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- PDB-37rr: Plasmodium falciparum 17-PF subpellicular microtubule associated ... -

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Basic information

Entry
Database: PDB / ID: 37rr
TitlePlasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin (composite map)
Components
  • (Hemoglobin subunit ...) x 2
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsOXYGEN TRANSPORT/Structural Protein / human hemoglobin / Tubulin / Microtubule / Microtubule-associated Protein / STRUCTURAL PROTEIN / OXYGEN TRANSPORT-Structural Protein complex
Function / homology
Function and homology information


Cargo trafficking to the periciliary membrane / Carboxyterminal post-translational modifications of tubulin / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / Neutrophil degranulation / cellular oxidant detoxification / Heme assimilation / nitric oxide transport / carbon dioxide transport / hemoglobin alpha binding ...Cargo trafficking to the periciliary membrane / Carboxyterminal post-translational modifications of tubulin / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / Neutrophil degranulation / cellular oxidant detoxification / Heme assimilation / nitric oxide transport / carbon dioxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / erythrocyte development / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / oxygen carrier activity / microtubule-based process / hydrogen peroxide catabolic process / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / microtubule cytoskeleton organization / oxygen binding / Late endosomal microautophagy / platelet aggregation / positive regulation of nitric oxide biosynthetic process / structural constituent of cytoskeleton / Chaperone Mediated Autophagy / tertiary granule lumen / mitotic cell cycle / microtubule / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / inflammatory response / iron ion binding / heme binding / GTPase activity / Neutrophil degranulation / GTP binding / extracellular exosome / extracellular region / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Globin / Globin / Globin domain profile. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Globin-like superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / PROTOPORPHYRIN IX CONTAINING FE / TAXOL / Hemoglobin subunit beta / Hemoglobin subunit alpha / Tubulin alpha chain / Tubulin beta chain
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsZeng, J. / Zhang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138854 United States
CitationJournal: To Be Published
Title: Human hemoglobin protects the parasite cytoskeleton during Plasmodium falciparum gametocyte development
Authors: Wang, X. / Zeng, J. / Qian, P. / Hasan, M. / Goldberg, D. / Zhang, R.
History
DepositionAug 2, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / 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: Tubulin alpha chain
B: Tubulin beta chain
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
E: Tubulin alpha chain
F: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,91016
Polymers229,9876
Non-polymers4,92210
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein Tubulin alpha chain


Mass: 49741.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q25790
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49666.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q7KQL5

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Hemoglobin subunit ... , 2 types, 2 molecules CD

#3: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15281.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#4: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 1 / Fragment: Hb_alpha / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 5 types, 10 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy, alkaloid*YM
#9: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Plasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
Type: CELL / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239215 / Symmetry type: POINT

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