SAXSdb — 7y04

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

Heat shock protein HSP 90-beta

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–724 Chain B； UniProt 1–724	Not recorded	Prostaglandin E synthase 3 × 2 （Q9R0Q7） Aryl hydrocarbon receptor × 1 （P30561） ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

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 7Y04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H77 Hsp90-AhR-p23-XAP2 complex Deposited 2022-10-19	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–724（724 aa） Chain B 1–724（724 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

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

View Construct and Data Evidence

UniProt name	HS90B_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 33–756； UniProt 1–724 Author chain B； PDBConstruct 33–756； UniProt 1–724

Prostaglandin E synthase 3

Mus musculus

UniProt Q9R0Q7

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain C； UniProt 1–160 Chain D； UniProt 1–160	Not recorded	Heat shock protein HSP 90-beta × 2 （P11499） Aryl hydrocarbon receptor × 1 （P30561） ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

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 7Y04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H77 Hsp90-AhR-p23-XAP2 complex Deposited 2022-10-19	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–160（160 aa） Chain D 1–160（160 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

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

View Construct and Data Evidence

UniProt name	TEBP_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 13–172； UniProt 1–160 Author chain D； PDBConstruct 13–172； UniProt 1–160

Aryl hydrocarbon receptor

Mus musculus

UniProt P30561

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain E； UniProt 1–398	Not recorded	Heat shock protein HSP 90-beta × 2 （P11499） Prostaglandin E synthase 3 × 2 （Q9R0Q7） ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

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 7Y04	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4M4X Structure and Dimerization Properties of the Aryl Hydrocarbon Receptor (AHR) PAS-A Domain Deposited 2013-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 110–267（158 aa） Fragment：PAS-A domain, UNP residues 110-267 Chain B 110–267（158 aa） Fragment：PAS-A domain, UNP residues 110-267	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100 mM HEPES, 1.6 M Ammonium Sulfate and 2% PEG 1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.55 Å R-free 0.245
5V0L Crystal structure of the AHR-ARNT heterodimer in complex with the DRE Deposited 2017-02-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 29–267（239 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；277 K；10%-12% PEG 20000, 4-6% Tacsimate pH 7.0 or 0.1 M Bis-Tris pH 6.5	Resolution 4.00 Å R-free 0.323
8H77 Hsp90-AhR-p23-XAP2 complex Deposited 2022-10-19	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–437（437 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AHR_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 13–410； UniProt 1–398

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	7y04
Deposition date deposition_date	2022-06-03
Structure title title	Hsp90-AhR-p23 complex
Keywords keywords	Hsp90, AhR, complex, p23, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	40.80 Å
Radius of gyration Rg (electron density) rg_electron	40.25 Å
Forward intensity I(0) i0	440906000.00
Molecular weight molecular_weight	171470.0 kDa
Excluded volume excluded_volume	214730 Å³
Envelope volume envelope_volume	296910 Å³
Hydration-shell volume shell_volume	61362 Å³
Envelope diameter envelope_diameter	134.6 Å
Shell Rg shell_rg	46.01 Å
Envelope Rg envelope_rg	39.56 Å
Shape Rg shape_rg	40.22 Å
Total Rg total_rg	40.66 Å
Total atoms total_atoms	12050
Residues n_residues	1475
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	135.3 Å
Rg (real space) rg_real	40.79 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	4.4090e+08
I(0) uncertainty (real space) i0_real_error	7.1080e+06
Rg (reciprocal space) rg_reciprocal	40.80 Å
I(0) (reciprocal space) i0_reciprocal	440900000.0000
Solution quality estimate total_estimate	0.8905
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.6 Å
Skewness Skewness skewness	0.322
Kurtosis Kurtosis kurtosis	-0.488
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	113100000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.946

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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	Heat shock protein HSP 90-beta
Molecular weight formula_weight	86590.7 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	12050

MGAWSHPQFEKGGGSGGGSGGGSAWSHPQFEKMPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKEDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVTAEEPSAAVPDEIPPLEGDEDASRMEEVD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Prostaglandin E synthase 3
Molecular weight formula_weight	20134.0 kDa
EC 编号 ec_number	5.3.99.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAEQKLISEEDLMQPASAKWYDRRDYVFIEFCVEDSKDVNVNFEKSKLTFSCLGGSDNFKHLNEIDLFHCIDPNDSKHKRTDRSILCCLRKGESGQSWPRLTKERAKLNWLSVDFNNWKDWEDDSDEDMSNFDRFSEMMDHMGGDEDVDLPEVDGADDDSQDSDDEKMPDLE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Aryl hydrocarbon receptor
Molecular weight formula_weight	46138.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GPGASGGGSGAGMSSGANITYASRKRRKPVQKTVKPIPAEGIKSNPSKRHRDRLNTELDRLASLLPFPQDVINKLDKLSVLRLSVSYLRAKSFFDVALKSTPADRNGGQDQCRAQIRDWQDLQEGEFLLQALNGFVLVVTADALVFYASSTIQDYLGFQQSDVIHQSVYELIHTEDRAEFQRQLHWALNPDSAQGVDEAHGPPQAAVYYTPDQLPPENASFMERCFRCRLRCLLDNSSGFLAMNFQGRLKYLHGQNKKGKDGALLPPQLALFAIATPLQPPSILEIRTKNFIFRTKHKLDFTPIGCDAKGQLILGYTEVELCTRGSGYQFIHAADMLHCAESHIRMIKTGESGMTVFRLFAKHSRWRWVQSNARLIYRNGRPDYIIATQRPLTDEEGREHLQKRSTSLPF

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7y04C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	790 —

Domain ID domain_id	7y04D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	790 —

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8. Citations (1)

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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	—

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

Resolution resolution	3.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	291578

fit	/app/data/saxs_computation/y0/7y04/7y04.fit
pddf	/app/data/pr_computation/y0/7y04/7y04.pr.out
profile	/app/data/saxs_computation/y0/7y04/7y04.dat

Hsp90-AhR-p23 complex

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

Heat shock protein HSP 90-beta

State in the Current Structure

Other States of the Same Protein in the Database

Prostaglandin E synthase 3

State in the Current Structure

Other States of the Same Protein in the Database

Aryl hydrocarbon receptor

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)