SAXSdb — 6z5l

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

Matrix protein 1

Influenza A virus (strain A/Puerto Rico/8/1934 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 × 80 PDB declaration: 80-meric（80） Consistent with protein copy count	Chain A； UniProt 1–252	Mutation：R134K	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 10 cryo-EM vitrification conditions：Cryogen ETHANE；sample was applied 3 times each with 30s adsorption time	Resolution 3.80 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.

Other PDB	Difference from Current Entry 6Z5L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AA7 INFLUENZA VIRUS MATRIX PROTEIN CRYSTAL STRUCTURE AT PH 4.0 Deposited 1997-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–158（158 aa） Chain B 1–158（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；20% PEG 3350, 50MM NAH2PO4, PH 4.0	Resolution 2.08 Å R-free 0.280
1EA3 Influenza virus M1 protein Deposited 2000-11-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–164（164 aa） Fragment：N-TERMINAL DOMAIN RESIDUES 1-164	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M HEPES PH7.5, 5% V/V ISOPROPANOL,6-10% PEG4000, pH 7.00	Resolution 2.30 Å R-free 0.313
1EA3 Influenza virus M1 protein Deposited 2000-11-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–164（164 aa） Fragment：N-TERMINAL DOMAIN RESIDUES 1-164	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M HEPES PH7.5, 5% V/V ISOPROPANOL,6-10% PEG4000, pH 7.00	Resolution 2.30 Å R-free 0.313
1HHI THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2 Deposited 1993-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 58–66（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1HHI THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2 Deposited 1993-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 58–66（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
3VDX Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains Deposited 2012-01-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Chain B 3–164（162 aa） Chain C 3–164（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.00 Å R-free 0.281
4D9J Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains Deposited 2012-01-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Chain B 3–164（162 aa） Chain C 3–164（162 aa） Chain D 3–164（162 aa） Chain E 3–164（162 aa） Chain F 3–164（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.92 Å R-free 0.294
4D9J Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains Deposited 2012-01-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain G 3–164（162 aa） Chain H 3–164（162 aa） Chain I 3–164（162 aa） Chain J 3–164（162 aa） Chain K 3–164（162 aa） Chain L 3–164（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.3；298 K；1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS, pH 10.3, vapor diffusion, hanging drop, temperature 298K	Resolution 3.92 Å R-free 0.294
4IQ4 Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P21212 form Deposited 2013-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–165（163 aa） Chain B 3–165（163 aa） Chain C 3–165（163 aa） Chain D 3–165（163 aa） Chain E 3–165（163 aa） Chain F 3–165（163 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3,000, vapor diffusion, hanging drop, temperature 298K	Resolution 3.50 Å R-free 0.231
4ITV Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P212121 form Deposited 2013-01-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Chain B 3–164（162 aa） Chain C 3–164（162 aa） Chain D 3–164（162 aa） Chain E 3–164（162 aa） Chain F 3–164（162 aa） Chain G 3–164（162 aa） Chain H 3–164（162 aa） Chain I 3–164（162 aa） Chain J 3–164（162 aa） Chain K 3–164（162 aa） Chain L 3–164（162 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K	Resolution 3.60 Å R-free 0.240
4IVJ Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, I222 form Deposited 2013-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–165（163 aa） Chain B 3–165（163 aa） Chain C 3–165（163 aa）	Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T Mutation：K118A, L279Q, Q24T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K	Resolution 7.35 Å R-free 0.288
4QES Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, I222 form Deposited 2014-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Fragment：SEE REMARK 999 Chain B 3–164（162 aa） Fragment：SEE REMARK 999 Chain C 3–164（162 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.1 M sodium citrate, pH 4.4, 11% PEG3000, 200 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.19 Å R-free 0.295
4QF0 Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P21212 form Deposited 2014-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Fragment：SEE REMARK 999 Chain B 3–164（162 aa） Fragment：SEE REMARK 999 Chain C 3–164（162 aa） Fragment：SEE REMARK 999 Chain D 3–164（162 aa） Fragment：SEE REMARK 999 Chain E 3–164（162 aa） Fragment：SEE REMARK 999 Chain F 3–164（162 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1 M Tris, pH 7.0, 10% PEG8000, 0.2 M magnesium chloride, 3% trehalose, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 6.49 Å R-free 0.324
4QFF Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, quadruple mutant, P212121 form Deposited 2014-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 3–164（162 aa） Fragment：SEE REMARK 999 Chain B 3–164（162 aa） Fragment：SEE REMARK 999 Chain C 3–164（162 aa） Fragment：SEE REMARK 999 Chain D 3–164（162 aa） Fragment：SEE REMARK 999 Chain E 3–164（162 aa） Fragment：SEE REMARK 999 Chain F 3–164（162 aa） Fragment：SEE REMARK 999 Chain G 3–164（162 aa） Fragment：SEE REMARK 999 Chain H 3–164（162 aa） Fragment：SEE REMARK 999 Chain I 3–164（162 aa） Fragment：SEE REMARK 999 Chain J 3–164（162 aa） Fragment：SEE REMARK 999 Chain K 3–164（162 aa） Fragment：SEE REMARK 999 Chain L 3–164（162 aa） Fragment：SEE REMARK 999	Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A Mutation：K118A, L279Q, Q24T, Y51A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.1 M sodium/potassium phosphate, pH 5.8, 10% PEG8000, 0.2 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 7.81 Å R-free 0.339
5CQE 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from Influenza A virus (A/Puerto Rico/8/34(H1N1)) Deposited 2015-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa） Chain B 1–164（164 aa）	Not recorded	CL CHLORIDE ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；Protein: 12.8 mg/mL 10 mM Tris-HCl pH 8.3 500 mM NaCl 0.5 mM TCEP Crsytallization: The JCSG+ Suite (B9: 100 mM Citric acid pH 4.0 20% (w/v) PEG 6000; final pH 5.0 Cryocondition: Crystallization condition + sucrose (50%)	Resolution 2.10 Å R-free 0.197
5EUO PF6-M1-HLA-A2 Deposited 2015-11-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 58–66（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG3350, Imidazole	Resolution 2.10 Å R-free 0.281
5EUO PF6-M1-HLA-A2 Deposited 2015-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 58–66（9 aa）	Not recorded	IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG3350, Imidazole	Resolution 2.10 Å R-free 0.281

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	M1_I34A1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–252； UniProt 1–252

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	6z5l
Deposition date deposition_date	2020-05-26
Structure title title	Helical reconstruction of influenza A virus M1 in complex with nucleic acid.
Keywords keywords	M1, Matrix protein, Influenza virus, Assembly, ribonucleoprotein complex, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	23.47 Å
Radius of gyration Rg (electron density) rg_electron	22.53 Å
Forward intensity I(0) i0	14102900.00
Molecular weight molecular_weight	27724.0 kDa
Excluded volume excluded_volume	34577 Å³
Envelope volume envelope_volume	45017 Å³
Hydration-shell volume shell_volume	17670 Å³
Envelope diameter envelope_diameter	78.0 Å
Shell Rg shell_rg	27.78 Å
Envelope Rg envelope_rg	22.37 Å
Shape Rg shape_rg	22.51 Å
Total Rg total_rg	23.30 Å
Total atoms total_atoms	1936
Residues n_residues	251
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	75.0 Å
Rg (real space) rg_real	23.50 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.4100e+07
I(0) uncertainty (real space) i0_real_error	1.7760e+05
Rg (reciprocal space) rg_reciprocal	23.50 Å
I(0) (reciprocal space) i0_reciprocal	14100000.0000
Solution quality estimate total_estimate	0.9023
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.272
Kurtosis Kurtosis kurtosis	-0.672
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1412000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	17984

Description description	Matrix protein 1
Molecular weight formula_weight	28971.4 kDa
Mutation mutation	R134K
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1936

Helical reconstruction of influenza A virus M1 in complex with nucleic acid.

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
NCBI Class编号 ncbi_taxonomy_id	211044
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/z5/6z5l/6z5l.fit
pddf	/app/data/pr_computation/z5/6z5l/6z5l.pr.out
profile	/app/data/saxs_computation/z5/6z5l/6z5l.dat