[English] 日本語
Yorodumi
- EMDB-33529: Cryo-EM structure of TOC complex from Chlamydomonas reinhardtii. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33529
TitleCryo-EM structure of TOC complex from Chlamydomonas reinhardtii.
Map data
Sample
  • Complex: Structure of a outer membrane protein complex
    • Protein or peptide: Ctap3
    • Protein or peptide: Toc39
    • Protein or peptide: Toc75
    • Protein or peptide: Toc90
    • Protein or peptide: Tic214
    • Protein or peptide: Tic100
    • Protein or peptide: Toc34
    • Protein or peptide: Unknown peptide
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
Function / homology
Function and homology information


chloroplast outer membrane / chloroplast membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein transport / hydrolase activity / GTP binding / membrane / metal ion binding
Similarity search - Function
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 / Translocase of chloroplast 34 homolog, chloroplastic / Bacterial surface antigen (D15) domain-containing protein / Uncharacterized protein / Uncharacterized membrane protein ycf78
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant) / Chlamydomonas smithii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLiu H / Li AJ / Liu ZF
Funding support China, 4 items
OrganizationGrant numberCountry
Chinese Academy of SciencesYSBR-015 China
National Natural Science Foundation of China (NSFC)31925024 China
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
Chinese Academy of SciencesXDB37020101 China
CitationJournal: Nature / Year: 2023
Title: Architecture of chloroplast TOC-TIC translocon supercomplex.
Authors: Hao Liu / Anjie Li / Jean-David Rochaix / Zhenfeng Liu /
Abstract: Chloroplasts rely on the translocon complexes in the outer and inner envelope membranes (the TOC and TIC complexes, respectively) to import thousands of different nuclear-encoded proteins from the ...Chloroplasts rely on the translocon complexes in the outer and inner envelope membranes (the TOC and TIC complexes, respectively) to import thousands of different nuclear-encoded proteins from the cytosol. Although previous studies indicated that the TOC and TIC complexes may assemble into larger supercomplexes, the overall architectures of the TOC-TIC supercomplexes and the mechanism of preprotein translocation are unclear. Here we report the cryo-electron microscopy structure of the TOC-TIC supercomplex from Chlamydomonas reinhardtii. The major subunits of the TOC complex (Toc75, Toc90 and Toc34) and TIC complex (Tic214, Tic20, Tic100 and Tic56), three chloroplast translocon-associated proteins (Ctap3, Ctap4 and Ctap5) and three newly identified small inner-membrane proteins (Simp1-3) have been located in the supercomplex. As the largest protein, Tic214 traverses the inner membrane, the intermembrane space and the outer membrane, connecting the TOC complex with the TIC proteins. An inositol hexaphosphate molecule is located at the Tic214-Toc90 interface and stabilizes their assembly. Four lipid molecules are located within or above an inner-membrane funnel formed by Tic214, Tic20, Simp1 and Ctap5. Multiple potential pathways found in the TOC-TIC supercomplex may support translocation of different substrate preproteins into chloroplasts.
History
DepositionJun 2, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33529.png

Downloads & links

-
Map

FileDownload / File: emd_33529.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.675 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-4.5464926 - 4.0438027
Average (Standard dev.)-0.00045712656 (±0.015026036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_33529_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33529_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Structure of a outer membrane protein complex

EntireName: Structure of a outer membrane protein complex
Components
  • Complex: Structure of a outer membrane protein complex
    • Protein or peptide: Ctap3
    • Protein or peptide: Toc39
    • Protein or peptide: Toc75
    • Protein or peptide: Toc90
    • Protein or peptide: Tic214
    • Protein or peptide: Tic100
    • Protein or peptide: Toc34
    • Protein or peptide: Unknown peptide
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid

+
Supramolecule #1: Structure of a outer membrane protein complex

SupramoleculeName: Structure of a outer membrane protein complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

+
Macromolecule #1: Ctap3

MacromoleculeName: Ctap3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 51.982613 KDa
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 VTDEINHEKR LMTAAQLRRL EVEEWDKQRM KNFYLASFGG LRWFDQMEQA LHNPLFIESR GWTDPVQNWV GQNR TYMDD LPAGQYMAGV GNAAIRIKEA ELKRKLTDVE RAHVLARGGA VAGGLLPQQP TDPATLAVAV GGAFVPSVAG KR

+
Macromolecule #2: Toc39

MacromoleculeName: Toc39 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 39.025082 KDa
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 #3: Toc75

MacromoleculeName: Toc75 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 87.333289 KDa
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 GDSELEYSVY DEGKVVKADK IIEASGFQRG HHYHVEDGYD AMNSIFACGL LEDINIEPEQ DPSD VNKIN VKIRCEEVQP KSMELDLDWS FQLKNGIPSI NRQSLIPGGS VEVSHENLFG NSESATLSLS ASDWRNPSAD LGFSV AYSE PFYKPHTTRN AQLFNTRKTS TIFTPGGESE VPPVFVDRFG LKGWTSQITG QDNKVEHALM LQLVSTLDEN GQVVAK GTK VQRGYYADNG PPTTNSGNGR DLSLSYQGFF ALDNVRFING NQLGERMLFQ VDQGLNPSIS LPGGRKLGLS GGIYNRA TA SYTKFLEAPF LPKLTTEQLW KERKAPNTVV LHAKAGNALG DVAAYDYFSL GGPYSVRGYS HGEIGAARRF LELATEVR V PLKNYGLPGT AYGFVEYATD LGSGRELNGN PTEYYRKPGR GMSYGLGLKA LGACRFEYAR DCNAGTGTFL VNFGERF

+
Macromolecule #4: Toc90

MacromoleculeName: Toc90 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 102.415258 KDa
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 TEDEGAESFN HVYYRQMYEL AVAGDPWAQR EYAAMLRAYD KGCESYRASY EEADVDANVE YGVESYVVDP IDFGPSF DP EDMYSHRHAY AEAADAGVTV IPSQDYYGPE HDDPLNGIVF QYEAQPFSRH GWGGVPFDLT VCCEKDKTSL CLQGETHV S LVHSVPPFGP RHITQVTGSW EVLRPNIKDV MYQLEVDTFK DGLLGKSDHA GCGLMLARLG EGGDPRKGPT AVGVRLQDT LRVGPFKLEA CASKVAVQGP TGGKEEGWGA RAFVGYDWLP GLGMAFDFIQ ERTPEEGGKR LRGYGANFTY DWEALGAAFG MEVDYVAAS ESVFVSVNAF SGNDYRLGWL LLLPAVNYFK ETVSSLWARL RGAGGGEGEE GEELEEEGEG EEGDDEEAMM M MAQEGDL

+
Macromolecule #5: Tic214

MacromoleculeName: Tic214 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 232.535719 KDa
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 GVNKEFTLRK RVKPRRKYHR KRFIKKDGLI FPRRTKFNTN TTLTGNALIT NN VNSIEED DLRWRPSSRT KQKRKDNTRS SAASKTKSNK RVKTNPLRLR QLRRREFQQV LKPLQRYIPQ NGGFTWPGDY LRL EIVEMP KLKSINIKKT SLKQKINVQP VGIMPRKYLI EKHNIKVLKK KLSQAYSTQQ LTKVVQEYKN LIQNSPPAI

+
Macromolecule #6: Tic100

MacromoleculeName: Tic100 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 105.817695 KDa
SequenceString: MASKKGTDAP AALTDPLKED PTVIRDEAQF PEPSLYFKVF ESEAGEPEAK IRADVNKLYD RWIEKYGRRW PEDGINTEDM VWLAEEANK RKRAKPRPRG TVAAEKTEYE DEFMPDPTVG APVSAADAAK AARRAKKDRK KKKAAGGAEQ PAGPRTNYEK T VAGGKWVT ...String:
MASKKGTDAP AALTDPLKED PTVIRDEAQF PEPSLYFKVF ESEAGEPEAK IRADVNKLYD RWIEKYGRRW PEDGINTEDM VWLAEEANK RKRAKPRPRG TVAAEKTEYE DEFMPDPTVG APVSAADAAK AARRAKKDRK KKKAAGGAEQ PAGPRTNYEK T VAGGKWVT DEFESADYEA GNLEKLWDMY LWDREGKPTM MPDTPAAQQE GEESEDFDDF YTAYRPRDVD SEEAREAVWA TD EFESDED NTESEWAPEY VGAGLGLVAE DPLNPQYSLR HSNHPLAPFP GEPLKWASYV YPDFTTFEGL SKQSIPHGMG VMT FGTGTG AGFAMSQTRY GDKYEGEFQA GYAHGLGQFT SEASGEVYIG EFFAGQRHGC GMTLDMKPYF YLLERGVDPV EAYR RTAGA IMKNVEVRTW YRGNKLGDAK EDEVVEINVL KDELDDPFEI ALRNSLHDAK LRKWKAMSPQ DKAMDRIVSI IERVQ RRNP GRFGAYYRED EKGRVRPVLD SDGADTDFDS VDMIQGVDTD GDLGPGWEGA TDSEENPMDP RIRELMAAEG MDDKLE DEG FKDTVLGSAI INPYTGLDMK TYLDGKERHQ AELVSVYKAS REGRKYLNKV RKDKGGAAKD DESSYVEDDA ASGHPGA LL SREAEDDRLA RLYEQAGVSK EDERRVEGLA ARWRRLLAAD EEEVLGGAVG AFRRPGNPLA ANDSDTGFET ESDMMEMC D IPEILGTVQE ARQIVERARM WRFKPYGEVG LRMAQDANGS PVSLMQEPLH YPHGTKFMAP GPLGLCHAVP DDPSLRQEM AKVAHNYAAI YRMYNFDWDP EPGTVQYKID QRIRRAQELR NNAMARYLAA ADEVLRDGAA PAGEGDQALL LASTSTGAPE AFDGQGNAS GSGSSSALSS RGGSMFASMT LSRPAPMAGV VSLGRAARVV LGAFADAAKS VPMARPRLAR PSGRRQ

+
Macromolecule #7: Toc34

MacromoleculeName: Toc34 / type: protein_or_peptide / ID: 7 / 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 smithii (plant)
Molecular weightTheoretical: 44.598613 KDa
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 #8: Unknown peptide

MacromoleculeName: Unknown peptide / type: protein_or_peptide / ID: 8
Details: Chain X belongs to an unidentified protein, which contains an alpha helix. The input sequence is a tentative one based on the model. The identity of this chain remains to be revealed in the future.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 2.166432 KDa
SequenceString:
AAAAFAFFAG FAFAAFAAAA AAAA

+
Macromolecule #9: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 796731
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7xzj:
Cryo-EM structure of TOC complex from Chlamydomonas reinhardtii.

+
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