SAXSdb — 2lbf

▼

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

60S acidic ribosomal protein P1

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–69	Fragment：UNP residues 1-69	60S acidic ribosomal protein P2 × 1 （P05387）	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition：1 mM [U-100% 13C; U-100% 15N] protein_1-1, 1 mM [U-100% 13C; U-100% 15N] protein_2-2, 90% H2O/10% D2O \| 90% H2O/10% 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 2LBF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BEH Solution structure of human ribosomal protein P1.P2 heterodimer Deposited 2013-03-10	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1.0 NMR sample composition 10% WATER/90% D2O	Resolution not provided
4V6X Structure of the human 80S ribosome Deposited 2013-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric	Chain Cs 1–114（114 aa） Chain Ct 1–114（114 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV).	Resolution 5.00 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RLA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 1–69

60S acidic ribosomal protein P2

Homo sapiens

UniProt P05387

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–69	Fragment：UNP residues 1-69	60S acidic ribosomal protein P1 × 1 （P05386）	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition：1 mM [U-100% 13C; U-100% 15N] protein_1-1, 1 mM [U-100% 13C; U-100% 15N] protein_2-2, 90% H2O/10% D2O \| 90% H2O/10% 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 2LBF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1S4J NMR structure of cross-reactive peptides from Homo sapiens Deposited 2004-01-16	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 103–115（13 aa） Fragment：h13 - C-terminal domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；278 K；Ionic strength (raw mmCIF value) 10mM phosphate buffer；Pressure ambient NMR sample composition 2mM of peptide; 10% D2O; 10mM phosphate buffer at pH 5.5 \| 90% H2O/10% D2O	Resolution not provided
2W1O NMR structure of dimerization domain of human ribosomal protein P2 Deposited 2008-10-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–69（69 aa） Fragment：RESIDUES 1-69 Chain B 1–69（69 aa） Fragment：RESIDUES 1-69	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 200MM SODIUM SULFATE；Pressure 1.0 NMR sample composition 90% WATER / 10% D2O	Resolution not provided
4BEH Solution structure of human ribosomal protein P1.P2 heterodimer Deposited 2013-03-10	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1.0 NMR sample composition 10% WATER/90% D2O	Resolution not provided
4V6X Structure of the human 80S ribosome Deposited 2013-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric	Chain Cu 1–115（115 aa） Chain Cv 1–115（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV).	Resolution 5.00 Å
5DDZ Crystal structure of the RTA-c10-P2 complex Deposited 2015-08-25	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 106–115（10 aa） Fragment：UNP residues 106-115	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.4 M ammonium dihydrogen phosphate	Resolution 1.50 Å R-free 0.175

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RLA2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–70； UniProt 1–69

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2lbf
Deposition date deposition_date	2011-03-30
Structure title title	Solution structure of the dimerization domain of human ribosomal protein P1/P2 heterodimer
Keywords keywords	ribosome, stalk, P1/P2, RIBOSOMAL PROTEIN; RIBOSOMAL PROTEIN
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	14.52 Å
Radius of gyration Rg (electron density) rg_electron	13.72 Å
Forward intensity I(0) i0	278789000.00
Molecular weight molecular_weight	142780.0 kDa
Excluded volume excluded_volume	180140 Å³
Envelope volume envelope_volume	30908 Å³
Hydration-shell volume shell_volume	15801 Å³
Envelope diameter envelope_diameter	56.5 Å
Shell Rg shell_rg	22.68 Å
Envelope Rg envelope_rg	17.19 Å
Shape Rg shape_rg	13.71 Å
Total Rg total_rg	14.06 Å
Total atoms total_atoms	20310
Residues n_residues	1390
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

▼

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

Maximum dimension Dmax dmax	52.4 Å
Rg (real space) rg_real	14.45 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	2.7880e+08
I(0) uncertainty (real space) i0_real_error	3.1160e+06
Rg (reciprocal space) rg_reciprocal	14.46 Å
I(0) (reciprocal space) i0_reciprocal	278800000.0000
Solution quality estimate total_estimate	0.7241
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.027
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	831300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.482; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	60S acidic ribosomal protein P1
Molecular weight formula_weight	7088.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	20310

MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLICNVGAGGPA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	60S acidic ribosomal protein P2
Molecular weight formula_weight	7207.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AMRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2lbfA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1410 —

Domain ID domain_id	2lbfB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1410 —

▶

8. Citations (1)

▶

fit	/app/data/saxs_computation/lb/2lbf/2lbf.fit
pddf	/app/data/pr_computation/lb/2lbf/2lbf.pr.out
profile	/app/data/saxs_computation/lb/2lbf/2lbf.dat

Solution structure of the dimerization domain of human ribosomal protein P1/P2 heterodimer

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

60S acidic ribosomal protein P1

State in the Current Structure

Other States of the Same Protein in the Database

60S acidic ribosomal protein P2

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)