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6d05

Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2.

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transferrin receptor protein 1

Homo sapiens

UniProt P02786

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 6 其他Polymer 6 Serotransferrin × 2 （P02787） Reticulocyte binding protein 2, putative × 2 （A5K736） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CALCIUM ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE (III) ION × 4 CARBONATE ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6y76 6y76 8p0z

3 assemblies

Homodimer
11qc 1cx8 1cx8 1cx8 1cx8 2nsu

6 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
11rn 1de4 1de4 1suv 3kas 3s9l 3s9l 3s9m 3s9m 3s9n 3s9n 6d03

25 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TFR1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–659； UniProt 121–760 Author chain B； PDBConstruct 20–659； UniProt 121–760

Serotransferrin

OrganismNot specified

UniProt P02787

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 6 其他Polymer 6 Transferrin receptor protein 1 × 2 （P02786） Reticulocyte binding protein 2, putative × 2 （A5K736） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CALCIUM ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE (III) ION × 4 CARBONATE ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1a8e 1a8f 1b3e 1bp5 1bp5 1bp5 1bp5 1btj 1btj 1d3k 1d4n 1dtg

68 assemblies; showing the first 12

Homodimer
3skp

1 assemblies

Homotetramer
3skp

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1suv 3s9l 3s9l 3s9m 3s9m 3s9n 3s9n 3v89 3v8x 3ve1 3ve1 6d03

25 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TRFE_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–698； UniProt 1–698 Author chain D； PDBConstruct 1–698； UniProt 1–698

Reticulocyte binding protein 2, putative

Plasmodium vivax

UniProt A5K736

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 6 其他Polymer 6 Transferrin receptor protein 1 × 2 （P02786） Serotransferrin × 2 （P02787） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CALCIUM ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE (III) ION × 4 CARBONATE ION × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5w53 5w53 6bpe

3 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6bpa 6bpa 6bpc 6bpc 6bpe 6bpe 6bpe 6d03 6d04 6d05 6wm9 6wm9

34 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name A5K736_PLAVS
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 6–820； UniProt 1–815 Author chain F； PDBConstruct 6–820； UniProt 1–815

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id6d05
Deposition date deposition_date2018-04-10
Structure title titleCryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2.
Keywords keywordsmalaria, Plasmodium vivax, reticulocyte, invasion, CELL INVASION; CELL INVASION
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6d05__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6d05__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6d05__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）51.87 Å
Rg (electron density)51.52 Å
Total Rg51.77 Å
Atom count28748
Residues3572
Excluded volume511820 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6d05__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

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6. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

Domain ID domain_id6d05A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id6d05A02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id6d05A03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily40 — Transferrin receptor-like, dimerisation domain
Domain ID domain_id6d05B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id6d05B02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id6d05B03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily40 — Transferrin receptor-like, dimerisation domain
Domain ID domain_id6d05C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id6d05C02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id6d05C03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id6d05C04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id6d05D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id6d05D02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id6d05D03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id6d05D04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
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7. Citations (1)