2lkm

Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology

Method: SOLUTION NMR Dmax: 65.6 Å Quality: GOOD

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

PHD finger protein 12

Homo sapiens

UniProt Q96QT6

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 200–241 Fragment:UNP residues 200-241 Mortality factor 4-like protein 1 × 1 (Q9UBU8) SOLUTION NMR NMR measurement conditions:pH 6.8;298 K NMR sample composition:0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM potassium chloride, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O | 100% D2O NMR sample composition:0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O | 100% 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.

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

View Construct and Data Evidence
UniProt name PHF12_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–42; UniProt 200–241

Mortality factor 4-like protein 1

Homo sapiens

UniProt Q9UBU8

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 194–362 Fragment:UNP residues 194-362 Mutation:K201R PHD finger protein 12 × 1 (Q96QT6) SOLUTION NMR NMR measurement conditions:pH 6.8;298 K NMR sample composition:0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM potassium chloride, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O | 100% D2O NMR sample composition:0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O | 100% 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.

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MO4L1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–172; UniProt 194–362

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 2lkm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2lkm
Deposition date deposition_date2011-10-16
Structure title titleStructural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology
Keywords keywordsprotein-protein complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier18.47
Radius of gyration Rg (electron density) rg_electron17.74
Forward intensity I(0) i03054270000.00
Molecular weight molecular_weight491220.0 kDa
Excluded volume excluded_volume622530 ų
Envelope volume envelope_volume61272 ų
Hydration-shell volume shell_volume24029 ų
Envelope diameter envelope_diameter74.6
Shell Rg shell_rg28.58
Envelope Rg envelope_rg21.78
Shape Rg shape_rg17.73
Total Rg total_rg17.94
Total atoms total_atoms69460
Residues n_residues4280
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 dmax65.6
Rg (real space) rg_real18.44
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real3.0540e+09
I(0) uncertainty (real space) i0_real_error4.3090e+07
Rg (reciprocal space) rg_reciprocal18.44
I(0) (reciprocal space) i0_reciprocal3054000000.0000
Solution quality estimate total_estimate0.7581
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.4
Skewness Skewness skewness0.353
Kurtosis Kurtosis kurtosis-0.008
Angular range angular_range— – 0.4300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1527000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.623; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2lkmA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily220
Domain ID domain_id2lkmB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily30 — MRG domain

8. Citations (1)

9. Files and Curves (10)