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- EMDB-41586: Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin -

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Basic information

Entry
Database: EMDB / ID: EMD-41586
TitleCryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin
Map data
Sample
  • Complex: Didecameric complex of Pomacea canaliculata hemocyanin
    • Protein or peptide: Hemocyanin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGlycoprotein / Respiratory Pigment / Cooper Protein / Carbohydrates / OXYGEN TRANSPORT
Biological speciesPomacea canaliculata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsBrola TR / Chiumiento IR / Gragera M / Carazo JM / Heras H / Dreon MS / Otero LH
Funding support Argentina, 2 items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2021-00158 Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2020- SERIEA-03047 Argentina
CitationJournal: To Be Published
Title: Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin
Authors: Brola TR / Chiumiento IR / Gragera M / Carazo JM / Heras H / Dreon MS / Otero LH
History
DepositionAug 10, 2023-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41586.png

Downloads & links

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Map

FileDownload / File: emd_41586.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.99 Å/pix.
x 300 pix.
= 597.78 Å		1.99 Å/pix.
x 300 pix.
= 597.78 Å		1.99 Å/pix.
x 300 pix.
= 597.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.9926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.637
Minimum - Maximum-2.13575 - 3.8620927
Average (Standard dev.)0.03286052 (±0.2124453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 597.77997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41586_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41586_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Didecameric complex of Pomacea canaliculata hemocyanin

EntireName: Didecameric complex of Pomacea canaliculata hemocyanin
Components
  • Complex: Didecameric complex of Pomacea canaliculata hemocyanin
    • Protein or peptide: Hemocyanin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Didecameric complex of Pomacea canaliculata hemocyanin

SupramoleculeName: Didecameric complex of Pomacea canaliculata hemocyanin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pomacea canaliculata (invertebrata)

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Macromolecule #1: Hemocyanin

MacromoleculeName: Hemocyanin / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Molecular weightTheoretical: 388.727125 KDa
SequenceString: SLVRKNVDLL TDQEVLSLES YLRELEDDKT VNGYQNLAAF HGEPSMCTKD DGKRVACCVH GMATFPQWHR LYVVQLEQKL GKKGLADIG VPYWDWTKPI TALPRLVQEP IFKDPKGGLG QKNSWFSGEI NVDSMDVHTS TARAVDDRLF QSVAPGENTQ L FEMVLDAL ...String:
SLVRKNVDLL TDQEVLSLES YLRELEDDKT VNGYQNLAAF HGEPSMCTKD DGKRVACCVH GMATFPQWHR LYVVQLEQKL GKKGLADIG VPYWDWTKPI TALPRLVQEP IFKDPKGGLG QKNSWFSGEI NVDSMDVHTS TARAVDDRLF QSVAPGENTQ L FEMVLDAL EEDDYCHFEV QFEVAHNHIH YLVGGRHDHS LSTLEWSAYD PLFFLHHSNV DRIFVIWQEL QKKRGKTYDH AD CSVELFR KKLEPFDRDT NPIELTRTYS TAKSLFSYRQ LGYVYDDLSL NGLNIEQLYN LLEQRRARER ALASFTLHGL GFS ANVRIK VCDHDDDDDQ SHSHCEFAGD IFILGGANEM PWEFNLPYHF DISKAVEHLG KKLNGDYVVT AELYSVNGTS LNPN LLPRP VGVYRPAKGF TDPKPSESDV QSANVVIRKD VDTLTDEEVY ELRQALSRFQ NDTSVNGYQS VAEFHGLPAR CPRPD ARVR YACCVHGMAT FPHWHRLFVV QVEDALKSRG LHFGIPYWDW TRPGTTVPAI ASKETYVDPN SGSSVHNPFF NAPVAF LGE TTSRQVQPEL STKPEYGDHT ALFDGMLLAL EQRDFCDFEV QFEVVHNLPH FLVGGFASYS LSTLHYSAFD PIFILHH SN VDRLWAIWQA LQIKRGLPYK AHCAHTMTHE LLKPFGFAPP LNSNEKTYSH ARPTNIYDYE HELEYAYDNL QFGGMTID Q LDHYIDERRT KDRTFVGLHL QNIGTSALVI LSIKPKDGDS YEVAKLAVLG GEKEMPWNFD RLVKVEITDA LNKKGLKYD DEYDVVLSIK DVSGKDWPEN TFSHTTIIHE EGTTHEETGE HQELHVRSDV SSLTREQVQS LREALQSLED DTSINGFEHI AAFHGQPNW CPSPDAEKKF ACCAHGMAVF PHWHRLLTVQ AENALRAKGF QDGLPYWDWT LPMTALPEIV AGETYVNPET N LPEPNPFH HGLVEGKKTT RSVRDELFEK PKFGRLTKIA EMVLLAFEQT DFCTFEVQYE IAHNYIHALV GGNESYSMAS LR YTAYDPI FFLHHSNTDR IWAIWQALQH YRGLPYNSAN CAIASLRKPL QPFAQTSTIN PDHITRDHSV PFEVFDYERS FQY HYDDLE FNGFSIPQLQ REILHRQHDE RVFAGFMLHG IRKSALVTLE VCEPSGPCHP EGEFYILGDE YEIPWQYDRL FQYE ITDIL AKYKLEANDR YSVKYSVIDL DGKKISSEVF GKVTVVVRPG SETKKGEIDK NIVASSHIRR NLQDLSEGEV ESLKS ALRR MQDDGTFGKI ASFHGFPSLC THEGRKVACC VHGSAVFPHW HRLYVDQVEN ALLARGSAVS VPYWDWTQPI RQLPAL INE ASYFDSRSQT EESNPFFQVK ILDTGKVTTR DPQPELFNSD YLLNNVLLAL EQTSFCDFEI QFEIVHNALH SLVGGRG LY SLSSLDYSAF DPLFFLHHAN VDRIWAIWQA LQQYRGLPDD KSDCALNIMR QPLKPFNDKG QNEFDLTNRY SRPIDVFD Y SNHFDYHYDT LNFNSWTIPQ LEEVLKRQRA QDRLFAGFLL HNIGTSADVQ LFICVATGNG ERNCNHPAGS FSVLGGETE MPFIFDRLYK YDISDPVRKL GLKLDSAGDI DLEIKIRAYN GSYLESSVLR RPSLIFVPGE DNSQDQTGKT ERRLIRKSVT SLTIGERRS LVLALQSLEE DSSATGFQAL ASFHAVPPLC PYPEANQRYA CCVHGMATFP QWHRLYTVQF EDALRRRGAL V GIPYWDTV NPQNSLPAFF NEPIYRDPVL DVDIPNPWAG ADIAFENTTV ERDFKRNRLS DDGEHGYDNW LWKQFLFALE QE NYCDFEV QFEIAHNAIH AWVGGSKEHS MAHLHYASYD PIFLLHHSST DRIYALWQEL QRLRGHDPNE ANCALELMRE PLK PFSFGA PYNLDPITKE YSKPEDVFDY KSHFNYEYDT LELAGINAEL LLSLINKQKE KSRAFAGFLL GGIKTSAHVD IKVC TPEDV CKDAGDFDVL GGTAEMPWSF DRLYRYEITE VLEKKGLSVD DAFTVKVELR ALNGSILSSS LIPTPSVLYE PKSRV TSIQ ELPPNRVRHE ISHLDARATM SLKAALRDLQ KDGTKSGWQA LAAFHGVPAL CPSPEAPKYA CCLHGVPTFP HWHRLY TLQ VEQALLKHGS TVALPYWDWT LPISQLPSLF TEQTFYDAWK DEVLENPFAR GYIKESKGYT VRDPQPELFK LSADGKH SV LFDEVLLVLE QTDYCDFEVQ FEVTHNAIHY LVGGHQSYSL SSLHYSSYDP IFFTHHTFVD KIWAVWQELQ KRRGLPYD R ADCAVNYMSD AMQPFNSVVL NENAFTRTHA LPKEVFNYQD LNFRYDDMKL GGLNLDELEE EIRQHQSKAR VFAGFLLHG IGTSAEVRFS VCQENGKCTR AGAIFVLGGS LEMPWAFDRL YKYDITDTLN ELHIRPEDVF NADAPFSLRY EIIAVNGTAL PPSSLSKPT IIFKPAVGAR TEEASYSVSG IGVRKNINTL TVAETESLKK ALRAVQQQSG PRGYQEIAAA HGYPGLCKDN G HTVACCHH GSASFPQWHR LFVVTLERAL TLQGARVGIP YWDWTESFTS LPTLLTDKDD NPFEHGEIAS LNEKTTRSPR PQ LFSDPER GEESFFYRQI LLAFEQRDYC NFEVQYEVTH NAIHSWIGGT SPYGMSTLEY SAYDPIFFIH HSNVDRQFAI WQA LQRYRG LDYNSANCNI QELRQPLEPF NWDSNPNDFI RENARAVDAF DYDQFNYQYD DLNFHGLTIP QLEEAIEKRR SEDR VFANF MLQGFKASAD VTFDLCDADN HCSFAGTFAV LGGPLEMDWH FDRLFQYDVT SVFNQMHLRP DSVYHFDVHI TAING TQLA SSLLESPSVS FVPGKGKTGS RAVAKEDPQP TKTKDVVRYE VSALSLEQVS NLRNALYKLQ NDDGPNGYEA IASFHG APK LCPENATDRY ACCTHGMPVF PHWHRLLTVQ FEMALRDKGA LLGIPYWDWT RPSKALPSLL TSTDNNPFST YQIKFAQ HQ VTRDVQPGLY NRRKQSGLDS LFYQTLETLE ETNYCDFEVQ FEMLHNTIHA LVGGQGTYSM STLEYSAFDP FFMIHHSS I DRIWQIWQTL QKLRHRSFNY ARCALRNLYR PLEPFNYESK NPNPVTRANS RPVQIFDASK FHYNFDNLNL NGHSVSEIN TIIENLRDHD RVYAGFVLSG IGVSATANVK LVPQGGDPVD VGSFYILGGD GEMPWAYERV YKYDVTDALE KLGLNAYSNF GFQVTLTKY NGEQLDASLA TPVVISRPAN ADYDVLILPL LEENKLPPKV IVSRGTRVRF HSPVSSLNAN VKEVGSYTSL S LCSIPPGD ANSYDPDVNY SLEPGDYFFV SSNKARCEQG TRVQISIDDE

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 20 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration3.0 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormula
20.0 mMTris-HCl
20.0 mMCaCl2
20.0 mMMgCl2
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 4584 / Average electron dose: 36.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 64970
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC, Scipion) / Number images used: 29935
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 1

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 110 / Target criteria: Correlation coefficient
Output model

PDB-8trz:
Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin

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