SAXSdb — 5v8a

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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)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–165	Mutation：G88R, R101S, R105S	No other associated polymer	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

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 5V8A	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 oligomeric state 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
5V6G Crystal structure of Influenza A virus Matrix Protein M1(NLS-88R) Deposited 2017-03-16	Different construct Different mutation/modification Different oligomeric state 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：G88R, R101S, R105S Mutation：G88R, R101S, R105S	No recorded non-water small molecule	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
5V6G Crystal structure of Influenza A virus Matrix Protein M1(NLS-88R) Deposited 2017-03-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–165（164 aa） Chain D 2–165（164 aa）	Mutation：G88R, R101S, R105S Mutation：G88R, R101S, R105S	No recorded non-water small molecule	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
5V6G Crystal structure of Influenza A virus Matrix Protein M1(NLS-88R) Deposited 2017-03-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–165（164 aa） Chain B 2–165（164 aa） Chain C 2–165（164 aa） Chain D 2–165（164 aa）	Mutation：G88R, R101S, R105S Mutation：G88R, R101S, R105S Mutation：G88R, R101S, R105S Mutation：G88R, R101S, R105S	No recorded non-water small molecule	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
5V7B Crystal structure of Influenza A virus matrix protein M1 (NLS-88E) Deposited 2017-03-20	Different construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
6I3H Crystal structure of influenza A virus M1 N-terminal domain (G18A mutation) Deposited 2018-11-06	Different construct Different mutation/modification 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 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 11 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

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_id	5v8a
Deposition date deposition_date	2017-03-21
Structure title title	Crystal structure of Influenza A virus matrix protein M1 (NLS-88R, pH 7.3)
Keywords keywords	Influenza A, Matrix protein, NLS-88R mutant, pH 7.3, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.10 Å
Radius of gyration Rg (electron density) rg_electron	14.64 Å
Forward intensity I(0) i0	4727380.00
Molecular weight molecular_weight	16098.0 kDa
Excluded volume excluded_volume	20458 Å³
Envelope volume envelope_volume	23434 Å³
Hydration-shell volume shell_volume	13505 Å³
Envelope diameter envelope_diameter	50.9 Å
Shell Rg shell_rg	20.50 Å
Envelope Rg envelope_rg	14.87 Å
Shape Rg shape_rg	14.64 Å
Total Rg total_rg	15.84 Å
Total atoms total_atoms	1129
Residues n_residues	148
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	51.5 Å
Rg (real space) rg_real	15.97 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	4.7270e+06
I(0) uncertainty (real space) i0_real_error	5.3140e+04
Rg (reciprocal space) rg_reciprocal	15.99 Å
I(0) (reciprocal space) i0_reciprocal	4727000.0000
Solution quality estimate total_estimate	0.8778
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.074
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1027000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.989

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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5v8aa_
Class class	a — All alpha proteins
Fold Fold fold	a.95 — Influenza virus matrix protein M1
Superfamily Superfamily superfamily	a.95.1 — Influenza virus matrix protein M1
Family Family family	a.95.1.1 — Influenza virus matrix protein M1

CATH v4.4 (2 domains)

Domain ID domain_id	5v8aA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Influenza matrix M1, N-terminal subdomain 1

Domain ID domain_id	5v8aA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	180 — Influenza matrix protein M1, N-terminal subdomain 2

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8. Citations (1)

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Unit-cell length a length_a	27.664 Å
Unit-cell length b length_b	33.341 Å
Unit-cell length c length_c	36.151 Å
Unit-cell angle α angle_alpha	112.18 °
Unit-cell angle β angle_beta	100.38 °
Unit-cell angle γ angle_gamma	94.21 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	21.926 Å
R factor r_factor	0.2751
R_work r_work	0.2719
R_free r_free	0.3213

Description description	Matrix protein 1
Molecular weight formula_weight	19098.1 kDa
Mutation mutation	G88R, R101S, R105S
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1131

Crystal structure of Influenza A virus matrix protein M1 (NLS-88R, pH 7.3)

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

Matrix protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Influenza A virus (strain A/Wilson-Smith/1933 H1N1)
NCBI Class编号 ncbi_taxonomy_id	381518
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

fit	/app/data/saxs_computation/v8/5v8a/5v8a.fit
pddf	/app/data/pr_computation/v8/5v8a/5v8a.pr.out
profile	/app/data/saxs_computation/v8/5v8a/5v8a.dat