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2cqk

Solution structure of the La domain of c-Mpl binding protein

Method: SOLUTION NMR Dmax: 58.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

C-Mpl binding protein

Homo sapiens

UniProt Q71RC2

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 43–130 Fragment：La domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.4mM 13C/15N-PROTEIN; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3 | 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 2CQK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3PKN Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4) Deposited 2010-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–26（14 aa） Fragment：PABP-binding region (UNP residues 13-26)
Not recorded SO4 SULFATE ION × 1 IOD IODIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.25 M potassium iodide, 1.9 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.80 Å R-free 0.269
3PKN Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4) Deposited 2010-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 13–26（14 aa） Fragment：PABP-binding region (UNP residues 13-26)
Not recorded SO4 SULFATE ION × 2 IOD IODIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.25 M potassium iodide, 1.9 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.80 Å R-free 0.269
6I9B NMR structure of the La module from human LARP4A Deposited 2018-11-22 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–287（177 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.25；298 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure 1
NMR sample composition 400 uM [U-99% 15N] RNA binding protein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 400 uM [U-99% 13C; U-99% 15N] RNA binding protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LARP4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–95； UniProt 43–130

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 2cqk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2cqk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2cqk
Deposition date deposition_date2005-05-20
Structure title titleSolution structure of the La domain of c-Mpl binding protein
Keywords keywords;La domain, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.00 Å
Radius of gyration Rg (electron density) rg_electron14.33 Å
Forward intensity I(0) i0735327000.00
Molecular weight molecular_weight224040.0 kDa
Excluded volume excluded_volume278830 ų
Envelope volume envelope_volume45839 ų
Hydration-shell volume shell_volume19798 ų
Envelope diameter envelope_diameter68.9 Å
Shell Rg shell_rg26.05 Å
Envelope Rg envelope_rg20.10 Å
Shape Rg shape_rg14.32 Å
Total Rg total_rg14.67 Å
Total atoms total_atoms31360
Residues n_residues2020
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.3 Å
Rg (real space) rg_real15.02 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real7.3530e+08
I(0) uncertainty (real space) i0_real_error8.2230e+06
Rg (reciprocal space) rg_reciprocal15.01 Å
I(0) (reciprocal space) i0_reciprocal735300000.0000
Solution quality estimate total_estimate0.6792
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary17.0 Å
Skewness Skewness skewness0.421
Kurtosis Kurtosis kurtosis0.082
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha428400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.337; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.815; 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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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2cqka1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.46 — La domain
Domain ID domain_idd2cqka2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2cqka3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2cqkA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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8. Citations (1)

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9. Files and Curves (10)