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- PDB-22jw: Perinereis linea erythrocruorin -

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Basic information

Entry
Database: PDB / ID: 22jw
TitlePerinereis linea erythrocruorin
Components
  • (Extracellular globin ...) x 4
  • (Hemoglobin linker ...) x 2
KeywordsOXYGEN TRANSPORT / invertebrate / annelid / hemoglobin / erythrocruorin
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesPerinereis linea (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsDeng, J.X. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 1items
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, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular globin A
B: Extracellular globin B
C: Extracellular globin C
D: Extracellular globin D
E: Extracellular globin A
F: Extracellular globin B
G: Extracellular globin C
H: Extracellular globin D
I: Extracellular globin A
J: Extracellular globin B
K: Extracellular globin C
L: Extracellular globin D
M: Hemoglobin linker 1
N: Hemoglobin linker 1
O: Hemoglobin linker 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,37230
Polymers271,85415
Non-polymers7,51815
Water00
1
A: Extracellular globin A
B: Extracellular globin B
C: Extracellular globin C
D: Extracellular globin D
E: Extracellular globin A
F: Extracellular globin B
G: Extracellular globin C
H: Extracellular globin D
I: Extracellular globin A
J: Extracellular globin B
K: Extracellular globin C
L: Extracellular globin D
M: Hemoglobin linker 1
N: Hemoglobin linker 1
O: Hemoglobin linker 2
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)3,352,467360
Polymers3,262,250180
Non-polymers90,217180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D6 (2x6 fold dihedral))

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Components

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Extracellular globin ... , 4 types, 12 molecules AEIBFJCGKDHL

#1: Protein Extracellular globin A


Mass: 16438.650 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Perinereis linea (invertebrata)
#2: Protein Extracellular globin B


Mass: 16476.941 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Perinereis linea (invertebrata)
#3: Protein Extracellular globin C


Mass: 16570.662 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Perinereis linea (invertebrata)
#4: Protein Extracellular globin D


Mass: 16101.162 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Perinereis linea (invertebrata)

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Hemoglobin linker ... , 2 types, 3 molecules MNO

#5: Protein Hemoglobin linker 1


Mass: 24846.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Perinereis linea (invertebrata)
#6: Protein Hemoglobin linker 2


Mass: 25398.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perinereis linea (invertebrata)

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Non-polymers , 2 types, 15 molecules

#7: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Perinereis linea erythrocruorin / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Perinereis linea (invertebrata)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 833216 / Symmetry type: POINT
RefinementHighest resolution: 2.84 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00320157
ELECTRON MICROSCOPYf_angle_d0.55627452
ELECTRON MICROSCOPYf_dihedral_angle_d8.2752716
ELECTRON MICROSCOPYf_chiral_restr0.0392844
ELECTRON MICROSCOPYf_plane_restr0.0033565

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