7nik

1918 H1N1 Viral influenza polymerase heterotrimer with Nb8189 core

Method: ELECTRON MICROSCOPY Dmax: 121.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Polymerase acidic protein

Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)

UniProt Q3HM39

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 RNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain A; UniProt 1–716 Not recorded RNA-directed RNA polymerase catalytic subunit × 1 (Q3HM40) Polymerase basic protein 2,Immunoglobulin G-binding protein A × 1 (Q3HM41,P38507) ;RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') ; × 1 ;RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3') ; × 1 Nanobody8189 core × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 6.20 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.

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PA_I18A0
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–716; UniProt 1–716

RNA-directed RNA polymerase catalytic subunit

Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)

UniProt Q3HM40

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 RNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain B; UniProt 1–757 Not recorded Polymerase acidic protein × 1 (Q3HM39) Polymerase basic protein 2,Immunoglobulin G-binding protein A × 1 (Q3HM41,P38507) ;RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') ; × 1 ;RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3') ; × 1 Nanobody8189 core × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 6.20 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.

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RDRP_I18A0
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–757; UniProt 1–757

Polymerase basic protein 2,Immunoglobulin G-binding protein A

Staphylococcus aureus

UniProt P38507

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 RNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain C; UniProt 158–271 Not recorded Polymerase acidic protein × 1 (Q3HM39) RNA-directed RNA polymerase catalytic subunit × 1 (Q3HM40) ;RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') ; × 1 ;RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3') ; × 1 Nanobody8189 core × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 6.20 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.

66 other PDB entries and 127 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPA_STAAU
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 784–897; UniProt 158–271

Polymerase basic protein 2,Immunoglobulin G-binding protein A

Staphylococcus aureus

UniProt Q3HM41

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 4 RNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain C; UniProt 1–759 Not recorded Polymerase acidic protein × 1 (Q3HM39) RNA-directed RNA polymerase catalytic subunit × 1 (Q3HM40) ;RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') ; × 1 ;RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3') ; × 1 Nanobody8189 core × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 6.20 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.

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PB2_I18A0
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–759; UniProt 1–759

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 7nik

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7nik
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7nik
Deposition date deposition_date2021-02-12
Structure title title1918 H1N1 Viral influenza polymerase heterotrimer with Nb8189 core
Keywords keywordsInfluenza, RNA polymerase, H1N1, 1918, VIRAL PROTEIN, nanobody; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.17
Radius of gyration Rg (electron density) rg_electron35.51
Forward intensity I(0) i0591369000.00
Molecular weight molecular_weight190060.0 kDa
Excluded volume excluded_volume234860 ų
Envelope volume envelope_volume298840 ų
Hydration-shell volume shell_volume66780 ų
Envelope diameter envelope_diameter132.3
Shell Rg shell_rg44.16
Envelope Rg envelope_rg35.44
Shape Rg shape_rg35.51
Total Rg total_rg36.01
Total atoms total_atoms25547
Residues n_residues1622
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax121.2
Rg (real space) rg_real35.97
Rg uncertainty (real space) rg_real_error0.88
I(0) (real space) i0_real5.9140e+08
I(0) uncertainty (real space) i0_real_error9.4120e+06
Rg (reciprocal space) rg_reciprocal36.10
I(0) (reciprocal space) i0_reciprocal591400000.0000
Solution quality estimate total_estimate0.8668
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.8
Skewness Skewness skewness0.207
Kurtosis Kurtosis kurtosis-0.265
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha129600000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.946

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)