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))

Method: X-RAY DIFFRACTION Dmax: 67.2 Å Quality: GOOD

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

Matrix protein 1

Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)

UniProt P03485

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 1–164 Chain B; UniProt 1–164 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

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.

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 25–188; UniProt 1–164 Author chain B; PDBConstruct 25–188; UniProt 1–164

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 5cqe

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5cqe
Deposition date deposition_date2015-07-21
Structure title title2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from Influenza A virus (A/Puerto Rico/8/34(H1N1))
Keywords keywords;matrix protein 1, Influenza A virus (A/Puerto Rico/8/34(H1N1)), CSGID, virulence, pathogenesis, Structural Genomics, Center for Structural Genomics of Infectious Diseases, VIRAL PROTEIN ;; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.39
Radius of gyration Rg (electron density) rg_electron20.67
Forward intensity I(0) i020851000.00
Molecular weight molecular_weight35369.0 kDa
Excluded volume excluded_volume44620 ų
Envelope volume envelope_volume51468 ų
Hydration-shell volume shell_volume20955 ų
Envelope diameter envelope_diameter68.0
Shell Rg shell_rg27.01
Envelope Rg envelope_rg20.90
Shape Rg shape_rg20.70
Total Rg total_rg21.44
Total atoms total_atoms2473
Residues n_residues319
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax67.2
Rg (real space) rg_real21.37
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real2.0850e+07
I(0) uncertainty (real space) i0_real_error2.8900e+05
Rg (reciprocal space) rg_reciprocal21.38
I(0) (reciprocal space) i0_reciprocal20850000.0000
Solution quality estimate total_estimate0.8200
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.7
Skewness Skewness skewness0.350
Kurtosis Kurtosis kurtosis-0.370
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5846000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5cqea1
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_idd5cqea2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5cqeb1
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_idd5cqeb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id5cqeA01
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_id5cqeA02
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_id5cqeB01
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_id5cqeB02
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

8. Citations (1)

9. Files and Curves (10)