SAXSdb — 5lmy

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

Matrix protein p10

Mason-Pfizer monkey 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 2–118	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 600；Pressure 1 NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 300；Pressure 1 NMR sample composition：1.2 mM [U-99% 13C; U-99% 15N] Matrix protein p10, 100 mM potassium phosphate, 300 mM sodium chloride, 5 mM DTT, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.2 mM [U-99% 15N] Matrix protein p10, 50 mM potassium phosphate, 150 mM sodium chloride, 5 mM DTT, 10 mg/mL Pf1 phage, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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 5LMY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BAX MASON-PFIZER MONKEY VIRUS MATRIX PROTEIN, NMR, AVERAGE STRUCTURE Deposited 1998-04-20	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–94（94 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K	Resolution not provided
1CL4 NUCLEOCAPSID PROTEIN FROM MASON-PFIZER MONKEY VIRUS (MPMV) Deposited 1999-05-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 546–605（60 aa） Fragment：GAG RESIDUES 574-605 (P14 RESIDUES 49-80)	Mutation：C23S	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Pressure 1	Resolution not provided
2KGF N-terminal domain of capsid protein from the Mason-Pfizer monkey virus Deposited 2009-03-10	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 300–439（140 aa） Fragment：UNP residues 300-439	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；295 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient NMR sample composition 0.7-1.0 mM [U-100% 13C; U-100% 15N] MPMV NTD CA, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-1.0 mM [U-100% 13C; U-100% 15N] MPMV NTD CA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MV4 Solution structure of myristoylated Y28F/Y67F mutant of the Mason-Pfizer monkey virus matrix protein Deposited 2014-09-23	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–118（117 aa） Fragment：UNP residues 2-118	Mutation：Y28F, Y67F Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.600；Pressure ambient NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N; NA-MYR] MPMV_MA_Y28F_Y67F, 300.0 mM NaCl, 2.5 mM TCEP, 50.0 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N; NA-MYR,H] MPMV_MA_Y28F_Y67F, 300.0 mM NaCl, 2.5 mM TCEP, 50.0 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] MPMV_MA_Y28F_Y67F, 300.0 mM NaCl, 2.5 mM TCEP, 50.0 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM [U-99% 13C]-MYR MPMV_MA_Y28F_Y67F, 300.0 mM NaCl, 2.5 mM TCEP, 50.0 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4ARD Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy Deposited 2012-04-23	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 318–433（116 aa） Fragment：M-PMV CA-NTD, RESIDUES 318-433 Chain B 318–433（116 aa） Fragment：M-PMV CA-NTD, RESIDUES 318-433	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100MM NACL, 50MM TRIS-HCL, 1UM ZN；pH 7.7；100MM NACL, 50MM TRIS-HCL, 1UM ZN cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 7.00 Å
5LDL Myristoylated T41I/T78I mutant of M-PMV matrix protein Deposited 2016-06-27	Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–118（117 aa）	Mutation：T41I, T78I	MYR MYRISTIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 600；Pressure 1 NMR sample composition 1 mM [U-13C; U-15N] myristoylated retroviral matrix protein, 100 mM phosphate, 300 mM sodium choride, 5 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 400 mM [U-15N] myristoylated retroviral matrix protein, 50 mM phosphate, 150 mM sodium choride, 5 mM DTT, 10 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GAG_MPMV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–118； UniProt 2–118

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	5lmy
Deposition date deposition_date	2016-08-02
Structure title title	Solution structure of the m-pmv myristoylated matrix protein
Keywords keywords	Matrix, M-PMV, Myristoylated, Retrovirus, Viral protein; VIRAL PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	19.09 Å
Radius of gyration Rg (electron density) rg_electron	18.23 Å
Forward intensity I(0) i0	669166000.00
Molecular weight molecular_weight	223490.0 kDa
Excluded volume excluded_volume	281670 Å³
Envelope volume envelope_volume	69573 Å³
Hydration-shell volume shell_volume	24131 Å³
Envelope diameter envelope_diameter	81.7 Å
Shell Rg shell_rg	31.41 Å
Envelope Rg envelope_rg	26.72 Å
Shape Rg shape_rg	18.26 Å
Total Rg total_rg	18.50 Å
Total atoms total_atoms	31455
Residues n_residues	1860
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	76.6 Å
Rg (real space) rg_real	19.32 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	6.6920e+08
I(0) uncertainty (real space) i0_real_error	9.7920e+06
Rg (reciprocal space) rg_reciprocal	19.29 Å
I(0) (reciprocal space) i0_reciprocal	669200000.0000
Solution quality estimate total_estimate	0.7043
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.2 Å
Skewness Skewness skewness	0.687
Kurtosis Kurtosis kurtosis	0.279
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	711800.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.236; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.448; Smooth: 0.994

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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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Description description	Matrix protein p10
Molecular weight formula_weight	14924.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	31455

来源生物 organism	Mason-Pfizer monkey virus
通用名 common_name	MPMV
NCBI Class编号 ncbi_taxonomy_id	11855
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/lm/5lmy/5lmy.fit
pddf	/app/data/pr_computation/lm/5lmy/5lmy.pr.out
profile	/app/data/saxs_computation/lm/5lmy/5lmy.dat

Solution structure of the m-pmv myristoylated matrix protein

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

Matrix protein p10

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

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)