SAXSdb — 6i3h

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

Matrix protein 1

Influenza A virus

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 1–158	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–158	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

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 6I3H	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 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 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 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 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 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 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 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 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
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 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
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 20–177； UniProt 1–158 Author chain B； PDBConstruct 20–177； UniProt 1–158

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	6i3h
Deposition date deposition_date	2018-11-06
Structure title title	Crystal structure of influenza A virus M1 N-terminal domain (G18A mutation)
Keywords keywords	Matrix protein 1 N-terminal domain G18A mutation, 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	24.22 Å
Radius of gyration Rg (electron density) rg_electron	23.97 Å
Forward intensity I(0) i0	20600900.00
Molecular weight molecular_weight	35494.0 kDa
Excluded volume excluded_volume	44907 Å³
Envelope volume envelope_volume	56334 Å³
Hydration-shell volume shell_volume	20630 Å³
Envelope diameter envelope_diameter	97.9 Å
Shell Rg shell_rg	29.43 Å
Envelope Rg envelope_rg	24.24 Å
Shape Rg shape_rg	23.98 Å
Total Rg total_rg	24.63 Å
Total atoms total_atoms	2486
Residues n_residues	322
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	94.2 Å
Rg (real space) rg_real	24.37 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	2.0600e+07
I(0) uncertainty (real space) i0_real_error	3.4220e+05
Rg (reciprocal space) rg_reciprocal	24.34 Å
I(0) (reciprocal space) i0_reciprocal	20600000.0000
Solution quality estimate total_estimate	0.7725
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.517
Kurtosis Kurtosis kurtosis	-0.128
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5091000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.506; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.526; Smooth: 0.995

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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	19532.6 kDa
Mutation mutation	G18A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2675

MAHHHHHHSSGLEVLFQGPMSLLTEVETYVLSIVPSAPLKAEIAQRLEDVFAGKNTDLEVLMEWLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDKAVKLYRKLKREITFHGAKEIALSYSAGALASCMGLIYNRMGAVTTEVAFGLVCATCEQIADSQ

来源 Source

来源生物 organism	Influenza A virus
NCBI Class编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	153

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6i3ha1
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	d6i3ha2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6i3hb1
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	d6i3hb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	6i3hA02
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	6i3hB02
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	35.560 Å
Unit-cell length b length_b	35.580 Å
Unit-cell length c length_c	69.290 Å
Unit-cell angle α angle_alpha	89.71 °
Unit-cell angle β angle_beta	84.40 °
Unit-cell angle γ angle_gamma	69.02 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	21.370 Å
R factor r_factor	0.2072
R_work r_work	0.2059
R_free r_free	0.2327

fit	/app/data/saxs_computation/i3/6i3h/6i3h.fit
pddf	/app/data/pr_computation/i3/6i3h/6i3h.pr.out
profile	/app/data/saxs_computation/i3/6i3h/6i3h.dat

Crystal structure of influenza A virus M1 N-terminal domain (G18A mutation)

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