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2k6q

LC3 p62 complex structure

Method: SOLUTION NMR Dmax: 49.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Microtubule-associated proteins 1A/1B light chain 3B

Rattus norvegicus

UniProt Q62625

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 1–120 Not recorded p62_peptide from Sequestosome-1 × 1 （O08623） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.125；Pressure ambient NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] LC3, 1.2 mM p62 peptide, 25 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] p62 peptide, 1.2 mM LC3, 25 mM sodium phosphate, 100 mM sodium chloride, 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 2K6Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1UGM Crystal Structure of LC3 Deposited 2003-06-16 Different construct 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 0–119（120 aa） Fragment：residues -4-120
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；PEG 3350, Sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.05 Å R-free 0.249
2Z0D The crystal structure of human Atg4B- LC3(1-120) complex Deposited 2007-05-07 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–120（120 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG 3350, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.227
2Z0E The crystal structure of human Atg4B- LC3(1-124) complex Deposited 2007-05-07 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–124（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG 3350, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.229
2ZZP The crystal structure of human Atg4B(C74S)- LC3(1-124) complex Deposited 2009-02-22 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–124（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% PEG 3350, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.05 Å R-free 0.251

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MLP3B_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–121； UniProt 1–120

p62_peptide from Sequestosome-1

Rattus norvegicus

UniProt O08623

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 331–346 Not recorded Microtubule-associated proteins 1A/1B light chain 3B × 1 （Q62625） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.125；Pressure ambient NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] LC3, 1.2 mM p62 peptide, 25 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] p62 peptide, 1.2 mM LC3, 25 mM sodium phosphate, 100 mM sodium chloride, 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 2K6Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KKC NMR structure of the p62 PB1 domain Deposited 2009-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–100（98 aa） Fragment：PB1 domain, OPR domain, residues 3-100
Mutation：D67A, D69R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 1mM [U-99% 13C; U-99% 15N] p62 PB1-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KTR NMR structure of p62 PB1 dimer determined based on PCS Deposited 2010-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–100（98 aa） Fragment：PB1 domain, OPR domain, residues 3-100
Chain B 3–100（98 aa） Fragment：PB1 domain, OPR domain, residues 3-100
Mutation：C42S, D67A, D69R Mutation：K207E, C226S, C242S, R294A TB TERBIUM(III) ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 0.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name SQSTM_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–17； UniProt 331–346

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 2k6q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2k6q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2k6q
Deposition date deposition_date2008-07-17
Structure title titleLC3 p62 complex structure
Keywords keywords;LC3, p62, Alternative splicing, Autophagy, Cytoplasm, Cytoplasmic vesicle, Lipoprotein, Membrane, Microtubule, Ubl conjugation pathway, Apoptosis, Differentiation, Endosome, Immune response, Metal-binding, Nucleus, Phosphoprotein, Zinc, Zinc-finger, APOPTOSIS INHIBITOR-APOPTOSIS COMPLEX ;; APOPTOSIS INHIBITOR/APOPTOSIS
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.51 Å
Radius of gyration Rg (electron density) rg_electron14.77 Å
Forward intensity I(0) i01448290000.00
Molecular weight molecular_weight321450.0 kDa
Excluded volume excluded_volume401640 ų
Envelope volume envelope_volume37813 ų
Hydration-shell volume shell_volume17972 ų
Envelope diameter envelope_diameter56.6 Å
Shell Rg shell_rg24.01 Å
Envelope Rg envelope_rg18.05 Å
Shape Rg shape_rg14.72 Å
Total Rg total_rg15.07 Å
Total atoms total_atoms45160
Residues n_residues2760
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 dmax49.6 Å
Rg (real space) rg_real15.40 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real1.4480e+09
I(0) uncertainty (real space) i0_real_error1.5250e+07
Rg (reciprocal space) rg_reciprocal15.42 Å
I(0) (reciprocal space) i0_reciprocal1448000000.0000
Solution quality estimate total_estimate0.8850
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.3 Å
Skewness Skewness skewness0.101
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha646200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2k6qa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.3 — GABARAP-like
Domain ID domain_idd2k6qa3
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_id2k6qA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)