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- EMDB-4750: CryoEM structure and molecular model of squid hemocyanin (Todarod... -

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Basic information

Entry
Database: EMDB / ID: EMD-4750
TitleCryoEM structure and molecular model of squid hemocyanin (Todarodes pacificus , TpH)
Map dataCryoEM map of Todarodes pacificus hemocyanin (TpH)
Sample
  • Complex: Squid Hemocyanin
    • Protein or peptide: Hemocyanin subunit 1
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity
Similarity search - Function
Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
Hemocyanin subunit 1
Similarity search - Component
Biological speciesTodarodes pacificus (Japanese flying squid) / Japanese flying squid (Japanese flying squid)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsTanaka Y / Kato S / Stabrin M / Raunser S / Matsui T / Gatsogiannis C
Funding support Germany, Japan, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
Japan Society for the Promotion of Science26291008;24000011;15KK0248;16H00748;17K07942 Japan
German Research FoundationFOR1905 Germany
CitationJournal: 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
DepositionMar 31, 2019-
Header (metadata) releaseMay 8, 2019-
Map releaseMay 8, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r83
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4750.png

Downloads & links

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Map

FileDownload / File: emd_4750.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of Todarodes pacificus hemocyanin (TpH)
Voxel sizeX=Y=Z: 1.14 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.020640383 - 0.06369496
Average (Standard dev.)0.000850192 (±0.0041214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 513.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z513.000513.000513.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.0210.0640.001

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Supplemental data

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Sample components

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Entire : Squid Hemocyanin

EntireName: Squid Hemocyanin
Components
  • Complex: Squid Hemocyanin
    • Protein or peptide: Hemocyanin subunit 1

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Supramolecule #1: Squid Hemocyanin

SupramoleculeName: 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.
Source (natural)Organism: Todarodes pacificus (Japanese flying squid)
Molecular weightTheoretical: 3.8 MDa

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Macromolecule #1: Hemocyanin subunit 1

MacromoleculeName: Hemocyanin subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Japanese flying squid (Japanese flying squid)
Molecular weightTheoretical: 379.741188 KDa
SequenceString: 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

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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

Concentration2.9 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
100.0 mMHEPES
200.0 mMcalcium chlorideCaCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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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 / Cs: 0.0 mm
Specialist opticsSpherical aberration corrector: Microscope equipped with Cs corrector
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 359250
CTF correctionSoftware - Name: SPHIRE (ver. 1.0)
Startup modelType of model: OTHER
Details: Initial model was computed from 2D class averages using VIPER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.0)
Final 3D classificationSoftware - Name: SPHIRE (ver. 1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 196315

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-6r83:
CryoEM structure and molecular model of squid hemocyanin (Todarodes pacificus , TpH)

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