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6mx7

CryoEM structure of chimeric Eastern Equine Encephalitis Virus: Genome-Binding Capsid N-terminal Domain

Method: ELECTRON MICROSCOPY Dmax: 112.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid

Eastern equine encephalitis virus

UniProt P27284

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 240 PDB declaration: 240-meric（240） Consistent with protein copy count Chain C； UniProt 1–260 Chain F； UniProt 1–260 Chain I； UniProt 1–260 Chain L； UniProt 1–260 Fragment：N-terminal domain (UNP residues 1-260) No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen HELIUM Resolution 4.80 Å
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–260 Chain F； UniProt 1–260 Chain I； UniProt 1–260 Chain L； UniProt 1–260 Fragment：N-terminal domain (UNP residues 1-260) No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen HELIUM Resolution 4.80 Å
3 Protein homooligomer Homooligomer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count Chain C； UniProt 1–260 Chain F； UniProt 1–260 Chain I； UniProt 1–260 Chain L； UniProt 1–260 Fragment：N-terminal domain (UNP residues 1-260) No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen HELIUM Resolution 4.80 Å
4 Protein homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain C； UniProt 1–260 Chain F； UniProt 1–260 Chain I； UniProt 1–260 Chain L； UniProt 1–260 Fragment：N-terminal domain (UNP residues 1-260) No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen HELIUM Resolution 4.80 Å
5 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–260 Chain F； UniProt 1–260 Chain I； UniProt 1–260 Chain L； UniProt 1–260 Fragment：N-terminal domain (UNP residues 1-260) No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen HELIUM Resolution 4.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6MX7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6MX4 CryoEM structure of chimeric Eastern Equine Encephalitis Virus Deposited 2018-10-30 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 720 PDB declaration: 720-meric
Chain C 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain F 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain I 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain L 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 240 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen HELIUM
Resolution 4.40 Å
6MX4 CryoEM structure of chimeric Eastern Equine Encephalitis Virus Deposited 2018-10-30 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain F 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain I 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain L 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen HELIUM
Resolution 4.40 Å
6MX4 CryoEM structure of chimeric Eastern Equine Encephalitis Virus Deposited 2018-10-30 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 60 PDB declaration: 60-meric
Chain C 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain F 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain I 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain L 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen HELIUM
Resolution 4.40 Å
6MX4 CryoEM structure of chimeric Eastern Equine Encephalitis Virus Deposited 2018-10-30 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 72 PDB declaration: 72-meric
Chain C 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain F 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain I 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain L 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen HELIUM
Resolution 4.40 Å
6MX4 CryoEM structure of chimeric Eastern Equine Encephalitis Virus Deposited 2018-10-30 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 5 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain F 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain I 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Chain L 1–260（260 aa） Fragment：N-terminal domain (UNP residues 1-260)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen HELIUM
Resolution 4.40 Å

1 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLS_EEEV3
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–260； UniProt 1–260 Author chain F； PDBConstruct 1–260； UniProt 1–260 Author chain I； PDBConstruct 1–260； UniProt 1–260 Author chain L； PDBConstruct 1–260； UniProt 1–260

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6mx7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6mx7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6mx7
Deposition date deposition_date2018-10-30
Structure title titleCryoEM structure of chimeric Eastern Equine Encephalitis Virus: Genome-Binding Capsid N-terminal Domain
Keywords keywordsAlphavirus, EEEV, Eastern Equine Encephalitis Virus, Sindbis, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.57 Å
Radius of gyration Rg (electron density) rg_electron34.14 Å
Forward intensity I(0) i098405100.00
Molecular weight molecular_weight77472.0 kDa
Excluded volume excluded_volume96791 ų
Envelope volume envelope_volume148350 ų
Hydration-shell volume shell_volume36914 ų
Envelope diameter envelope_diameter123.8 Å
Shell Rg shell_rg40.11 Å
Envelope Rg envelope_rg33.14 Å
Shape Rg shape_rg34.13 Å
Total Rg total_rg34.70 Å
Total atoms total_atoms5445
Residues n_residues699
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.1 Å
Rg (real space) rg_real34.51 Å
Rg uncertainty (real space) rg_real_error1.08 Å
I(0) (real space) i0_real9.8410e+07
I(0) uncertainty (real space) i0_real_error1.7280e+06
Rg (reciprocal space) rg_reciprocal34.55 Å
I(0) (reciprocal space) i0_reciprocal98410000.0000
Solution quality estimate total_estimate0.7986
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.7 Å
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.343
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15080000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.796; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)