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5v6g

Crystal structure of Influenza A virus Matrix Protein M1(NLS-88R)

Method: X-RAY DIFFRACTION Dmax: 80.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Matrix protein 1

Influenza A virus (strain A/Wilson-Smith/1933 H1N1)

UniProt P05777

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–165 Chain B； UniProt 2–165 Mutation：G88R, R101S, R105S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；Protein solution: 13.7 mg/ml in 55 mM K2HPO4/KH2PO4/H3PO4, 0.2M NaCl, 10 mM BME, pH 4.0 Reservoir solution: 75 mM Tris-HCl, pH 7.0, 15% PEG-1000 Resolution 2.00 Å R-free 0.236
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 2–165 Chain D； UniProt 2–165 Mutation：G88R, R101S, R105S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；Protein solution: 13.7 mg/ml in 55 mM K2HPO4/KH2PO4/H3PO4, 0.2M NaCl, 10 mM BME, pH 4.0 Reservoir solution: 75 mM Tris-HCl, pH 7.0, 15% PEG-1000 Resolution 2.00 Å R-free 0.236
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 2–165 Chain B； UniProt 2–165 Chain C； UniProt 2–165 Chain D； UniProt 2–165 Mutation：G88R, R101S, R105S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；Protein solution: 13.7 mg/ml in 55 mM K2HPO4/KH2PO4/H3PO4, 0.2M NaCl, 10 mM BME, pH 4.0 Reservoir solution: 75 mM Tris-HCl, pH 7.0, 15% PEG-1000 Resolution 2.00 Å R-free 0.236

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 5V6G Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4PUS Crystal Structure of Influenza A Virus Matrix Protein M1 Deposited 2014-03-13 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–165（164 aa） Fragment：N-terminal domain (UNP residues 2-165)
Chain B 2–165（164 aa） Fragment：N-terminal domain (UNP residues 2-165)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；298 K；protein in 55 mM phosphate, 0.2 M sodium chloride, 2 mM TCEP, pH 4.0, precipitant: 15% PEG3000, 75 mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.264
5V7B Crystal structure of Influenza A virus matrix protein M1 (NLS-88E) Deposited 2017-03-20 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–165（164 aa）
Chain B 2–165（164 aa）
Mutation：G88E, R101S, R105S Mutation：G88E, R101S, R105S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 7；277 K；16.7 mg/ml protein in 25mM Hepes/NaOH, 0.2M NaCl, 2mM TCEP, pH 7.0
Resolution 2.50 Å R-free 0.308
5V7S Crystal structure of Influenza A virus matrix protein M1 (NLS-88E, pH 6.2) Deposited 2017-03-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 2–165（164 aa）
Chain C 2–165（164 aa）
Mutation：G88E, R101S, R105S Mutation：G88E, R101S, R105S PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；Protein solution: 8 mg/ml in 50mM K2HPO4/KH2PO4/H3PO4, 0.2M NaCl, 10mM bME, pH 3.2 Reservoir solution: 0.1M Tris-HCl, pH 8.2, 8% PEG-8K
Resolution 2.50 Å R-free 0.311
5V7S Crystal structure of Influenza A virus matrix protein M1 (NLS-88E, pH 6.2) Deposited 2017-03-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–165（164 aa）
Mutation：G88E, R101S, R105S PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；Protein solution: 8 mg/ml in 50mM K2HPO4/KH2PO4/H3PO4, 0.2M NaCl, 10mM bME, pH 3.2 Reservoir solution: 0.1M Tris-HCl, pH 8.2, 8% PEG-8K
Resolution 2.50 Å R-free 0.311
5V8A Crystal structure of Influenza A virus matrix protein M1 (NLS-88R, pH 7.3) Deposited 2017-03-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–165（164 aa）
Mutation：G88R, R101S, R105S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；Protein solution: 10 mg/ml in K2HPO4/KH2PO4, 0.2M NaCl, 10bME, pH 7.2. Reservoir solution: 0.2M NaF, 20% PEG-3350, pH 7.3
Resolution 3.00 Å R-free 0.321
6I3H Crystal structure of influenza A virus M1 N-terminal domain (G18A mutation) Deposited 2018-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–158（158 aa）
Mutation：G18A PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；30% EDO_P8K, 0.1 M MB2 pH 7.5, 10% NPS
Resolution 1.90 Å R-free 0.233
6I3H Crystal structure of influenza A virus M1 N-terminal domain (G18A mutation) Deposited 2018-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–158（158 aa）
Mutation：G18A PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；30% EDO_P8K, 0.1 M MB2 pH 7.5, 10% NPS
Resolution 1.90 Å R-free 0.233
6QZD HLA-DR1 with SGP Influenza Matrix Peptide Deposited 2019-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 17–30（14 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000
Resolution 2.66 Å R-free 0.254
6QZD HLA-DR1 with SGP Influenza Matrix Peptide Deposited 2019-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 17–30（14 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000
Resolution 2.66 Å R-free 0.254

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name M1_I33A0
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–171； UniProt 2–165 Author chain B； PDBConstruct 8–171； UniProt 2–165 Author chain C； PDBConstruct 8–171； UniProt 2–165 Author chain D； PDBConstruct 8–171； UniProt 2–165

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 5v6g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5v6g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5v6g
Deposition date deposition_date2017-03-16
Structure title titleCrystal structure of Influenza A virus Matrix Protein M1(NLS-88R)
Keywords keywordsInfluenza virus, Matrix protein, NLS-88R mutant, pH 5.5, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.73 Å
Radius of gyration Rg (electron density) rg_electron24.85 Å
Forward intensity I(0) i073399800.00
Molecular weight molecular_weight68668.0 kDa
Excluded volume excluded_volume86828 ų
Envelope volume envelope_volume101140 ų
Hydration-shell volume shell_volume33038 ų
Envelope diameter envelope_diameter82.6 Å
Shell Rg shell_rg33.00 Å
Envelope Rg envelope_rg24.76 Å
Shape Rg shape_rg24.87 Å
Total Rg total_rg25.66 Å
Total atoms total_atoms4816
Residues n_residues628
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 dmax80.4 Å
Rg (real space) rg_real25.58 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real7.3400e+07
I(0) uncertainty (real space) i0_real_error1.0570e+06
Rg (reciprocal space) rg_reciprocal25.63 Å
I(0) (reciprocal space) i0_reciprocal73400000.0000
Solution quality estimate total_estimate0.7091
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.4 Å
Skewness Skewness skewness0.150
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15920000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 0.164; Positv: 1.000; Valcen: 0.987; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5v6ga_
Class classa — All alpha proteins
Fold Fold folda.95 — Influenza virus matrix protein M1
Superfamily Superfamily superfamilya.95.1 — Influenza virus matrix protein M1
Family Family familya.95.1.1 — Influenza virus matrix protein M1
Domain ID domain_idd5v6gb_
Class classa — All alpha proteins
Fold Fold folda.95 — Influenza virus matrix protein M1
Superfamily Superfamily superfamilya.95.1 — Influenza virus matrix protein M1
Family Family familya.95.1.1 — Influenza virus matrix protein M1
Domain ID domain_idd5v6gc_
Class classa — All alpha proteins
Fold Fold folda.95 — Influenza virus matrix protein M1
Superfamily Superfamily superfamilya.95.1 — Influenza virus matrix protein M1
Family Family familya.95.1.1 — Influenza virus matrix protein M1
Domain ID domain_idd5v6gd_
Class classa — All alpha proteins
Fold Fold folda.95 — Influenza virus matrix protein M1
Superfamily Superfamily superfamilya.95.1 — Influenza virus matrix protein M1
Family Family familya.95.1.1 — Influenza virus matrix protein M1

CATH v4.4 (8 domains)

Domain ID domain_id5v6gA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Influenza matrix M1, N-terminal subdomain 1
Domain ID domain_id5v6gA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily180 — Influenza matrix protein M1, N-terminal subdomain 2
Domain ID domain_id5v6gB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Influenza matrix M1, N-terminal subdomain 1
Domain ID domain_id5v6gB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily180 — Influenza matrix protein M1, N-terminal subdomain 2
Domain ID domain_id5v6gC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Influenza matrix M1, N-terminal subdomain 1
Domain ID domain_id5v6gC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily180 — Influenza matrix protein M1, N-terminal subdomain 2
Domain ID domain_id5v6gD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Influenza matrix M1, N-terminal subdomain 1
Domain ID domain_id5v6gD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily180 — Influenza matrix protein M1, N-terminal subdomain 2
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8. Citations (1)

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9. Files and Curves (10)