SAXSdb — 5v7s

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2–165 Chain C； UniProt 2–165	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–165	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

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 5V7S	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 ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 ligand/ion 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 ligand/ion 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
5V8A Crystal structure of Influenza A virus matrix protein M1 (NLS-88R, pH 7.3) Deposited 2017-03-21	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 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 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 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 10 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

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	5v7s
Deposition date deposition_date	2017-03-20
Structure title title	Crystal structure of Influenza A virus matrix protein M1 (NLS-88E, pH 6.2)
Keywords keywords	Influenza A, Matrix protein, NLS-88E mutant, pH 6.2, 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	25.42 Å
Radius of gyration Rg (electron density) rg_electron	24.54 Å
Forward intensity I(0) i0	43883100.00
Molecular weight molecular_weight	52018.0 kDa
Excluded volume excluded_volume	65480 Å³
Envelope volume envelope_volume	79296 Å³
Hydration-shell volume shell_volume	27241 Å³
Envelope diameter envelope_diameter	96.6 Å
Shell Rg shell_rg	31.38 Å
Envelope Rg envelope_rg	24.67 Å
Shape Rg shape_rg	24.55 Å
Total Rg total_rg	25.26 Å
Total atoms total_atoms	3645
Residues n_residues	473
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	89.3 Å
Rg (real space) rg_real	25.39 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	4.3880e+07
I(0) uncertainty (real space) i0_real_error	6.6690e+05
Rg (reciprocal space) rg_reciprocal	25.40 Å
I(0) (reciprocal space) i0_reciprocal	43880000.0000
Solution quality estimate total_estimate	0.7896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.222
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9702000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.761; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Matrix protein 1
Molecular weight formula_weight	19070.0 kDa
Mutation mutation	G88E, R101S, R105S
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3658

MHHHHHHSLLTEVETYVLSIVPSGPLKAEIAQRLEDVFAGKNTDLEVLMEWLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNEDPNNMDKAVKLYSKLKSEITFHGAKEIALSYSAGALASCMGLIYNRMGAVTTEVAFGLVCATCEQIADSQHRSHRQM

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5v7sa_
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

Domain ID domain_id	d5v7sb_
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

Domain ID domain_id	d5v7sc_
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 (6 domains)

Domain ID domain_id	5v7sA01
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	5v7sA02
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

Domain ID domain_id	5v7sB01
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	5v7sB02
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

Domain ID domain_id	5v7sC01
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	5v7sC02
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	85.612 Å
Unit-cell length b length_b	133.260 Å
Unit-cell length c length_c	39.308 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	26.230 Å
R factor r_factor	0.2251
R_work r_work	0.2203
R_free r_free	0.3115

fit	/app/data/saxs_computation/v7/5v7s/5v7s.fit
pddf	/app/data/pr_computation/v7/5v7s/5v7s.pr.out
profile	/app/data/saxs_computation/v7/5v7s/5v7s.dat

Crystal structure of Influenza A virus matrix protein M1 (NLS-88E, pH 6.2)

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