SAXSdb — 6wms

▼

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

Nuclear receptor Rev-ErbA beta variant 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	NCOR isoform c × 2 （Q86YY1） PROTOPORPHYRIN IX CONTAINING FE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F1D8P2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–199； UniProt 381–579 Author chain B； PDBConstruct 1–199； UniProt 381–579

NCOR isoform c

OrganismNot specified

UniProt Q86YY1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nuclear receptor Rev-ErbA beta variant 1 × 2 （F1D8P2） PROTOPORPHYRIN IX CONTAINING FE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q86YY1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–23； UniProt 776–798 Author chain F； PDBConstruct 1–23； UniProt 776–798

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6wms
Deposition date deposition_date	2020-04-21
Structure title title	Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR ID2 Peptide
Keywords keywords	Nuclear receptor, heme-binding protein, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6wms__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6wms__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wms__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	23.30 Å
Rg (electron density)	22.06 Å
Total Rg	22.95 Å
Atom count	3370
Residues	415
Excluded volume	60604 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wms__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nuclear receptor Rev-ErbA beta variant 1
Molecular weight formula_weight	22494.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3610

HLVCPMSKSPYVDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFKVHP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	NCOR isoform c
Molecular weight formula_weight	2508.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

DPASNLGLEDIIRKALMGSFDDK

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

▶

Unit-cell length a length_a	55.586 Å
Unit-cell length b length_b	73.400 Å
Unit-cell length c length_c	59.673 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	43.699 Å
R factor r_factor	0.1913
R_work r_work	0.1880
R_free r_free	0.2395

Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR ID2 Peptide

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

Nuclear receptor Rev-ErbA beta variant 1

State in the Current Structure

Other States of the Same Protein in the Database

NCOR isoform c

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6wms__assembly_1__model_1

6wms__assembly_1__model_1 | I(q)

6wms__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR ID2 Peptide

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

Nuclear receptor Rev-ErbA beta variant 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NCOR isoform c

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6wms__assembly_1__model_1

6wms__assembly_1__model_1 | I(q)

6wms__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)