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4jzy

Crystal structures of Drosophila Cryptochrome

Method: X-RAY DIFFRACTION Dmax: 119.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cryptochrome-1

Drosophila melanogaster

UniProt O77059

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 1–540 Chain B； UniProt 1–540 Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NH4 AMMONIUM ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.2 M NH4OAc, 20% PEG 3350 , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.34 Å R-free 0.222

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 4JZY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GU5 Structure of Full-length Drosophila Cryptochrome Deposited 2012-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–539（539 aa）
Not recorded MG MAGNESIUM ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；298 K；50 MM HEPES PH 8.0; 150 MM NACL 5MG/ML PROTEIN MIXED 1:1 WITH 18% PDG 4K, 150 MM MGACETATE, 100 MM TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Resolution 2.30 Å R-free 0.247
4GU5 Structure of Full-length Drosophila Cryptochrome Deposited 2012-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–539（539 aa）
Not recorded MG MAGNESIUM ION × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；298 K；50 MM HEPES PH 8.0; 150 MM NACL 5MG/ML PROTEIN MIXED 1:1 WITH 18% PDG 4K, 150 MM MGACETATE, 100 MM TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Resolution 2.30 Å R-free 0.247
4K03 Crystal structure of Drosophila Cryprochrome Deposited 2013-04-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–542（542 aa）
Chain B 1–542（542 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM TrisHCl pH 8.0, 17% PEG 3350, 120 mM Mg-Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.269
6WTB Sort-Tagged Drosophila Cryptochrome Deposited 2020-05-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–539（539 aa）
Chain B 1–539（539 aa）
Not recorded MG MAGNESIUM ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；4 microliter drop (2 microliter protein solution, 2 microliter well solution) 100 mM Tris (pH 9) 150 mM Magneisum Acetate Tetrahydrate 17% PEG-4000 8 mg/mL sort-tagged WT Drosophila Cryptochrome
Resolution 2.58 Å R-free 0.287
7UD0 Room Temperature Drosophila Cryptochrome Deposited 2022-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–539（539 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 8.5；298 K；5 mg/mL twin-strep tagged dCRY (1-539) 100 mM Tris (pH 8.5) 150 mM Magnesium acetate tetrahydrate 18% PEG-4000 Mixed 1:1 in Eppendorf tube; no vortexing
Resolution 3.50 Å R-free 0.294
7UD0 Room Temperature Drosophila Cryptochrome Deposited 2022-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–539（539 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 8.5；298 K；5 mg/mL twin-strep tagged dCRY (1-539) 100 mM Tris (pH 8.5) 150 mM Magnesium acetate tetrahydrate 18% PEG-4000 Mixed 1:1 in Eppendorf tube; no vortexing
Resolution 3.50 Å R-free 0.294
8DD7 The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–520（520 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å

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

View Construct and Data Evidence
UniProt name CRY1_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–536； UniProt 1–540 Author chain B； PDBConstruct 2–536； UniProt 1–540

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 4jzy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4jzy
Deposition date deposition_date2013-04-03
Structure title titleCrystal structures of Drosophila Cryptochrome
Keywords keywordsCryptochrome, Rossmann Fold, Photoreceptor, FAD, CIRCADIAN CLOCK PROTEIN; CIRCADIAN CLOCK 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_guinier36.01 Å
Radius of gyration Rg (electron density) rg_electron35.60 Å
Forward intensity I(0) i0237455000.00
Molecular weight molecular_weight124260.0 kDa
Excluded volume excluded_volume155230 ų
Envelope volume envelope_volume190760 ų
Hydration-shell volume shell_volume45474 ų
Envelope diameter envelope_diameter126.1 Å
Shell Rg shell_rg40.99 Å
Envelope Rg envelope_rg35.69 Å
Shape Rg shape_rg35.58 Å
Total Rg total_rg36.02 Å
Total atoms total_atoms8771
Residues n_residues1070
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 dmax119.0 Å
Rg (real space) rg_real36.09 Å
Rg uncertainty (real space) rg_real_error0.92 Å
I(0) (real space) i0_real2.3750e+08
I(0) uncertainty (real space) i0_real_error4.2140e+06
Rg (reciprocal space) rg_reciprocal36.04 Å
I(0) (reciprocal space) i0_reciprocal237400000.0000
Solution quality estimate total_estimate0.8846
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.1 Å
Skewness Skewness skewness0.358
Kurtosis Kurtosis kurtosis-0.506
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha107600000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.884
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4jzyA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id4jzyA02
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily80 —
Domain ID domain_id4jzyA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3
Domain ID domain_id4jzyB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id4jzyB02
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily80 —
Domain ID domain_id4jzyB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3
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8. Citations (1)

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9. Files and Curves (10)