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3ixx

The pseudo-atomic structure of West Nile immature virus in complex with Fab fragments of the anti-fusion loop antibody E53

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

Envelope protein E

West Nile virus

UniProt Q9Q6P4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 600 Peptide pr × 180 （Q9WHD2） E53 Fab Fragment (chain H) × 120 E53 Fab Fragment (chain L) × 120 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 10 Peptide pr × 3 （Q9WHD2） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 50 Peptide pr × 15 （Q9WHD2） E53 Fab Fragment (chain H) × 10 E53 Fab Fragment (chain L) × 10 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 60 Peptide pr × 18 （Q9WHD2） E53 Fab Fragment (chain H) × 12 E53 Fab Fragment (chain L) × 12 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 10 Peptide pr × 3 （Q9WHD2） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2oy0 2oy0 3lkz 3lkz

4 assemblies

Homodimer
8co8

1 assemblies

Homotetramer

None

Other homooligomers
2of6 2of6 2of6 2of6 2of6 3j0b 3j0b 3j0b 3j0b 3j0b

10 assemblies

Heteromeric or nucleic-acid complex
3ixx 3ixx 3ixx 3ixx 3ixx

5 assemblies

View Construct and Data Evidence
UniProt name Q9Q6P4_WNV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–400； UniProt 291–690 Author chain B； PDBConstruct 1–400； UniProt 291–690 Author chain C； PDBConstruct 1–400； UniProt 291–690

Peptide pr

West Nile virus

UniProt Q9WHD2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 600 Envelope protein E × 180 （Q9Q6P4） E53 Fab Fragment (chain H) × 120 E53 Fab Fragment (chain L) × 120 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 10 Envelope protein E × 3 （Q9Q6P4） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 50 Envelope protein E × 15 （Q9Q6P4） E53 Fab Fragment (chain H) × 10 E53 Fab Fragment (chain L) × 10 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 60 Envelope protein E × 18 （Q9Q6P4） E53 Fab Fragment (chain H) × 12 E53 Fab Fragment (chain L) × 12 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 10 Envelope protein E × 3 （Q9Q6P4） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3ixx 3ixx 3ixx 3ixx 3ixx

5 assemblies

View Construct and Data Evidence
UniProt name Q9WHD2_WNV
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–80； UniProt 101–180 Author chain E； PDBConstruct 1–80； UniProt 101–180 Author chain F； PDBConstruct 1–80； UniProt 101–180

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_id3ixx
Deposition date deposition_date2009-02-26
Structure title titleThe pseudo-atomic structure of West Nile immature virus in complex with Fab fragments of the anti-fusion loop antibody E53
Keywords keywords;West Nile Virus, WNV, immature, fusion loop, Fab, E53, ATP-binding, Envelope protein, Helicase, Hydrolase, Membrane, Nucleotide-binding, RNA replication, Transmembrane, Virion, Icosahedral virus, VIRUS ;; VIRUS
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.

3ixx__assembly_1__model_1

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

Download this curve (.dat)

3ixx__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 108 109 1010 1011 1012 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3ixx__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）0.00 Å
Rg (electron density)249.70 Å
Total Rg249.80 Å
Atom count0
Residues0
Excluded volume18208000 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3ixx__assembly_1__model_1 600-MERIC （600） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3ixx__assembly_2__model_1 decameric （10） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 3ixx__assembly_3__model_1 50-meric （50） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 3ixx__assembly_4__model_1 60-meric （60） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 3ixx__assembly_5__model_1 decameric （10） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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7. Citations (1)