4umm

The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclear receptor reveals an asymmetric organization with allosteric domain positioning

Method: ELECTRON MICROSCOPY

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

ECDYSONE RECEPTOR

HELIOTHIS VIRESCENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	ECR-USP × 1 ;5'-D(CPAPAPGPGPGPTPTPCPAPAPTPGPCP APCPTPTPGPTP)-3' ; × 1 ;5'-D(DGPAPCPAPAPGPTPGPCPAPTPTPGPDAP APCPCPCPTPT)-3' ; × 1 GENE REGULATION PROTEIN × 1 （Q7SIF6） L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ECR_HELVI
Isoform	—
PDB entities	4, 6
Chains and sequence ranges	Author chain E； PDBConstruct 1–87； UniProt 157–243 Author chain G； PDBConstruct 18–266； UniProt 305–550

GENE REGULATION PROTEIN

HELIOTHIS VIRESCENS

UniProt Q7SIF6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	ECR-USP × 1 ;5'-D(CPAPAPGPGPGPTPTPCPAPAPTPGPCP APCPTPTPGPTP)-3' ; × 1 ;5'-D(DGPAPCPAPAPGPTPGPCPAPTPTPGPDAP APCPCPCPTPT)-3' ; × 1 ECDYSONE RECEPTOR × 1 （O18473） ECDYSONE RECEPTOR × 1 （O18473） L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7SIF6_HELVI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–264； UniProt 1–264

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	4umm
Deposition date deposition_date	2014-05-19
Structure title title	The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclear receptor reveals an asymmetric organization with allosteric domain positioning
Keywords keywords	NUCLEAR RECEPTOR, TRANSCRIPTION, ECDYSONE, USP-ECR, DNA RESPONSE ELEMENT, ALLOSTERY, CRYO ELECTRON MICROSCOPY; NUCLEAR RECEPTOR
Experimental Method method	ELECTRON MICROSCOPY

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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.

4umm__assembly_1__model_1

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

Download this curve (.dat)

4umm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4umm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.66 Å
Rg (electron density)	34.91 Å
Total Rg	35.38 Å
Atom count	6022
Residues	682
Excluded volume	105520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4umm__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	ECR-USP
Molecular weight formula_weight	9256.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6030

KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACREERNCIIDKRQRNRCQYCRYQKCLACGMKREAVQEER

Source Source

Source organism organism	HELIOTHIS VIRESCENS
Common name common_name	TOBACCO BUDWORM
NCBI taxonomy ID ncbi_taxonomy_id	7102
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;5'-D(CPAPAPGPGPGPTPTPCPAPAPTPGPCP APCPTPTPGPTP)-3' ;
Molecular weight formula_weight	6149.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CAAGGGTTCAATGCACTTGT

Entity 3 Entity 3 polymer

Description description	;5'-D(DGPAPCPAPAPGPTPGPCPAPTPTPGPDAP APCPCPCPTPT)-3' ;
Molecular weight formula_weight	6118.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GACAAGTGCATTGAACCCTT

Entity 4 Entity 4 polymer

Description description	ECDYSONE RECEPTOR
Molecular weight formula_weight	10100.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

RQQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKNAVYICKFGHACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMKR

Source Source

Source organism organism	HELIOTHIS VIRESCENS
NCBI taxonomy ID ncbi_taxonomy_id	7102
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 5 Entity 5 polymer

Description description	GENE REGULATION PROTEIN
Molecular weight formula_weight	29962.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

AAVQELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNHAPPIDTNMM

Source Source

Source organism organism	HELIOTHIS VIRESCENS
Common name common_name	TOBACCO BUDWORM
NCBI taxonomy ID ncbi_taxonomy_id	7102
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 6 Entity 6 polymer

Description description	ECDYSONE RECEPTOR
Molecular weight formula_weight	30369.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GSHMASMTGGQQMGRDPLKNVPPLTANQKSLIARLVWYQEGYEQPSEEDLKRVTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFSDRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKNRKLPPFLEEIWDVADVA

Source Source

Source organism organism	HELIOTHIS VIRESCENS
Common name common_name	TOBACCO BUDWORM
NCBI taxonomy ID ncbi_taxonomy_id	7102
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 7 Entity 7 non-polymer

Description description	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	709.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE
Molecular weight formula_weight	464.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	11.600 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	11.60 Å
Resolution测定Method resolution_method	CROSS-COMMON LINES
颗粒数 num_particles	50000

The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclear receptor reveals an asymmetric organization with allosteric domain positioning

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

ECDYSONE RECEPTOR

State in the Current Structure

Other States of the Same Protein in the Database

GENE REGULATION PROTEIN

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

4umm__assembly_1__model_1

4umm__assembly_1__model_1 | I(q)

4umm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclear receptor reveals an asymmetric organization with allosteric domain positioning

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

ECDYSONE RECEPTOR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GENE REGULATION PROTEIN

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

4umm__assembly_1__model_1

4umm__assembly_1__model_1 | I(q)

4umm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)