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9cyx

Cryo-EM structure of MRV full core

Method: ELECTRON MICROSCOPY Dmax: 238.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lambda 1

OrganismNot specified

UniProt F1ARN3

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain B； UniProt 1–1275 Chain H； UniProt 1–1275 Chain I； UniProt 1–1275 Not recorded Outer capsid protein lambda-2 × 1 （P11079） Inner capsid protein sigma-2 × 2 （P03525） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；Phosphate-buffered saline cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9CYX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ELH In situ structure of transcriptional enzyme complex and capsid shell protein of mammalian reovirus at initiation state Deposited 2021-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 17 PDB declaration: 26-meric
Chain D 181–1275（1095 aa）
Chain E 181–1275（1095 aa）
Chain F 181–1275（1095 aa）
Chain G 181–1275（1095 aa）
Chain H 181–1275（1095 aa）
Chain I 181–1275（1095 aa）
Chain J 181–1275（1095 aa）
Chain K 181–1275（1095 aa）
Chain L 181–1275（1095 aa）
Chain M 181–1275（1095 aa）
Chain e 1–180（180 aa）
Chain g 1–180（180 aa）
Chain i 1–180（180 aa）
Chain k 1–180（180 aa）
Chain m 1–180（180 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9CYY Cryo-EM structure of MRV virion Deposited 2024-08-03 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain K 1–1275（1275 aa）
Chain M 1–1275（1275 aa）
Chain Y 1–1275（1275 aa）
Chain Z 1–1275（1275 aa）
Chain a 1–1275（1275 aa）
Chain b 1–1275（1275 aa）
Chain c 1–1275（1275 aa）
Chain d 1–1275（1275 aa）
Chain e 1–1275（1275 aa）
Chain f 1–1275（1275 aa）
Chain g 1–1275（1275 aa）
Chain h 1–1275（1275 aa）
Chain i 1–1275（1275 aa）
Chain k 1–1275（1275 aa）
Chain m 1–1275（1275 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Phosphate-buffered saline
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F1ARN3_9REOV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–1275； UniProt 1–1275 Author chain H； PDBConstruct 1–1275； UniProt 1–1275 Author chain I； PDBConstruct 1–1275； UniProt 1–1275

Outer capsid protein lambda-2

OrganismNot specified

UniProt P11079

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 2–1289 Not recorded Lambda 1 × 3 （F1ARN3） Inner capsid protein sigma-2 × 2 （P03525） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；Phosphate-buffered saline cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9CYX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: complete icosahedral assembly
Chain A 1–1289（1289 aa）
Not recorded ZN ZINC ION × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1289（1289 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain A 1–1289（1289 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 1–1289（1289 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1289（1289 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain A 1–1289（1289 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
2CSE Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution Deposited 2005-05-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 1620 PDB declaration: 1620-MERIC
Chain U 1–1289（1289 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM TRIS；pH 7.5；10 mM TRIS
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGED INTO ETHANE
Resolution 7.00 Å
2CSE Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution Deposited 2005-05-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric
Chain U 1–1289（1289 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM TRIS；pH 7.5；10 mM TRIS
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGED INTO ETHANE
Resolution 7.00 Å
2CSE Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution Deposited 2005-05-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 135 PDB declaration: 135-meric
Chain U 1–1289（1289 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM TRIS；pH 7.5；10 mM TRIS
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGED INTO ETHANE
Resolution 7.00 Å
2CSE Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution Deposited 2005-05-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 162 PDB declaration: 162-meric
Chain U 1–1289（1289 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM TRIS；pH 7.5；10 mM TRIS
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGED INTO ETHANE
Resolution 7.00 Å
2CSE Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution Deposited 2005-05-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric
Chain U 1–1289（1289 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 10 mM TRIS；pH 7.5；10 mM TRIS
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGED INTO ETHANE
Resolution 7.00 Å
6ZTZ Assembly intermediates of orthoreovirus captured in the cell Deposited 2020-07-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain O 2–1289（1288 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 6.50 Å
9CYT Cryo-EM structure of MRV outer shell Deposited 2024-08-02 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain J 1–1289（1289 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Phosphate-buffered saline
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9CYY Cryo-EM structure of MRV virion Deposited 2024-08-03 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain J 1–1289（1289 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Phosphate-buffered saline
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

5 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LMBD2_REOVD
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–1288； UniProt 2–1289

Inner capsid protein sigma-2

OrganismNot specified

UniProt P03525

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain Q； UniProt 2–418 Chain R； UniProt 2–418 Not recorded Lambda 1 × 3 （F1ARN3） Outer capsid protein lambda-2 × 1 （P11079） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；Phosphate-buffered saline cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9CYX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: complete icosahedral assembly
Chain D 1–418（418 aa）
Chain E 1–418（418 aa）
Not recorded ZN ZINC ION × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–418（418 aa）
Chain E 1–418（418 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain D 1–418（418 aa）
Chain E 1–418（418 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain D 1–418（418 aa）
Chain E 1–418（418 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–418（418 aa）
Chain E 1–418（418 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
1EJ6 Reovirus core Deposited 2000-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain D 1–418（418 aa）
Chain E 1–418（418 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；sodium chloride, sodium acetate, magnesium chloride, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.60 Å R-free 0.208
9CYY Cryo-EM structure of MRV virion Deposited 2024-08-03 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain 0 1–418（418 aa）
Chain C 1–418（418 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Phosphate-buffered saline
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

2 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SIGM2_REOVD
Isoform —
PDB entities 3
Chains and sequence ranges Author chain Q； PDBConstruct 1–417； UniProt 2–418 Author chain R； PDBConstruct 1–417； UniProt 2–418

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 9cyx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9cyx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9cyx
Deposition date deposition_date2024-08-02
Structure title titleCryo-EM structure of MRV full core
Keywords keywordsMammalian reovirus, outer shell, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier70.60 Å
Radius of gyration Rg (electron density) rg_electron70.94 Å
Forward intensity I(0) i03329190000.00
Molecular weight molecular_weight490220.0 kDa
Excluded volume excluded_volume613830 ų
Envelope volume envelope_volume951430 ų
Hydration-shell volume shell_volume114510 ų
Envelope diameter envelope_diameter255.6 Å
Shell Rg shell_rg68.05 Å
Envelope Rg envelope_rg70.50 Å
Shape Rg shape_rg70.99 Å
Total Rg total_rg70.71 Å
Total atoms total_atoms34537
Residues n_residues4377
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 dmax238.3 Å
Rg (real space) rg_real70.78 Å
Rg uncertainty (real space) rg_real_error3.63 Å
I(0) (real space) i0_real3.3290e+09
I(0) uncertainty (real space) i0_real_error8.7620e+07
Rg (reciprocal space) rg_reciprocal69.83 Å
I(0) (reciprocal space) i0_reciprocal3323000000.0000
Solution quality estimate total_estimate0.8475
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary65.0 Å
Skewness Skewness skewness0.334
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.1100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha169700000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.379
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)