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2z0e

The crystal structure of human Atg4B- LC3(1-124) complex

Method: X-RAY DIFFRACTION Dmax: 93.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine protease ATG4B

Homo sapiens

UniProt Q9Y4P1

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 1–354 Fragment：residues (-2)-354 Mutation：H280A Microtubule-associated proteins 1A/1B light chain 3B × 1 （Q62625） 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

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 2Z0E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CY7 The crystal structure of human Atg4B Deposited 2005-07-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–393（393 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；potassium phosphate, sodium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.247
2D1I Structure of human Atg4b Deposited 2005-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–393（393 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.65M tri-Sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.00 Å R-free 0.283
2D1I Structure of human Atg4b Deposited 2005-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–393（393 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.65M tri-Sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.00 Å R-free 0.283
2Z0D The crystal structure of human Atg4B- LC3(1-120) complex Deposited 2007-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–354（354 aa） Fragment：residues (-2)-354
Mutation：H280A 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
2ZZP The crystal structure of human Atg4B(C74S)- LC3(1-124) complex Deposited 2009-02-22 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–354（354 aa） Fragment：residues in database 1-354
Mutation：C74S 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
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 384–393（10 aa） Fragment：UNP residues 384-393
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol
Resolution 1.58 Å R-free 0.237
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 384–393（10 aa） Fragment：UNP residues 384-393
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol
Resolution 1.58 Å R-free 0.237
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 384–393（10 aa） Fragment：UNP residues 384-393
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol
Resolution 1.58 Å R-free 0.237
5LXI GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 384–393（10 aa） Fragment：UNP residues 384-393
Chain E 384–393（10 aa） Fragment：UNP residues 384-393
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 3 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 PER PEROXIDE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MgCl2, 24.6 % PEG 400, 29.5 % PEG 8000, 0.1M TRIS 8.5
Resolution 1.44 Å R-free 0.230

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

View Construct and Data Evidence
UniProt name ATG4B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–357； UniProt 1–354

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 B； UniProt 1–124 Not recorded Cysteine protease ATG4B × 1 （Q9Y4P1） 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

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 2Z0E 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 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
2K6Q LC3 p62 complex structure Deposited 2008-07-17 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–120（120 aa）
Not recorded No recorded non-water small molecule 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
2Z0D The crystal structure of human Atg4B- LC3(1-120) complex Deposited 2007-05-07 Different construct 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
2ZZP The crystal structure of human Atg4B(C74S)- LC3(1-124) complex Deposited 2009-02-22 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 2
Chains and sequence ranges Author chain B； PDBConstruct 6–129； UniProt 1–124

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 2z0e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2z0e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2z0e
Deposition date deposition_date2007-05-07
Structure title titleThe crystal structure of human Atg4B- LC3(1-124) complex
Keywords keywordspapain-like fold, ubiquitin fold, HYDROLASE-STRUCTURAL PROTEIN COMPLEX; HYDROLASE/STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.39 Å
Radius of gyration Rg (electron density) rg_electron23.54 Å
Forward intensity I(0) i037843900.00
Molecular weight molecular_weight48095.0 kDa
Excluded volume excluded_volume60356 ų
Envelope volume envelope_volume71375 ų
Hydration-shell volume shell_volume25917 ų
Envelope diameter envelope_diameter98.3 Å
Shell Rg shell_rg29.98 Å
Envelope Rg envelope_rg24.25 Å
Shape Rg shape_rg23.56 Å
Total Rg total_rg24.20 Å
Total atoms total_atoms3393
Residues n_residues433
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 dmax93.7 Å
Rg (real space) rg_real24.49 Å
Rg uncertainty (real space) rg_real_error0.88 Å
I(0) (real space) i0_real3.7840e+07
I(0) uncertainty (real space) i0_real_error6.1660e+05
Rg (reciprocal space) rg_reciprocal24.47 Å
I(0) (reciprocal space) i0_reciprocal37840000.0000
Solution quality estimate total_estimate0.7848
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.2 Å
Skewness Skewness skewness0.546
Kurtosis Kurtosis kurtosis0.153
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10490000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.503; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.729; Smooth: 0.961
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2z0ea_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.22 — Autophagin-like
Domain ID domain_idd2z0eb_
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

CATH v4.4 (1 domains)

Domain ID domain_id2z0eB00
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)