SAXSdb — 5vji

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

Circadian locomoter output cycles protein kaput

Mus musculus

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 516–560 Chain B； UniProt 516–560	Fragment：UNP Residues 516-560 Non-standard monomer：Yes (specific site not provided by mmCIF)	CLOCK-interacting pacemaker × 1 （Q8R0W1）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7.3；291 K；100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM	Resolution 1.86 Å R-free 0.280
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 516–560 Chain E； UniProt 516–560	Fragment：UNP Residues 516-560 Non-standard monomer：Yes (specific site not provided by mmCIF)	CLOCK-interacting pacemaker × 1 （Q8R0W1）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7.3；291 K；100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM	Resolution 1.86 Å R-free 0.280

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 5VJI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4F3L Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex Deposited 2012-05-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–384（359 aa） Fragment：UNP residues 26-384	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；100 mM Hepes pH 8.0, 6% PEG 3350 and 75 mM NaF., VAPOR DIFFUSION, temperature 293K	Resolution 2.27 Å R-free 0.217
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 515–560（46 aa） Fragment：UNP Residues 516-560 Chain C 515–560（46 aa） Fragment：UNP Residues 516-560 Chain b 515–560（46 aa） Fragment：UNP Residues 516-560 Chain c 515–560（46 aa） Fragment：UNP Residues 516-560	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 515–560（46 aa） Fragment：UNP Residues 516-560 Chain F 515–560（46 aa） Fragment：UNP Residues 516-560 Chain K 515–560（46 aa） Fragment：UNP Residues 516-560 Chain L 515–560（46 aa） Fragment：UNP Residues 516-560	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 515–560（46 aa） Fragment：UNP Residues 516-560 Chain I 515–560（46 aa） Fragment：UNP Residues 516-560 Chain V 515–560（46 aa） Fragment：UNP Residues 516-560 Chain W 515–560（46 aa） Fragment：UNP Residues 516-560	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain N 515–560（46 aa） Fragment：UNP Residues 516-560 Chain O 515–560（46 aa） Fragment：UNP Residues 516-560 Chain S 515–560（46 aa） Fragment：UNP Residues 516-560 Chain T 515–560（46 aa） Fragment：UNP Residues 516-560	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain Y 515–560（46 aa） Fragment：UNP Residues 516-560 Chain Z 515–560（46 aa） Fragment：UNP Residues 516-560 Chain e 515–560（46 aa） Fragment：UNP Residues 516-560 Chain f 515–560（46 aa） Fragment：UNP Residues 516-560	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain M 26–395（370 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.20 Å
8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain M 26–395（370 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain M 26–395（370 aa） Chain O 26–395（370 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLOCK_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–51； UniProt 516–560 Author chain B； PDBConstruct 7–51； UniProt 516–560 Author chain D； PDBConstruct 7–51； UniProt 516–560 Author chain E； PDBConstruct 7–51； UniProt 516–560

CLOCK-interacting pacemaker

Mus musculus

UniProt Q8R0W1

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 352–414	Fragment：UNP residues 352-414 Non-standard monomer：Yes (specific site not provided by mmCIF)	Circadian locomoter output cycles protein kaput × 2 （O08785）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7.3；291 K；100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM	Resolution 1.86 Å R-free 0.280
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 352–414	Fragment：UNP residues 352-414 Non-standard monomer：Yes (specific site not provided by mmCIF)	Circadian locomoter output cycles protein kaput × 2 （O08785）	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7.3；291 K；100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM	Resolution 1.86 Å R-free 0.280

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 5VJI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 352–414（63 aa） Fragment：UNP Residues 352-414 Chain a 352–414（63 aa） Fragment：UNP Residues 352-414	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 352–414（63 aa） Fragment：UNP Residues 352-414 Chain J 352–414（63 aa） Fragment：UNP Residues 352-414	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 352–414（63 aa） Fragment：UNP Residues 352-414 Chain U 352–414（63 aa） Fragment：UNP Residues 352-414	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain M 352–414（63 aa） Fragment：UNP Residues 352-414 Chain R 352–414（63 aa） Fragment：UNP Residues 352-414	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275
5VJX Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain X 352–414（63 aa） Fragment：UNP Residues 352-414 Chain d 352–414（63 aa） Fragment：UNP Residues 352-414	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)	Resolution 2.69 Å R-free 0.275

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

View Construct and Data Evidence

UniProt name	CIPC_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–64； UniProt 352–414 Author chain F； PDBConstruct 2–64； UniProt 352–414

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5vji
Deposition date deposition_date	2017-04-19
Structure title title	Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor
Keywords keywords	circadian rhythm, CLOCK protein, transcription activation, repressor, coiled coil, CIPC, circadian clock, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.51 Å
Radius of gyration Rg (electron density) rg_electron	24.24 Å
Forward intensity I(0) i0	24221000.00
Molecular weight molecular_weight	35257.0 kDa
Excluded volume excluded_volume	42995 Å³
Envelope volume envelope_volume	54434 Å³
Hydration-shell volume shell_volume	20004 Å³
Envelope diameter envelope_diameter	104.7 Å
Shell Rg shell_rg	29.30 Å
Envelope Rg envelope_rg	24.75 Å
Shape Rg shape_rg	24.15 Å
Total Rg total_rg	25.06 Å
Total atoms total_atoms	2409
Residues n_residues	280
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	101.3 Å
Rg (real space) rg_real	24.76 Å
Rg uncertainty (real space) rg_real_error	1.25 Å
I(0) (real space) i0_real	2.4220e+07
I(0) uncertainty (real space) i0_real_error	3.7630e+05
Rg (reciprocal space) rg_reciprocal	24.70 Å
I(0) (reciprocal space) i0_reciprocal	24220000.0000
Solution quality estimate total_estimate	0.7232
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.621
Kurtosis Kurtosis kurtosis	0.139
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7750000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.385; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.251; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Circadian locomoter output cycles protein kaput
Molecular weight formula_weight	6196.4 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	2562

GAMDPEFSAQLGAMQHLKDQLEQRTRMIEANIHRQQEELRKIQEQLQMVHG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CLOCK-interacting pacemaker
Molecular weight formula_weight	7205.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

GNTLVVLHKSGLLEITLKTKELIRQNQATQAELDQLKEQTQMFIEATKSRAPQAWAKLQASLTS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	118

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8. Citations (1)

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Unit-cell length a length_a	24.339 Å
Unit-cell length b length_b	77.585 Å
Unit-cell length c length_c	150.363 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	28.040 Å
R factor r_factor	0.2174
R_work r_work	0.2139
R_free r_free	0.2802

fit	/app/data/saxs_computation/vj/5vji/5vji.fit
pddf	/app/data/pr_computation/vj/5vji/5vji.pr.out
profile	/app/data/saxs_computation/vj/5vji/5vji.dat

Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor

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

Circadian locomoter output cycles protein kaput

State in the Current Structure

Other States of the Same Protein in the Database

CLOCK-interacting pacemaker

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)