exact molecular ...The TOC and TIC complexes are essential translocons that facilitate the import of the nuclear genome-encoded preproteins across the two envelope membranes of chloroplast, but their exact molecular identities and assembly remain unclear. Here, we report a cryoelectron microscopy structure of TOC-TIC supercomplex from Chlamydomonas, containing a total of 14 identified components. The preprotein-conducting pore of TOC is a hybrid β-barrel co-assembled by Toc120 and Toc75, while the potential translocation path of TIC is formed by transmembrane helices from Tic20 and YlmG, rather than a classic model of Tic110. A rigid intermembrane space (IMS) scaffold bridges two chloroplast membranes, and a large hydrophilic cleft on the IMS scaffold connects TOC and TIC, forming a pathway for preprotein translocation. Our study provides structural insights into the TOC-TIC supercomplex composition, assembly, and preprotein translocation mechanism, and lays a foundation to interpret the evolutionary conservation and diversity of this fundamental translocon machinery.
History
DepositionSep 2, 2021-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31890.png

Downloads & links

-
Map

FileDownload / File: emd_31890.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.2131057 - 12.515656
Average (Standard dev.)0.03682045 (±0.1441328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 417.40802 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Map1 (Overall map)

Fileemd_31890_additional_1.map
AnnotationMap1 (Overall map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map4 (TIC IMS region map)

Fileemd_31890_additional_2.map
AnnotationMap4 (TIC IMS region map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map2 (TOCL region map)

Fileemd_31890_additional_3.map
AnnotationMap2 (TOCL region map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map3 (TOCS region map)

Fileemd_31890_additional_4.map
AnnotationMap3 (TOCS region map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Composite map (deepEMhancer)

Fileemd_31890_additional_5.map
AnnotationComposite map (deepEMhancer)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map5 (TIC YlmG map)

Fileemd_31890_additional_6.map
AnnotationMap5 (TIC YlmG map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Overall map half1

Fileemd_31890_half_map_1.map
AnnotationOverall map half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Overall map half2

Fileemd_31890_half_map_2.map
AnnotationOverall map half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : TOC-TIC supercomplex

EntireName: TOC-TIC supercomplex
Components
  • Complex: TOC-TIC supercomplex
    • Protein or peptide: Tic214
    • Protein or peptide: Toc75
    • Protein or peptide: Toc52
    • Protein or peptide: Tic13
    • Protein or peptide: Toc120
    • Protein or peptide: Toc34
    • Protein or peptide: YlmG
    • Protein or peptide: Toc39
    • Protein or peptide: Toc10
    • Protein or peptide: Tic12
    • Protein or peptide: Unknown fragment
    • Protein or peptide: Tic35
    • Protein or peptide: Tic56
    • Protein or peptide: Tic100
    • Protein or peptide: Tic20-Venus-Flag
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
  • Ligand: MAGNESIUM ION
  • Ligand: water

+
Supramolecule #1: TOC-TIC supercomplex

SupramoleculeName: TOC-TIC supercomplex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

+
Macromolecule #1: Tic214

MacromoleculeName: Tic214 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 232.615688 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MITFTFMSLV TSVKDYVEIT HKLIEIEPLK NYTEFGAVFT YFIFSIGEFF KNFFSFSFLN NIWSIPIIIP DIASAMISEV SVLDGYFHN AFTFLETSVN TTTNPSLVIF EKFVIGIINS LFLILPTSTS HLITLRRFVM QGLEAGYMAG LGTLAGNFLW L ASIILGWR ...String:
MITFTFMSLV TSVKDYVEIT HKLIEIEPLK NYTEFGAVFT YFIFSIGEFF KNFFSFSFLN NIWSIPIIIP DIASAMISEV SVLDGYFHN AFTFLETSVN TTTNPSLVIF EKFVIGIINS LFLILPTSTS HLITLRRFVM QGLEAGYMAG LGTLAGNFLW L ASIILGWR FFVIPWLSLD IFRYLLGFVL LVKYIWDSSK ERRMALEDLS KWKIFLLNFL LALTEQSCIY PFISNLSFGP DA SILEGFP VDNYPQFLLI HGAYLLGILF GSFSLLQFTC WFWENPAFSI YLWITTKSSL KISTSSYYKI LNFTFLYATM LCA IASIPY YGLDYTITNP IGLVPQDRIL NQKKSQSDPD KLITETAFLN LNPTDKNSRI RDGVHARRER WKQRLIKYQA FDAS TYDQG VYDFLTIEDL NYGFDRFWLR RKMRNHQIRF RLFPGPWMRS LKKQLNNPAN PSLETSTKAA SGPRVEFFRI LFEQF YHPN FHDRAAMQTN PAEARNKFIS TSPLASTESK KALNSTFSLG NINNSSTGIE GLVLTNTQAT LLPTDLQTKR TIKPGL IYT NSALRKFVRN VNTRLNLKLL NSKETNLTTK YKSQFIYSKR WKSIFSKIQP LQNGTTRKSY QLFRNVAKQI LVTPDAK SL KLITINQKLS LKERKLLELR TQYNNNSTLT TTAPLTLVRP LNVYLQKEEA FKRKLRYYGT MPMRKLTVGN QAPYFKAL M KRGFYYYKPT LRWRKTLYVA SLRRGFRKKS RKQRILVMPS NQQNFNNTLD NTKTNINQNN LANPLGGNEV PMYGADGEN SLITKPTHSY TVLGKRASRY RHQIYKDVLQ HWYYTPFNRL LMKFDVDAFI NRQPKSHFLT KNEERALHIR RFLLSEHYDT LRWYTYMQH YKTMKTNIGG TKSFANRAYN QQFQGTFKKI RHLFAITPKQ GDFYTLKFDQ PLYNDNKLKD NLYFHEELLT D YYNGTNLQ TNQTSNISVN STTTFIDNSL RTTQLPVPSS SFDIVNQSST LIGLTTMQNA LRKNVVESTL TSLNSDGEAA TS QPKLNFV YSELFVKLIK ECKKRIHDQT FLKNYITHRI EKREQLNQEQ TKELNKRLEK LKVWLNSDKG SISKLQNTPV QDP NISSPD KVLTTAMQKA VNESISLSGI MPSDKIKTTY GNLTNAYTIK TENAILTKLN VINQLTNNET TTQKNTLIKS IGVN KIQTV LQTIITNFKS SLYNQTQLLR VKTDKDLQWW RTKQRVITKR KSARKRDRFK KQIAVVNKKL AALSKKVETE KSNLY QTLY GNYEISDYLL RNVPTGSSAV IDSTVLRKKQ DNQAYLPKET NNVQFNSFVD SNNNVWQTFF AKKLRKKISS KGRRYR SLS LARYLTATRK PRLVGLDNLT KIDNITTLQG AFITKEEKQD SLNLTIQRKQ ELTNSLKKSQ IKKRSRHSWK KRSRHQF SR NHYKYRKRHT HGNGKLRVMN KKLKKFKATN ELRQWWWNSF LPRYLSNLQV NNSTLTNKNV SFKPLSNTNS VPSTNMAS P TTSRNLLDNL NSSNQISTSA SMNQNIVTES VKVETNQVYL PEGEKSFDIT SMTTTLPFYA GWDESLKKFV VTNRLLSRR DAGLSVNNNP QEINFTNPPI QGLNEGSFLY WQTEMPFNSY NIDQFITTNQ SFYAPLGWRR FEFRHSILKT WVNNTKAGNN NIKKKTLII SLKNLQPLKS SQQKQNQIKT KKLVARRIKK RYKLLKQMPN QLMYSPTGPL LTEVLPSHYI SVFDQQYRLP R NRYLKRNP LKTLKKTTLL ALMDSSKQTN GVNKEF(TPO)LRK RVKPRRKYHR KRFIKKDGLI FPRRTKFNTN TTLTGNAL I TNNVNSIEED DLRWRPSSRT KQKRKDNTRS SAASKTKSNK RVKTNPLRLR QLRRREFQQV LKPLQRYIPQ NGGFTWPGD YLRLEIVEMP KLKSINIKKT SLKQKINVQP VGIMPRKYLI EKHNIKVLKK KLSQAYSTQQ LTKVVQEYKN LIQNSPPAI

+
Macromolecule #2: Toc75

MacromoleculeName: Toc75 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 87.493242 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MQGLKATPGL RASSGRPTLR TARTALVVRA HASQPSSSNH AEQQECSSSG SGVSVNQPSA LGRLGKFGLS SALSAFVLVP NFGGFGGNG GNRGGGGGGG GGGGSGGQGQ PDGGLPLPLY ELAEESSDEK EKQQKDDKRN WKNLVTDSED LEEKPGERSG T NRCVEIVI ...String:
MQGLKATPGL RASSGRPTLR TARTALVVRA HASQPSSSNH AEQQECSSSG SGVSVNQPSA LGRLGKFGLS SALSAFVLVP NFGGFGGNG GNRGGGGGGG GGGGSGGQGQ PDGGLPLPLY ELAEESSDEK EKQQKDDKRN WKNLVTDSED LEEKPGERSG T NRCVEIVI EGWPDVGNLP TADELKDLLT VQEGHIFEKQ DLLDDRRKLE IQYEDYIAEV EIRTEYVDGK SNHQRVVYKF TP HQFRGIN AIDIKGAALM PASEVERICN ECLPKQPYMV DIAVMDKVRN RIEQWYQSRG LPFCYVGFFD GMDDGILRAN VTE AKIDNV SVRFVRPKLT GD(SEP)ELEY(SEP)VY DEGKVVKADK IIEASGFQRG HHYHVEDGYD AMNSIFACGL LEDINI EPE QDPSDVNKIN VKIRCEEVQP KSMELDLDWS FQLKNGIPSI NRQSLIPGGS VEVSHENLFG NSESATLSLS ASDWRNP SA DLGFSVAYSE PFYKPHTTRN AQLFNTRKTS TIFTPGGESE VPPVFVDRFG LKGWTSQITG QDNKVEHALM LQLVSTLD E NGQVVAKGTK VQRGYYADNG PPTTNSGNGR DLSLSYQGFF ALDNVRFING NQLGERMLFQ VDQGLNPSIS LPGGRKLGL SGGIYNRATA SYTKFLEAPF LPKLTTEQLW KERKAPNTVV LHAKAGNALG DVAAYDYFSL GGPYSVRGYS HGEIGAARRF LELATEVRV PLKNYGLPGT AYGFVEYATD LGSGRELNGN PTEYYRKPGR GMSYGLGLKA LGACRFEYAR DCNAGTGTFL V NFGERF

+
Macromolecule #3: Toc52

MacromoleculeName: Toc52 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 52.062594 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MADGPSPIRI VLWNDGGESL AAGVEDEEQQ QVLHSFADLV GSAIDAVLEL PQFRHVEAVT AEAEEDEPGL SIGFDAGSGD GEVDIDNLK GRLDIAGLLL GSAQLPEELA EVAAVEVTDE EEGTTELQFT DEGLVQQLQA VVKRAKLEKR YNDWVAGVAE S LGPALDAA ...String:
MADGPSPIRI VLWNDGGESL AAGVEDEEQQ QVLHSFADLV GSAIDAVLEL PQFRHVEAVT AEAEEDEPGL SIGFDAGSGD GEVDIDNLK GRLDIAGLLL GSAQLPEELA EVAAVEVTDE EEGTTELQFT DEGLVQQLQA VVKRAKLEKR YNDWVAGVAE S LGPALDAA AGGVEVTEMP VDPYDVLQAV VAQLIRVAGV SPPAPSLFSR TGALVGGVLG APRSAVRQVT KRLGRAQRLW WR LEDVVVD GSKLALRLAV KAARPVLVGF VLHRVLKTLD RSRQLEYRLA RMGPEEAREA YYEAVLGKDW KQQLQADWDK ALE DVDAGL V(TPO)DEINHEKR LMTAAQLRRL EVEEWDKQRM KNFYLASFGG LRWFDQMEQA LHNPLFIESR GWTDPVQNWV GQNRTYMDD LPAGQYMAGV GNAAIRIKEA ELKRKLTDVE RAHVLARGGA VAGGLLPQQP TDPATLAVAV GGAFVPSVAG K R

+
Macromolecule #4: Tic13

MacromoleculeName: Tic13 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 13.426158 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
MSSDVQAKLS GLLGDIGVKC TLAFAGTVAA GAAIVVPSGK QVEAASLDIY GRPPSQLLPN ERRAAEFAAG HRRWKGFVDN SIYSWTRTL PGHDNPIVNP YKGPRRPQRP QQKLEEEVEA AAKQE

+
Macromolecule #5: Toc120

MacromoleculeName: Toc120 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 102.495242 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MGGGLPPKRS EVAESQPASS ASSSAAAPAP AAETAGPKLP PRPAGLGLGG AGLLPSRGAA AAPSAGSATG TPAAAASSSL QQQQQQPAP PATQPAAHAA PAAPAGLGGA GLKPMLPPRP AAAAGAGAAG AAAAKPTPAP APAAAPVPAA APPPRPAMPN P AAGMSLPP ...String:
MGGGLPPKRS EVAESQPASS ASSSAAAPAP AAETAGPKLP PRPAGLGLGG AGLLPSRGAA AAPSAGSATG TPAAAASSSL QQQQQQPAP PATQPAAHAA PAAPAGLGGA GLKPMLPPRP AAAAGAGAAG AAAAKPTPAP APAAAPVPAA APPPRPAMPN P AAGMSLPP RPVVAAAPPV LAAAGSDAVV DPSEDRRVQR VQRIAHDTRV RLIRAASRLG LAPRTDQVAQ FLQAIERSER MV GAQHYKG SRRVDLLAAA EREARLAEER EGAAAEAVAG LRVKILVLGM TGTGKTELIN SLLNRPAGSR TNAFREATRR VRV VRGDHN GIPLTFIDTP GLHASASRTA DNRAILRAVR AAYRWHKPDY VFYVDRLDAT RPGFGEMGLL GLITESLGAG VWRN TMAVL THAHAARTAF GGQYDVNSRQ RRNIVSQLLR QAAGDQQSRN PVFLADCHPA CPTNSLGQPV ILEGPTAVPW KQQLL VQLV GYKSYNVATS AFKDLAKAKA GKAAAGAAGG ARGPQDIFKQ MMRSRLPPMT FFVEQMSEGV LKPEGWATME TVAGLG EEV (TPO)EDEGAESFN HVYYRQMYEL AVAGDPWAQR EYAAMLRAYD KGCESYRASY EEADVDANVE YGVESYVVDP IDF GPSFDP EDMYSHRHAY AEAADAGVTV IPSQDYYGPE HDDPLNGIVF QYEAQPFSRH GWGGVPFDLT VCCEKDKTSL CLQG ETHVS LVHSVPPFGP RHITQVTGSW EVLRPNIKDV MYQLEVDTFK DGLLGKSDHA GCGLMLARLG EGGDPRKGPT AVGVR LQDT LRVGPFKLEA CASKVAVQGP TGGKEEGWGA RAFVGYDWLP GLGMAFDFIQ ERTPEEGGKR LRGYGANFTY DWEALG AAF GMEVDYVAAS ESVFVSVNAF SGNDYRLGWL LLLPAVNYFK ETVSSLWARL RGAGGGEGEE GEELEEEGEG EEGDDEE AM MMMAQEGDL

+
Macromolecule #6: Toc34

MacromoleculeName: Toc34 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 44.598613 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MAQPPRPAEE YDDDVQEDED ELKEGELDDD ESHEAASEGG EAAAGDEEAE DDEQDEEDGD EDSQPWAGLN RLPERDDMLD ILNELRAEG RKQLTVLLLG KSSVGKSSLI NSLLGEAVVR VQAFKLQADT DITTTVVRQV AVGNSEVDGF RLKLIDTCGL E DPEAGDTV ...String:
MAQPPRPAEE YDDDVQEDED ELKEGELDDD ESHEAASEGG EAAAGDEEAE DDEQDEEDGD EDSQPWAGLN RLPERDDMLD ILNELRAEG RKQLTVLLLG KSSVGKSSLI NSLLGEAVVR VQAFKLQADT DITTTVVRQV AVGNSEVDGF RLKLIDTCGL E DPEAGDTV NLGALSKIAE DVRGVGIDVV LYCDRLDLYR VDPLDKAIID AISSTFGRGI WRRTVVALTH ANLVQTPPGT DY DSFVNGR VRLIRGAVRG PLFFRPSLPV ALVENSETCP VSSESGFRVL PDGEPWLVAL VSQLVDMAAA RRRPYKYHPR LSS KPSHRF RWLLPVAIAA EVLFYRRFLH PRLDDNQRRV EREEERVWAL RGQQRRALGL HRPHRPDKDA AWRLEQMYDD D

+
Macromolecule #7: YlmG

MacromoleculeName: YlmG / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 21.425592 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MATCAAVSLA TAVFQVAAKY VNKARDAVAS ALPSPSNIDG VQQDWRQQVK ELKKHTRVLG FVLPLAKAFA AESLTSVYAR TFERAAFGF AKMYLFCLFM RVLLSWFPSI DWNSQPWAFL RLITEPYLQI YRGILPPLFG QLDFTPLFGF LILQDVVELM S PVYTLGHA ...String:
MATCAAVSLA TAVFQVAAKY VNKARDAVAS ALPSPSNIDG VQQDWRQQVK ELKKHTRVLG FVLPLAKAFA AESLTSVYAR TFERAAFGF AKMYLFCLFM RVLLSWFPSI DWNSQPWAFL RLITEPYLQI YRGILPPLFG QLDFTPLFGF LILQDVVELM S PVYTLGHA KDTSMFW(TPO)(TPO)(TPO) DIMCYFDGH

+
Macromolecule #8: Toc39

MacromoleculeName: Toc39 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.025082 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MGASQESELD FVPRLSFLPI EWRSIGSAFG LKDKSGAAAN GRATFTVRQG VDAAELTSTG RVIDGQADVG ASLKLNTLAI GVSASNITF HSGLDDPTAA AAQRSSLIPS LKLTAAKQFK RDNYIAVSYD LKHQKPELSA CWTGEAGADR ATLLVNVDPV M RSVKLAAA ...String:
MGASQESELD FVPRLSFLPI EWRSIGSAFG LKDKSGAAAN GRATFTVRQG VDAAELTSTG RVIDGQADVG ASLKLNTLAI GVSASNITF HSGLDDPTAA AAQRSSLIPS LKLTAAKQFK RDNYIAVSYD LKHQKPELSA CWTGEAGADR ATLLVNVDPV M RSVKLAAA VRTPGPEWRK VLYNDETDLL EYPADDGARH TLYVQHEVRG RDLLHATRLG CRLDLGRLVN YVVDFVDYRI EE NIPSFVW NVPLLPQLYS LLVPADNDEQ VRHRITGWEL DVSHDFARSG LLPVVAISKT SKKLLGGGTL TASYDAAARE AGV SLSRKG VSVGARVARA EGAAGGLSAG WGRPSIHVAV EPLGLLQ

+
Macromolecule #9: Toc10

MacromoleculeName: Toc10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 10.569109 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
MKLVKTVSKL AGAAVGMLPA GQAGLAVKVA LGVAFAFWWT SGPGADEEMD AKAQQEPDRR SQYTRHYAFK GRGRKEFLRS DMKNDANEL VPTRGAAGL

+
Macromolecule #10: Tic12

MacromoleculeName: Tic12 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 14.662776 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
MDEEPPFNLA LNVYKGPASI PHASAEVFGA FFLATNTALL AHMFPGKLFG SELHVRKWDP DYLASCCNEQ GMRREALSGK KPNLWLLGG GPRLVNDSWE RMWWNNLHWK RWKVPRTGPA FPQDMYWQ

+
Macromolecule #11: Unknown fragment

MacromoleculeName: Unknown fragment / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 2.188521 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
KFIFWAAMVY ATLYGNYE

+
Macromolecule #12: Tic35

MacromoleculeName: Tic35 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 35.63302 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MQLGQLRQPL RACQDQRLTR GVPLARRQLV VVSNWNPLGG KGGGNSKDKE DAARRALEQS LGQKKFGADA SKKTPAAKPA EPSKPAGED ASKNPLQNLF GGGGPKPPAG GGGGGGGDGG GGFFSGGNAE QPGGEEPIQD ELLKLLRGGW VLLSNLALFL V FSSFLHRS ...String:
MQLGQLRQPL RACQDQRLTR GVPLARRQLV VVSNWNPLGG KGGGNSKDKE DAARRALEQS LGQKKFGADA SKKTPAAKPA EPSKPAGED ASKNPLQNLF GGGGPKPPAG GGGGGGGDGG GGFFSGGNAE QPGGEEPIQD ELLKLLRGGW VLLSNLALFL V FSSFLHRS LNWFVQTELL VAVGAPQQAG ERVVGKFFEA IEWVERNILG WKLPGDEEAE DATSKVYEVL QNYTPAEAAY SF AQLKYKD LTHKERELFH KAYALRHFER RDGRPGDVDA AELQAVKDRL DPLEADRRAY AAAKAAGRLD EYWAAPGREA TYQ RIVGAP RIA

+
Macromolecule #13: Tic56

MacromoleculeName: Tic56 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 28.046527 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MSEPGAGPSD GQVVTRKIRL HKVMRPLDES SPSSQEQHMD RRLAEILPAI ADLPVPGPSG AGGSPADARA VEMRRLRGTQ QELAQMEAM ELATLFDMSK PHPLDNAAPA TPWKGELRPV PRKIVLSPYQ YEMINYQRML MRKNIWYYRD RMNVPRGPCP L HVVKEAWV ...String:
MSEPGAGPSD GQVVTRKIRL HKVMRPLDES SPSSQEQHMD RRLAEILPAI ADLPVPGPSG AGGSPADARA VEMRRLRGTQ QELAQMEAM ELATLFDMSK PHPLDNAAPA TPWKGELRPV PRKIVLSPYQ YEMINYQRML MRKNIWYYRD RMNVPRGPCP L HVVKEAWV SGIVDENTLF WGHGLYDWLP AKNIKLLLPM VRTPEVRFAT WIKRTFSLKP SLNRIREQRK EHRDPQEASL QV ELMR

+
Macromolecule #14: Tic100

MacromoleculeName: Tic100 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 107.337312 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MASKKGTDAP AALTDPLKED PTVIRDEAQF PEPSLYFKVF E(SEP)EAGEPEAK IRADVNKLYD RWIEKYGRRW PEDGIN (TPO)ED MVWLAEEANK RKRAKPRPRG TVAAEKTEYE DEFMPDPTVG APVSAADAAK AARRAKKDRK KKKAAGGAEQ PAG PRTNYE ...String:
MASKKGTDAP AALTDPLKED PTVIRDEAQF PEPSLYFKVF E(SEP)EAGEPEAK IRADVNKLYD RWIEKYGRRW PEDGIN (TPO)ED MVWLAEEANK RKRAKPRPRG TVAAEKTEYE DEFMPDPTVG APVSAADAAK AARRAKKDRK KKKAAGGAEQ PAG PRTNYE KTVAGGKWV(TPO) DEFE(SEP)ADYEA GNLEKLWDMY LWDREGKPTM MPDTPAAQQE GEE(SEP)EDFDDF YT AYRPRDV D(SEP)EEAREAVW A(TPO)DEFE(SEP)DED N(TPO)E(SEP)EWAPEY VGAGLGLVAE DPLNPQYSLR HSN HPLAPF PGEPLKWASY VYPDFTTFEG LSKQSIPHGM GVMTFGTGTG AGFAMSQTRY GDKYEGEFQA GYAHGLGQFT SEAS GEVYI GEFFAGQRHG CGMTLDMKPY FYLLERGVDP VEAYRRTAGA IMKNVEVRTW YRGNKLGDAK EDEVVEINVL KDELD DPFE IALRNSLHDA KLRKWKAMSP QDKAMDRIVS IIERVQRRNP GRFGAYYRED EKGRVRPVLD (SEP)DGAD(TPO)DF D (SEP)VDMIQGVD(TPO) DGDLGPGWEG ATD(SEP)EENPMD PRIRELMAAE GMDDKLEDEG FKDTVLGSAI INPYTGL DM KTYLDGKERH QAELVSVYKA SREGRKYLNK VRKDKGGAAK DDESSYVEDD AASGHPGALL SREAEDDRLA RLYEQAGV S KEDERRVEGL AARWRRLLAA DEEEVLGGAV GAFRRPGNPL AAND(SEP)D(TPO)GFE (TPO)E(SEP)DMMEMCD IPE ILGTVQ EARQIVERAR MWRFKPYGEV GLRMAQDANG SPVSLMQEPL HYPHGTKFMA PGPLGLCHAV PDDPSLRQEM AKVA HNYAA IYRMYNFDWD PEPGTVQYKI DQRIRRAQEL RNNAMARYLA AADEVLRDGA APAGEGDQAL LLASTSTGAP EAFDG QGNA SGSGSSSALS SRGGSMFASM TLSRPAPMAG VVSLGRAARV VLGAFADAAK SVPMARPRLA RPSGRRQ

+
Macromolecule #15: Tic20-Venus-Flag

MacromoleculeName: Tic20-Venus-Flag / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 60.260367 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString: MSALLSQASG FSGLALGSSA SSKRLCKPLC RRPAVCVQAA HRPASAVSSG VPSTGFGPVS PLQRRPTLPT RKLVVASSQS GGRAEDAEK QDWKFGRNEG PMTWPWKLMC AILYMLPWVD VTEKTVYFVE RFPAFVWTEY FSEPFEHWYN IHEYAPLFIF F ATYLGIVR ...String:
MSALLSQASG FSGLALGSSA SSKRLCKPLC RRPAVCVQAA HRPASAVSSG VPSTGFGPVS PLQRRPTLPT RKLVVASSQS GGRAEDAEK QDWKFGRNEG PMTWPWKLMC AILYMLPWVD VTEKTVYFVE RFPAFVWTEY FSEPFEHWYN IHEYAPLFIF F ATYLGIVR NKKIPHVARY HVMMGVMLDI VAMILIVTEE NLPTGVLWTP WSDLFYALMF WFIFLLVIYC LFFCFLGWYC EI PLISEGV YLQIEQAEQL GQNGDLGGSG GRMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKLI CTT GKLPVP WPTLVTTLGY GLQCFARYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDF KEDGN ILGHKLEYNY NSHNVYITAD KQKNGIKANF KIRHNIEDGG VQLADHYQQN TPIGDGPVLL PDNHYLSYQS ALSKD PNEK RDHMVLLEFV TAAGITLGMD ELYKDYKDDD DKDYKDDDDK DYKDDDDK

+
Macromolecule #16: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 16 / Number of copies: 4 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

+
Macromolecule #17: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 17 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

+
Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 82000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.0) / Number images used: 595638

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more