SAXSdb — 4ard

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

CAPSID PROTEIN P27

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 318–433 Chain B； UniProt 318–433	Fragment：M-PMV CA-NTD, RESIDUES 318-433	No other associated polymer	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

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 4ARD	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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–94（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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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
5LDL Myristoylated T41I/T78I mutant of M-PMV matrix protein Deposited 2016-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
5LMY Solution structure of the m-pmv myristoylated matrix protein Deposited 2016-08-02	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 2–118（117 aa）	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) 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

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 1–83； UniProt 318–433 Author chain B； PDBConstruct 1–83； UniProt 318–433

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	4ard
Deposition date deposition_date	2012-04-23
Structure title title	Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy
Keywords keywords	VIRAL PROTEIN, RETROVIRUS, GAG; 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	17.67 Å
Radius of gyration Rg (electron density) rg_electron	16.94 Å
Forward intensity I(0) i0	11480000.00
Molecular weight molecular_weight	25749.0 kDa
Excluded volume excluded_volume	31115 Å³
Envelope volume envelope_volume	20623 Å³
Hydration-shell volume shell_volume	11311 Å³
Envelope diameter envelope_diameter	51.2 Å
Shell Rg shell_rg	20.81 Å
Envelope Rg envelope_rg	15.83 Å
Shape Rg shape_rg	17.04 Å
Total Rg total_rg	17.38 Å
Total atoms total_atoms	—
Residues n_residues	—
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	53.4 Å
Rg (real space) rg_real	17.55 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	1.1480e+07
I(0) uncertainty (real space) i0_real_error	1.2680e+05
Rg (reciprocal space) rg_reciprocal	17.57 Å
I(0) (reciprocal space) i0_reciprocal	11480000.0000
Solution quality estimate total_estimate	0.8303
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.105
Kurtosis Kurtosis kurtosis	-0.528
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1789000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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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 (1)

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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	1

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

Resolution resolution	7.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	7.00 Å
Resolution测定方法 resolution_method	HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING
颗粒数 num_particles	—

Description description	CAPSID PROTEIN P27
Molecular weight formula_weight	12885.2 kDa
Source method src_method	man
Copy count entity_count	2

Structure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy

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

CAPSID PROTEIN P27

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

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 (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	232

来源生物 organism	MASON-PFIZER MONKEY VIRUS
NCBI Class编号 ncbi_taxonomy_id	11855
宿主生物 host_organism	ESCHERICHIA COLI

fit	/app/data/saxs_computation/ar/4ard/4ard.fit
pddf	/app/data/pr_computation/ar/4ard/4ard.pr.out
profile	/app/data/saxs_computation/ar/4ard/4ard.dat