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4co7

Crystal structure of human GATE-16

Method: X-RAY DIFFRACTION Dmax: 77.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2

HOMO SAPIENS

UniProt P60520

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 1–117 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；100 MM SODIUM PHOSPHATE PH 7.0, 50 MM POTASSIUM CHLORIDE, 10 MM DITHIOTHREITOL Resolution 2.00 Å R-free 0.212
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–117 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；100 MM SODIUM PHOSPHATE PH 7.0, 50 MM POTASSIUM CHLORIDE, 10 MM DITHIOTHREITOL Resolution 2.00 Å R-free 0.212

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 4CO7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6H8C Structure of the human GABARAPL2 protein in complex with the UBA5 LIR motif Deposited 2018-08-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3–116（114 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT
NMR sample composition 0.6 mM [U-99% 13C; U-99% 15N] GABARAPL2, 1.0 mM No Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, 50 mM No sodium phosphate, 100 mM No sodium chloride, 4.6 mM No sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.0 mM No GABARAPL2, 0.6 mM [U-99% 13C; U-99% 15N] Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, 50 mM No sodium phosphate, 100 mM No sodium chloride, 4.6 mM No sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7LK3 Crystal structure of untwinned human GABARAPL2 Deposited 2021-02-01 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M KBr, 30% (w/v) PEG monomethyl ether 2000
Resolution 1.90 Å R-free 0.233
7LK3 Crystal structure of untwinned human GABARAPL2 Deposited 2021-02-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–117（117 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M KBr, 30% (w/v) PEG monomethyl ether 2000
Resolution 1.90 Å R-free 0.233
7YO8 Crystal structure of fission yeast Hfl1 LIR fused to human GABARAPL2 Deposited 2022-08-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–116（116 aa）
Mutation：F28S V29T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；8% PEG 3000, 0.1 M sodium citrate
Resolution 1.80 Å R-free 0.205
8Q6Q Structure of human immunity related GTPase Q in complex with GABARAPL2. Deposited 2023-08-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % w/v Polyethylene glycol 3,350, 200 mM di-Ammonium hydrogen citrate; pH 5.0
Resolution 1.80 Å R-free 0.222
8Q6Q Structure of human immunity related GTPase Q in complex with GABARAPL2. Deposited 2023-08-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–117（117 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % w/v Polyethylene glycol 3,350, 200 mM di-Ammonium hydrogen citrate; pH 5.0
Resolution 1.80 Å R-free 0.222

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

View Construct and Data Evidence
UniProt name GBRL2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–119； UniProt 1–117 Author chain B； PDBConstruct 3–119； UniProt 1–117

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 4co7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4co7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4co7
Deposition date deposition_date2014-01-27
Structure title titleCrystal structure of human GATE-16
Keywords keywordsPROTEIN TRANSPORT, AUTOPHAGY, BETA-GRASP FOLD, UBIQUITIN SUPERFAMILY; PROTEIN TRANSPORT
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_guinier22.34 Å
Radius of gyration Rg (electron density) rg_electron21.50 Å
Forward intensity I(0) i012311000.00
Molecular weight molecular_weight27272.0 kDa
Excluded volume excluded_volume34588 ų
Envelope volume envelope_volume42198 ų
Hydration-shell volume shell_volume17403 ų
Envelope diameter envelope_diameter76.0 Å
Shell Rg shell_rg26.67 Å
Envelope Rg envelope_rg21.29 Å
Shape Rg shape_rg21.49 Å
Total Rg total_rg22.31 Å
Total atoms total_atoms1922
Residues n_residues236
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 dmax77.4 Å
Rg (real space) rg_real22.42 Å
Rg uncertainty (real space) rg_real_error0.60 Å
I(0) (real space) i0_real1.2310e+07
I(0) uncertainty (real space) i0_real_error1.6180e+05
Rg (reciprocal space) rg_reciprocal22.41 Å
I(0) (reciprocal space) i0_reciprocal12310000.0000
Solution quality estimate total_estimate0.6734
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.421
Kurtosis Kurtosis kurtosis-0.393
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2086000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 0.189; Positv: 1.000; Valcen: 0.904; Smooth: 0.986
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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) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4co7a1
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_idd4co7a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4co7b1
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_idd4co7b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id4co7A00
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
Domain ID domain_id4co7B00
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)