6mcv

Crystal Structure of Holo Retinal-Bound Domain-Swapped Dimer of Wild Type Human Cellular Retinol Binding Protein II

Method: X-RAY DIFFRACTION Dmax: 142.5 Å Quality: GOOD

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

Retinol-binding protein 2

Homo sapiens

UniProt P50120

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–134 Chain K; UniProt 2–134 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;4000 PEG, Ammonium acetate, Sodium acetate Resolution 3.30 Å R-free 0.266
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2–134 Chain L; UniProt 2–134 Not recorded RET RETINAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;4000 PEG, Ammonium acetate, Sodium acetate Resolution 3.30 Å R-free 0.266
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 2–134 Chain G; UniProt 2–134 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;4000 PEG, Ammonium acetate, Sodium acetate Resolution 3.30 Å R-free 0.266
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 2–134 Chain H; UniProt 2–134 Not recorded RET RETINAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;4000 PEG, Ammonium acetate, Sodium acetate Resolution 3.30 Å R-free 0.266
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 2–134 Chain I; UniProt 2–134 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;4000 PEG, Ammonium acetate, Sodium acetate Resolution 3.30 Å R-free 0.266
6 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 2–134 Chain J; UniProt 2–134 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;4000 PEG, Ammonium acetate, Sodium acetate Resolution 3.30 Å R-free 0.266

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.

101 other PDB entries and 195 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RET2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–133; UniProt 2–134 Author chain B; PDBConstruct 1–133; UniProt 2–134 Author chain C; PDBConstruct 1–133; UniProt 2–134 Author chain D; PDBConstruct 1–133; UniProt 2–134 Author chain E; PDBConstruct 1–133; UniProt 2–134 Author chain F; PDBConstruct 1–133; UniProt 2–134 Author chain G; PDBConstruct 1–133; UniProt 2–134 Author chain H; PDBConstruct 1–133; UniProt 2–134 Author chain I; PDBConstruct 1–133; UniProt 2–134 Author chain J; PDBConstruct 1–133; UniProt 2–134 Author chain K; PDBConstruct 1–133; UniProt 2–134 Author chain L; PDBConstruct 1–133; UniProt 2–134

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 6mcv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6mcv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6mcv
Deposition date deposition_date2018-09-02
Structure title titleCrystal Structure of Holo Retinal-Bound Domain-Swapped Dimer of Wild Type Human Cellular Retinol Binding Protein II
Keywords keywordsiLBP, Protein Switch, CYTOSOLIC PROTEIN, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.53
Radius of gyration Rg (electron density) rg_electron43.30
Forward intensity I(0) i0542877000.00
Molecular weight molecular_weight186720.0 kDa
Excluded volume excluded_volume231810 ų
Envelope volume envelope_volume336000 ų
Hydration-shell volume shell_volume65986 ų
Envelope diameter envelope_diameter147.3
Shell Rg shell_rg47.20
Envelope Rg envelope_rg42.34
Shape Rg shape_rg43.31
Total Rg total_rg43.47
Total atoms total_atoms13145
Residues n_residues1596
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 dmax142.5
Rg (real space) rg_real43.56
Rg uncertainty (real space) rg_real_error1.38
I(0) (real space) i0_real5.4290e+08
I(0) uncertainty (real space) i0_real_error1.0190e+07
Rg (reciprocal space) rg_reciprocal43.53
I(0) (reciprocal space) i0_reciprocal542900000.0000
Solution quality estimate total_estimate0.8741
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.5
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.361
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37450000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.802

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id6mcvA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvE00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvF00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvG00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvH00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvI00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvJ00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvK00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain
Domain ID domain_id6mcvL00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain

8. Citations (1)

9. Files and Curves (10)