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Yorodumi- EMDB-4750: CryoEM structure and molecular model of squid hemocyanin (Todarod... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4750 | ||||||||||||
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Title | CryoEM structure and molecular model of squid hemocyanin (Todarodes pacificus , TpH) | ||||||||||||
Map data | CryoEM map of Todarodes pacificus hemocyanin (TpH) | ||||||||||||
Sample |
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Keywords | oxygen transporter / mollusc / hemocyanin / copper / symmetry mismatch / OXYGEN TRANSPORT | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Todarodes pacificus (Japanese flying squid) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||||||||
Authors | Tanaka Y / Kato S | ||||||||||||
Funding support | Germany, Japan, 3 items
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Citation | Journal: IUCrJ / Year: 2019 Title: Cryo-EM reveals the asymmetric assembly of squid hemocyanin. Authors: Yoshikazu Tanaka / Sanae Kato / Markus Stabrin / Stefan Raunser / Takashi Matsui / Christos Gatsogiannis / Abstract: The oxygen transporter of molluscs, hemocyanin, consists of long pearl-necklace-like subunits of several globular domains. The subunits assemble in a complex manner to form cylindrical decamers. ...The oxygen transporter of molluscs, hemocyanin, consists of long pearl-necklace-like subunits of several globular domains. The subunits assemble in a complex manner to form cylindrical decamers. Typically, the first six domains of each subunit assemble together to form the cylinder wall, while the C-terminal domains form a collar that fills or caps the cylinder. During evolution, various molluscs have been able to fine-tune their oxygen binding by deleting or adding C-terminal domains and adjusting their inner-collar architecture. However, squids have duplicated one of the wall domains of their subunits instead. Here, using cryo-EM and an optimized refinement protocol implemented in , this work tackled the symmetry-mismatched structure of squid hemocyanin, revealing the precise effect of this duplication on its quaternary structure and providing a potential model for its structural evolution. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4750.map.gz | 24.7 MB | EMDB map data format | |
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Header (meta data) | emd-4750-v30.xml emd-4750.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_4750.png | 283.3 KB | ||
Filedesc metadata | emd-4750.cif.gz | 7.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4750 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4750 | HTTPS FTP |
-Validation report
Summary document | emd_4750_validation.pdf.gz | 420.4 KB | Display | EMDB validaton report |
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Full document | emd_4750_full_validation.pdf.gz | 420 KB | Display | |
Data in XML | emd_4750_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | emd_4750_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4750 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4750 | HTTPS FTP |
-Related structure data
Related structure data | 6r83MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4750.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of Todarodes pacificus hemocyanin (TpH) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Squid Hemocyanin
Entire | Name: Squid Hemocyanin |
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Components |
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-Supramolecule #1: Squid Hemocyanin
Supramolecule | Name: Squid Hemocyanin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: TpH is a decamer of a 400 kDa subunit. Each subunit is composed by 8 paralogous O2 binding functional units (A,B,C,D,D*,E,F,G). The ten subunits of TpH acquire 4 different overall conformations. |
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Source (natural) | Organism: Todarodes pacificus (Japanese flying squid) |
Molecular weight | Theoretical: 3.8 MDa |
-Macromolecule #1: Hemocyanin subunit 1
Macromolecule | Name: Hemocyanin subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Todarodes pacificus (Japanese flying squid) |
Molecular weight | Theoretical: 379.741188 KDa |
Sequence | String: NLLRKNVDTL TPDEILNLQV SLRAMQDDEG ASGYQAISAY HGEPADCKAA DGSTIVCCLH GMPTFPMWHR LYLVQFEQAL VAHGSTLGI PYWDWTKPMT QLPELVQHPL FIDPTGKKAK KNVFYSGEIK FENKVTARAV DARLYQASQE GQKNFLLEGV L NALEQEDF ...String: NLLRKNVDTL TPDEILNLQV SLRAMQDDEG ASGYQAISAY HGEPADCKAA DGSTIVCCLH GMPTFPMWHR LYLVQFEQAL VAHGSTLGI PYWDWTKPMT QLPELVQHPL FIDPTGKKAK KNVFYSGEIK FENKVTARAV DARLYQASQE GQKNFLLEGV L NALEQEDF CHFEVQLEVA HNPIHYLVGG RFTHSMSSLE YTSYDPLFFL HHSNVERHFA LWQALQKHRG LPTRPNCGLN LF HSPMEPF GRDTNPFAIT KDNSKASSLF DYEHLGYAFD DLSLNGMTIE ELEALLKQRR SGARAFANFR LGGIKTSANV RIK LCIPTE DKRQSDNCDN DAGQFFILGG TNEMPWNFAF PYLHEITDTV LSLGLALDSN YYVTAEVTAI NGTLMPTQTI PRPI VTYIP PQGFKDVNMV NMDTSSLRFR KDISSLTTEE EYELRVAMER FMSDKSINGY QALAEFHGLP AKCPRPDALN RVACC IHGM ATFPHWHRLV VMQFENALFT RGSPIGVPYW DWTKPFTALP SLLADETYVD PYTKETKPNP FFKAPIEFLK AGVHTS RQI DERLFKQPSK GDHGFLYDGL SLAFEQDDFC DFEVQFEVTH NSIHAWTGGS EPYSMSSLHY TSFDPMFWLH HSQVDRL WA IWQALQIQRG KPYKTYCANS EVYRPMKPFA FKSPLNNDEK TREHSVPTDV YDYQAELAYT YDTLFFGGLS IRELQRYV E EAKSKDRVFA GFLLMGIQTS ANVDLFVVAG GNEFFVGSIA VLGGSKEMTW RFDRVYKHEI TDALGALGVD MFAEYTLRV DIKDVNGTAL PPTAIPPPIV IFVPGIADAN VKFDEQHRSR KNVDSMTVSE MNALRTAMAA FAADKEVTGY QQVAAFHGST QWCPSPDAA QKYACCHHGM ATFPHWHRLI ALNFENGLRR NGWSGGLPYW DWTRPIDALP ALVLEAEYTD ANGEAKPNPF F SGAIDSIG ASTSRAPTEA LYEKPDFGKY THLANEIISA LEQEDFCDFE VQYEIAHNHI HALVGGTEAV SMASLEYSAF DP IFMLHHS NVDRIWATWQ ALQKFRGKAY NSANCAIEIL RKPMSPFSLA SDINPDAMTR EYSVPFDVFN YKKNFHYEYD TLE LNGLSI (UNK)QLSREINRR KAKNRV(UNK)VTF MLEGLKKSLL VEYFIAADGT DQKMKAGEFY VLGSENEMPW KFDRPY KSD ITYVMDAMKL HYTDKYHVEL RITDMTGAEV TDLKLVTSVI YEPGIGNFGE GRRWISPITS ASRIRKNLLD FEDGEME SL RNAFKQMADE GRYEEIASFH GVPAQCPSED GTMVHTCCLH GMPVFPHWHR LYVSLVEDEL LARGSGVAVP YWDWVEPF D ELPRLINEAT FYNSRTLQIE PNPFFKGKIS FENAETDRDT QPELFGNRYL YDHTLFVFEQ TDFCEFEVHY EVLHNTIHS WLGGRDVHSM SSLDYAAYDP VFFLHHSNVD RLWAIWQELQ RYRKLSYNEA NCALPLMNQP MRPFSNSTAN NDRLTFTNSR PNDVFDYQN VLHYKYDTLN FAGLSIPQLE RILQKNQGRD RIFAGFLLHG IKASADVRIY ICVPTGIGEE NCGNYAGIFS V LGGETEMP WQFDRLFRYE ITDELKKLGL NQNSHFRVEM ELTAVNGSKI TQKIFPNPTI IFVPSDVEFE EDTWRDVVTS AN RIRRNLK DLSKEDMFSL RAAFKRMTDD GRYEEIAAFH GLPAQCPNAD GSNIHTCCLH GMPTFPHWHR LYLSLVENEL LAR GSDVAV PYWDWIEPFD SLPGLISDET YKHPKTNEDI ENPFHHGKIS FADAVTVRKP RDQLFNNRYL YEHALFAFEH TDFC DFEVH FEVLHNSIHS WIGGPNPHSM SSLDFAAYDP IFFLHHSTVD RLWAIWQDLQ RYRKLDYNVA NCALNLLNDP MRPFN NKTA NQDHLTFTNS RPNDVFDYQN SLNYKFDSLS FSGLSIPRLD DLLESRQSHD RVFAGFWLSG IKASADVNIH ICVPIG VEH EDCDNYAGTF AVLGGETEMP WAFDRLFRYE ISDEMKKLQL TEDSKFRLTT NIIASNGSKV SNDIFPTPTV IFVPKKE RT EQVSTTKSVR GNLVRKNVDR LSLQEINSLI HALKRMQKDR SSDGFETIAS FHALPPLCPN PTAKHRHACC LHGMATFP Q WHRLYVVQFE HSLNRHGAIV GVPYWDWTYP MTEVPGLLTS EKYTDPFTGI ETFNPFNHGH ISFISPETMT TREVSEHLF EQPALGKQTW LFNNIILALE QTDYCDFEVQ FEIVHNSIHS WLGGKELYSL NHLHYAAYDP AFFLHHSNVD RLWVVWQELQ KFRGLPAYE SNCAIELMSQ PLKPFSFGAP YNLNPVTTKY SKPSDVFNYK QNFHYEYDML EMNGMSIAQL ESYIRQERQK D RVFAGFLL EGFGSSAYAT FQVCPDVGDC YEGSHFSVLG GSTEMPWAFD RLYKMEITDI LQAMDLKFDS HFTIKTKIVA HN GTELPES LLPEATIVRI PPSAQNLEVA IPLNRIRRNI NSLESRDVQN LMSALKRLKE DESDFGFQTI AGYHGSLMCP TPE APEYAC CLHGMPTFMH WHRVYLLHFE ESMRRHGASV AVPYWDWTMP SDNLPSLLGD ADYYDAWTDS VIENPFLRGH IKYE DTYTV REIQPELFAL AEGQKESTLF KDVMLMFEQE DYCDFEVQAE VIHNSIHYLI GGHQKYAMSS LMFSSFDPIF YVHHS MVDR LWAIWQELQK HRKLPHDKAY CALDQMAFPM KPFIWESNPN PTTRAVSTPS KLFDYKSLGY DYDHLNFHGM SIGQLE ALI QKQKKADRVF AGFLLHGIKI SADVHLKICI EADCQEAGVI FVLGGETEMP WHFDRNYKMD ITDVLKKRNI PPEALFE HD SKIRLEVEIK SVDGAVLDPN SLPKPSLIYA PAKGLIIQQV GEYDAGSMVR KNVNSLTPSE IENLRNALAA VQADKTDA G YQKIASFHGM PLSCQYPDGT AFACCQHGMV TFPHWHRLYM KQMEDALKAK GAKIGIPYWD WTTAFHSLPI LVTEPKNNP FHHGYIDVAD TKTTRDPRPQ LFDDPEQGDQ SFFYRQIAFA LEQRDFCDFE IQFEMGHNAI HSWVGGPSPY GMSTLHYTSY DPLFYVHHS NTDRIWAIWQ ALQKYRGLPY NSANCEINKL KKPMMPFSSE DNPNEVTKAH STGYKSFDYQ QLNYEYDNLN F HGMTIPQL EVHLKKIQEK DRVFAGFLLR AIGQSADVNF DVCRKDGECT FGGTFCVLGG DYEMPWAFDR LFLYDISKSL VH LRLDAHD DFDIKVTIMG IDGKSLPPNL LPSPTILFKP GTGKI UniProtKB: Hemocyanin subunit 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.9 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Microscope equipped with Cs corrector |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 1-24 / Number grids imaged: 1 / Number real images: 5092 / Average exposure time: 1.0 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
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Output model | PDB-6r83: |