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- EMDB-68387: Perinereis linea erythrocruorin -

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Basic information

Entry
Database: EMDB / ID: EMD-68387
TitlePerinereis linea erythrocruorin
Map data
Sample
  • Complex: Perinereis linea erythrocruorin
    • Protein or peptide: Extracellular globin A
    • Protein or peptide: Extracellular globin B
    • Protein or peptide: Extracellular globin C
    • Protein or peptide: Extracellular globin D
    • Protein or peptide: Hemoglobin linker 1
    • Protein or peptide: Hemoglobin linker 2
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CALCIUM ION
Keywordsinvertebrate / annelid / hemoglobin / erythrocruorin / OXYGEN TRANSPORT
Biological speciesPerinereis linea (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsDeng JX / Jiang YL / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32241025 China
CitationJournal: Structure / Year: 2026
Title: Structure of Perinereis linea erythrocruorin reveals a compact extracellular globin megacomplex.
Authors: Jia-Xin Deng / Wen-Bin Cheng / Kang Xu / Pu Hou / Yuxing Chen / Yong-Liang Jiang / Cong-Zhao Zhou /
Abstract: Many invertebrates lack erythrocytes and instead rely on extracellular hemoglobin assemblies, termed erythrocruorins, for oxygen transport. Here we report a 2.84 Å cryo-electron microscopy (cryo-EM) ...Many invertebrates lack erythrocytes and instead rely on extracellular hemoglobin assemblies, termed erythrocruorins, for oxygen transport. Here we report a 2.84 Å cryo-electron microscopy (cryo-EM) structure of Perinereis linea erythrocruorin (PlEc). PlEc is a ∼3.3 MDa megacomplex composed of 180 polypeptide chains organized into 12 protomers, forming a hexagonal bilayer with D6 symmetry. Each protomer consists of 12 globin subunits and three linker subunits, adopting a mushroom-like architecture. The cap of the mushroom is formed by a globin dodecamer associated with a heterotrimeric linker head, and the stem consists of a triple-stranded coiled coil derived from the N-terminal helices of three linker subunits. Biochemical assays show that PlEc has thermal stability and auto-oxidation rate comparable to those of other erythrocruorins, but displays relatively lower oxygen-binding affinity. These findings provide mechanistic insights into the quaternary assembly of invertebrate erythrocruorins and lay the groundwork for the potential biomedical applications.
History
DepositionJan 14, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68387.png

Downloads & links

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Map

FileDownload / File: emd_68387.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.217
Minimum - Maximum-1.6656394 - 2.4463594
Average (Standard dev.)-0.0010590766 (±0.07764154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 547.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68387_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_68387_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_68387_half_map_2.map
Projections & Slices
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Sample components

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Entire : Perinereis linea erythrocruorin

EntireName: Perinereis linea erythrocruorin
Components
  • Complex: Perinereis linea erythrocruorin
    • Protein or peptide: Extracellular globin A
    • Protein or peptide: Extracellular globin B
    • Protein or peptide: Extracellular globin C
    • Protein or peptide: Extracellular globin D
    • Protein or peptide: Hemoglobin linker 1
    • Protein or peptide: Hemoglobin linker 2
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CALCIUM ION

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Supramolecule #1: Perinereis linea erythrocruorin

SupramoleculeName: Perinereis linea erythrocruorin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Perinereis linea (invertebrata)

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Macromolecule #1: Extracellular globin A

MacromoleculeName: Extracellular globin A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Perinereis linea (invertebrata)
Molecular weightTheoretical: 16.43865 KDa
SequenceString:
DQCCSIEDRH EVQALWQSIW SAENTGKRTL IGRRIFEELF DINPGTKALF GRVNVDDMGS PEFKAHVLRV MNGLDTLIGV LDDPATGTS LIQHLAEQHK ARDGFKAAYF KDIGVALRRV LPQVASCFNP EAWNHCFDGF VASITAAMA

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Macromolecule #2: Extracellular globin B

MacromoleculeName: Extracellular globin B / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Perinereis linea (invertebrata)
Molecular weightTheoretical: 16.476941 KDa
SequenceString:
DTHCGPLQRL KVKQQWAKAY GVGHERVELG IALWKSMFSQ DPEARKLFDR VHGEDVRSPA FEAHIARVFN GFDRIISSLT DEDVLNAQL AHLKEQHIKL GITAHHFKLM RTGLGYVLPA QLGRCFDKAA WSACWDEVIY PGIKSL

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Macromolecule #3: Extracellular globin C

MacromoleculeName: Extracellular globin C / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Perinereis linea (invertebrata)
Molecular weightTheoretical: 16.570662 KDa
SequenceString:
DDCCSAADRH AVLSDWQNVW SAEFTGRRVA IGKAIFEELF AIDASAKGVF GRVHVDDQSS PEWAAHVIRV INGLDLAINL LEDPRALNE ELHHLARQHR ERDGVKAVYF DEIEKALLKV LPQVSSNFNA GAWDRCFTRI ASVIKAELP

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Macromolecule #4: Extracellular globin D

MacromoleculeName: Extracellular globin D / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Perinereis linea (invertebrata)
Molecular weightTheoretical: 16.101162 KDa
SequenceString:
DCNNLRRLKV KYQWSMVYDT THDRSQFATA VWRQFFKTYP DRSLFSNVRG ENIYSPEFRA HMVRVFAGFD ILISVLDSEP VLNAALAHY NTFHKQFDSI PFKQFGEVLL DTLSQFIPNE FDQDAWKECY AVIVAGIGA

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Macromolecule #5: Hemoglobin linker 1

MacromoleculeName: Hemoglobin linker 1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Perinereis linea (invertebrata)
Molecular weightTheoretical: 24.84693 KDa
SequenceString: WAGIASKADA QEARINRLAG RVESVAEKLR TGGERVKNFM GEFREMEFRV NELEGNGCDK RHFQCGGNSR ECISDLLTCD GSPDCQNGA DEADDICHIP IPAGTVLVGH LNTDHDFCTK RKPNEMDLYI TSVTRSKYMQ SRLKVKANLN IKYTAEGSEV E DVLPVSGY ...String:
WAGIASKADA QEARINRLAG RVESVAEKLR TGGERVKNFM GEFREMEFRV NELEGNGCDK RHFQCGGNSR ECISDLLTCD GSPDCQNGA DEADDICHIP IPAGTVLVGH LNTDHDFCTK RKPNEMDLYI TSVTRSKYMQ SRLKVKANLN IKYTAEGSEV E DVLPVSGY YNFGTHQLVI LPPEDDRLGI ICRFRAGNDN RCMASIVHEA SLTHCGDDFV FVAQH

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Macromolecule #6: Hemoglobin linker 2

MacromoleculeName: Hemoglobin linker 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Perinereis linea (invertebrata)
Molecular weightTheoretical: 25.39807 KDa
SequenceString: SAFSDPGVAE GRLANQDARL EQLENYLEGV ISKYEKFTQG REARVRRWNA LQDRVWGLEA HHCDDEHFSC RDDVYNCVGH QLVCDGTKD CLNGRDEDEE TCRVVPGVGS AFEGTLVKQD PCTSRKPRTF RFVVTSVDTS PNFPQEPKVK AAVIMQSDQT G ETVESSMT ...String:
SAFSDPGVAE GRLANQDARL EQLENYLEGV ISKYEKFTQG REARVRRWNA LQDRVWGLEA HHCDDEHFSC RDDVYNCVGH QLVCDGTKD CLNGRDEDEE TCRVVPGVGS AFEGTLVKQD PCTSRKPRTF RFVVTSVDTS PNFPQEPKVK AAVIMQSDQT G ETVESSMT ANGVYDYTHR RLILYSPDND SLVFTCTFDR YNDDLCRGEI RRESGTSCVE FGLARLG

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Macromolecule #7: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 7 / Number of copies: 12 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 833216
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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