6me7

XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin

Method: X-RAY DIFFRACTION Dmax: 107.8 Å Quality: GOOD

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

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

Homo sapiens

UniProt P00268

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 1–53 Mutation:M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate Resolution 3.20 Å R-free 0.250
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–53 Mutation:M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate Resolution 3.20 Å R-free 0.250

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.

44 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RUBR_CLOPA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 308–360; UniProt 1–53 Author chain B; PDBConstruct 308–360; UniProt 1–53

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

Homo sapiens

UniProt P0ABE7

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 23–128 Mutation:M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate Resolution 3.20 Å R-free 0.250
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 23–128 Mutation:M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate Resolution 3.20 Å R-free 0.250

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.

714 other PDB entries and 821 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–106; UniProt 23–128 Author chain B; PDBConstruct 1–106; UniProt 23–128

Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin

Homo sapiens

UniProt P49286

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 35–231 Chain A; UniProt 241–340 Mutation:M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate Resolution 3.20 Å R-free 0.250
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 35–231 Chain B; UniProt 241–340 Mutation:M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate Resolution 3.20 Å R-free 0.250

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.

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

View Construct and Data Evidence
UniProt name MTR1B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 111–307; UniProt 35–231 Author chain A; PDBConstruct 361–460; UniProt 241–340 Author chain B; PDBConstruct 111–307; UniProt 35–231 Author chain B; PDBConstruct 361–460; UniProt 241–340

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 6me7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6me7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6me7
Deposition date deposition_date2018-09-05
Structure title titleXFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin
Keywords keywords;GPCR, melatonin receptor type 1B (MT2), H208A mutation, membrane protein, 2-phenylmelatonin, XFEL, LCP, BRIL, Rubredoxin, circadian rhythm, jetlag, type 2 diabetes ;; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.25
Radius of gyration Rg (electron density) rg_electron32.77
Forward intensity I(0) i0108008000.00
Molecular weight molecular_weight87442.0 kDa
Excluded volume excluded_volume111130 ų
Envelope volume envelope_volume150730 ų
Hydration-shell volume shell_volume37972 ų
Envelope diameter envelope_diameter108.7
Shell Rg shell_rg39.99
Envelope Rg envelope_rg32.51
Shape Rg shape_rg32.77
Total Rg total_rg33.41
Total atoms total_atoms6188
Residues n_residues841
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 dmax107.8
Rg (real space) rg_real34.18
Rg uncertainty (real space) rg_real_error0.81
I(0) (real space) i0_real1.0800e+08
I(0) uncertainty (real space) i0_real_error1.7820e+06
Rg (reciprocal space) rg_reciprocal34.23
I(0) (reciprocal space) i0_reciprocal108000000.0000
Solution quality estimate total_estimate0.8377
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.2
Skewness Skewness skewness0.182
Kurtosis Kurtosis kurtosis-0.553
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8835000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6me7A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id6me7B01
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)