SAXSdb — 1a6y

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

ORPHAN NUCLEAR RECEPTOR NR1D1

Homo sapiens

UniProt P20393

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 123–216 Chain B； UniProt 123–216	Fragment：DNA BINDING DOMAIN CONSISTS OF RESIDUES A 101 TO A 164, B 101 TO B 164 Mutation：H116L	;DNA (5'-D(CPAPAPCPTPAPGPGPTPCPAPCP(5IT)PAPGPGPTPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPAPCPCPTPAPGPTPGPAPCPCPTPAPGPTPTPG)-3') ; × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；PROTEIN AND DNA COMPLEX WAS CRYSTALLIZED FROM 25-30% PEG 8000, 5 MM MGCL2, 400 MM NACL2, 100 MM TRIS, PH 7.5., VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.288

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 1A6Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GA5 CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT Deposited 2000-11-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION Chain B 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG8000, 5mM MgCl2, 400 mM NaCl, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.40 Å R-free 0.299
1GA5 CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT Deposited 2000-11-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain E 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION Chain F 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG8000, 5mM MgCl2, 400 mM NaCl, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.40 Å R-free 0.299
1HLZ CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT Deposited 2000-12-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION Chain B 123–216（94 aa） Fragment：DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG8000, 5 mM MgCl2, 400 mM NaCl, Tris buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.80 Å R-free 0.310
3N00 Crystal Structure of a deletion mutant of human Reverba ligand binding domain bound with an NCoR ID1 peptide determined to 2.60A Deposited 2010-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 281–323（43 aa） Chain A 423–614（192 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.60 Å R-free 0.266
3N00 Crystal Structure of a deletion mutant of human Reverba ligand binding domain bound with an NCoR ID1 peptide determined to 2.60A Deposited 2010-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 281–323（43 aa） Chain A 423–614（192 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH 7.5, VAPOR DIFFUSION, temperature 295K	Resolution 2.60 Å R-free 0.266
8D8I Crystal structure of Reverb alpha in complex with synthetic agonist Deposited 2022-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 281–323（43 aa） Chain A 425–614（190 aa）	Not recorded	QFX (4S)-6-[([1,1'-biphenyl]-2-yl)oxy]-3-chloro[1,2,4]triazolo[4,3-b]pyridazine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；80mM Na Hepes pH7.5, 200mM proline, 8% glycerol and 18% PEG3350	Resolution 2.50 Å R-free 0.239

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

View Construct and Data Evidence

UniProt name	NR1D1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 123–216 Author chain B； PDBConstruct 1–94； UniProt 123–216

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	1a6y
Deposition date deposition_date	1998-03-04
Structure title title	REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX
Keywords keywords	ORPHAN RECEPTOR, NUCLEAR RECEPTOR, DNA-BINDING, REVERB, REV-ERB, TRANSCRIPTION REGULATION, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	21.62 Å
Radius of gyration Rg (electron density) rg_electron	21.26 Å
Forward intensity I(0) i0	28281900.00
Molecular weight molecular_weight	31137.0 kDa
Excluded volume excluded_volume	34809 Å³
Envelope volume envelope_volume	44339 Å³
Hydration-shell volume shell_volume	18518 Å³
Envelope diameter envelope_diameter	80.0 Å
Shell Rg shell_rg	26.65 Å
Envelope Rg envelope_rg	21.67 Å
Shape Rg shape_rg	21.24 Å
Total Rg total_rg	21.89 Å
Total atoms total_atoms	2100
Residues n_residues	201
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	78.7 Å
Rg (real space) rg_real	21.80 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.8280e+07
I(0) uncertainty (real space) i0_real_error	3.6180e+05
Rg (reciprocal space) rg_reciprocal	21.77 Å
I(0) (reciprocal space) i0_reciprocal	28280000.0000
Solution quality estimate total_estimate	0.6525
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.574
Kurtosis Kurtosis kurtosis	-0.058
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3738000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.665; Stabil: 1.000; Sysdev: 0.281; Positv: 1.000; Valcen: 0.667; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(CPAPAPCPTPAPGPGPTPCPAPCP(5IT)PAPGPGPTPCPAPG)-3') ;
Molecular weight formula_weight	6254.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	2334

CAACTAGGTCACUAGGTCAG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPTPGPAPCPCPTPAPGPTPGPAPCPCPTPAPGPTPTPG)-3') ;
Molecular weight formula_weight	6125.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CTGACCTAGTGACCTAGTTG

Entity 3 Entity 3 polymer

Description description	ORPHAN NUCLEAR RECEPTOR NR1D1
Molecular weight formula_weight	10902.0 kDa
Mutation mutation	H116L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

TKLNGMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRM

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1a6ya_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d1a6yb_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

CATH v4.4 (2 domains)

Domain ID domain_id	1a6yA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	1a6yB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

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8. Citations (1)

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Unit-cell length a length_a	38.670 Å
Unit-cell length b length_b	45.690 Å
Unit-cell length c length_c	47.950 Å
Unit-cell angle α angle_alpha	75.16 °
Unit-cell angle β angle_beta	80.64 °
Unit-cell angle γ angle_gamma	85.58 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.1921
R_free r_free	0.2880

fit	/app/data/saxs_computation/a6/1a6y/1a6y.fit
pddf	/app/data/pr_computation/a6/1a6y/1a6y.pr.out
profile	/app/data/saxs_computation/a6/1a6y/1a6y.dat

REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX

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

ORPHAN NUCLEAR RECEPTOR NR1D1

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)