SAXSdb — 8u1m

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

Heat shock protein 83

OrganismNot specified

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–722 Chain B； UniProt 1–722	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.3 cryo-EM vitrification conditions：Cryogen ETHANE；Grids were blotted for 4.5 seconds before plunging	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 8U1M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8U1L Cryo-EM structure of the RAF1-HSP90-CDC37 complex in the closed state Deposited 2023-09-01	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–722（722 aa） Chain B 1–722（722 aa）	Mutation：0 Mutation：0	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 4.5 seconds before plunging	Resolution 3.70 Å
8U1N Cryo-EM structure of the cross-linked HSP90 dimer (NTD-MD) in the semi-open state Deposited 2023-09-01	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–722（722 aa） Chain B 1–722（722 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 4.5 seconds before plunging	Resolution 3.90 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7E5VSK5_TRINI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–722； UniProt 1–722 Author chain B； PDBConstruct 1–722； UniProt 1–722

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	8u1m
Deposition date deposition_date	2023-09-01
Structure title title	Cryo-EM structure of the HSP90 dimer (NTD-MD) in the semi-open state
Keywords keywords	HSP, HSP90, CHAPERONE; CHAPERONE
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	33.02 Å
Radius of gyration Rg (electron density) rg_electron	32.04 Å
Forward intensity I(0) i0	195143000.00
Molecular weight molecular_weight	112030.0 kDa
Excluded volume excluded_volume	140370 Å³
Envelope volume envelope_volume	177670 Å³
Hydration-shell volume shell_volume	45554 Å³
Envelope diameter envelope_diameter	123.5 Å
Shell Rg shell_rg	39.33 Å
Envelope Rg envelope_rg	32.31 Å
Shape Rg shape_rg	32.04 Å
Total Rg total_rg	32.63 Å
Total atoms total_atoms	7882
Residues n_residues	957
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	111.9 Å
Rg (real space) rg_real	32.86 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.9510e+08
I(0) uncertainty (real space) i0_real_error	2.7800e+06
Rg (reciprocal space) rg_reciprocal	32.93 Å
I(0) (reciprocal space) i0_reciprocal	195200000.0000
Solution quality estimate total_estimate	0.8857
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.3 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.500
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	78300000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 1.000

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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	Heat shock protein 83
Molecular weight formula_weight	83322.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7882

MPEEMQTDSGEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELYIKIIPNKSEGTFTIIDTGIGMTKADLVNNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSCYLVADRVTVHSKHNDDEQYMWESSAGGSFTVRTDHGEPLGRGTKIVLHIKEDLAEYLEVNKIKEIVKKHSQFIGYPIKLTVEKEREKELAYDEEEEKKEGEEDKKEDEKEDEKPKIEDVGEDDEEDKDKKKKKTIKEKYTEDEELNKTKPIWTRNADDITQEEYGDFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPFDLFENKKRKNNIKLYVRRVFIMDNCEDLIPEYLNFIKGVVDSEDLPLNISREMLQQNKILKVIRKNLVKKCLELFEELAEDKENYKKYYEQFSKNLKLGIHEDAQNRTKLADLLRYHTSASGDEACSLKEYVSRMKENQKHIYYITGENRDQVANSSFVERVKKRGYEVVYMTEPIDEYVVQQMREYDGKTLVSVTKEGLELPEDEEEKKKREEDKVKFEGLCKVMKNILDNKVEKVVVSNRLVESPCCIVTAQYGWSANMERIMKAQALRDTSTMGYMAAKKHLEINPDHSIVETLRQKAEADKNDKAVKDLVILLYETALLSSGFTLDEPQVHASRIYRMIKLGLGIDEDEPIQVEESSVGDVPPLEGDADDASRMEEVD

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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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	325732

fit	/app/data/saxs_computation/u1/8u1m/8u1m.fit
pddf	/app/data/pr_computation/u1/8u1m/8u1m.pr.out
profile	/app/data/saxs_computation/u1/8u1m/8u1m.dat

Cryo-EM structure of the HSP90 dimer (NTD-MD) in the semi-open state

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

Heat shock protein 83

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)