4zwj

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

Method: X-RAY DIFFRACTION Dmax: 223.9 Å Quality: GOOD

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

Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin

Mus musculus

UniProt P00720

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 2–161 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–161 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 2–161 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
4 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 2–161 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293

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.

721 other PDB entries and 843 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENLYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–160; UniProt 2–161 Author chain B; PDBConstruct 1–160; UniProt 2–161 Author chain C; PDBConstruct 1–160; UniProt 2–161 Author chain D; PDBConstruct 1–160; UniProt 2–161

Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin

Mus musculus

UniProt P08100

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–348 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–348 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–348 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
4 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–348 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293

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.

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OPSD_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 161–508; UniProt 1–348 Author chain B; PDBConstruct 161–508; UniProt 1–348 Author chain C; PDBConstruct 161–508; UniProt 1–348 Author chain D; PDBConstruct 161–508; UniProt 1–348

Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin

Mus musculus

UniProt P20443

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 10–392 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 10–392 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 10–392 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293
4 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 10–392 Mutation:R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5;293 K;PEG400, sodium acetate, magnesium acetate Resolution 3.30 Å R-free 0.293

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.

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

View Construct and Data Evidence
UniProt name ARRS_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 524–906; UniProt 10–392 Author chain B; PDBConstruct 524–906; UniProt 10–392 Author chain C; PDBConstruct 524–906; UniProt 10–392 Author chain D; PDBConstruct 524–906; UniProt 10–392

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 4zwj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4zwj
Deposition date deposition_date2015-05-19
Structure title titleCrystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
Keywords keywords;GPCR, rhodopsin, visual arrestin, X-ray free electron laser, serial femtosecond crystallography, SIGNALING PROTEIN, Structural Genomics, GPCR Network ;; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier72.91
Radius of gyration Rg (electron density) rg_electron73.18
Forward intensity I(0) i01538690000.00
Molecular weight molecular_weight350190.0 kDa
Excluded volume excluded_volume446350 ų
Envelope volume envelope_volume775050 ų
Hydration-shell volume shell_volume97296 ų
Envelope diameter envelope_diameter269.4
Shell Rg shell_rg62.11
Envelope Rg envelope_rg70.34
Shape Rg shape_rg73.21
Total Rg total_rg72.81
Total atoms total_atoms24665
Residues n_residues3128
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 dmax223.9
Rg (real space) rg_real72.40
Rg uncertainty (real space) rg_real_error1.51
I(0) (real space) i0_real1.5310e+09
I(0) uncertainty (real space) i0_real_error3.3140e+07
Rg (reciprocal space) rg_reciprocal71.55
I(0) (reciprocal space) i0_reciprocal1533000000.0000
Solution quality estimate total_estimate0.8333
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary85.3
Skewness Skewness skewness0.462
Kurtosis Kurtosis kurtosis-0.123
Angular range angular_range— – 0.1050 −1
Current regularization parameter α current_alpha0.0198
Highest regularization parameter α highest_alpha44070000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.819; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.385

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4zwjA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
Domain ID domain_id4zwjD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins

8. Citations (1)

9. Files and Curves (10)