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8eob

Cryo-EM structure of human HSP90B in the closed state

Method: ELECTRON MICROSCOPY Dmax: 127.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Heat shock protein HSP 90-beta

Homo sapiens

UniProt P08238

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 2–724 Chain B； UniProt 2–724 Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；25 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 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 8EOB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1QZ2 Crystal Structure of FKBP52 C-terminal Domain complex with the C-terminal peptide MEEVD of Hsp90 Deposited 2003-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain G 719–723（5 aa）
Chain H 719–723（5 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；Sodium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.287
1UYM Human Hsp90-beta with PU3 (9-Butyl-8(3,4,5-trimethoxy-benzyl)-9H-purin-6-ylamine) Deposited 2004-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–220（220 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-220
Not recorded PU3 9-BUTYL-8-(3,4,5-TRIMETHOXYBENZYL)-9H-PURIN-6-AMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；25% PEG MME 2000, 0.1M NA CACODYLATE, PH6.5, 0.2M MGCL2., pH 6.50
Resolution 2.45 Å R-free 0.294
3FWV Crystal Structure of a Redesigned TPR Protein, T-MOD(VMY), in Complex with MEEVF Peptide Deposited 2009-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 719–723（5 aa） Fragment：C-terminal residues
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris pH 8.5, 30% PEG MME 2000, 5-10 mM NiCl2, 10% xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.244
3FWV Crystal Structure of a Redesigned TPR Protein, T-MOD(VMY), in Complex with MEEVF Peptide Deposited 2009-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 719–723（5 aa） Fragment：C-terminal residues
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris pH 8.5, 30% PEG MME 2000, 5-10 mM NiCl2, 10% xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.244
3NMQ Hsp90b N-terminal domain in complex with EC44, a pyrrolo-pyrimidine methoxypyridine inhibitor Deposited 2010-06-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–223（223 aa） Fragment：N-terminal domain (UNP residues 1-223)
Not recorded 7PP 5-{2-amino-4-chloro-7-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-methylpent-4-yn-2 -ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；277 K；0.1M Na Cacodylate, 20% PEG 2000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.267
3PRY Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 284–543（260 aa） Fragment：middle domain (UNP residues 284-543)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；25.5% PEG3350, 0.17 M ammonium sulfate, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.28 Å R-free 0.217
3PRY Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 284–543（260 aa） Fragment：middle domain (UNP residues 284-543)
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；25.5% PEG3350, 0.17 M ammonium sulfate, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.28 Å R-free 0.217
3PRY Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 284–543（260 aa） Fragment：middle domain (UNP residues 284-543)
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；25.5% PEG3350, 0.17 M ammonium sulfate, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Resolution 2.28 Å R-free 0.217
5FWK Atomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex Deposited 2016-02-17 Different construct 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 1–724（724 aa） Fragment：FULL LENGTH
Chain B 1–724（724 aa） Fragment：FULL LENGTH
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS-HCL (PH 7.5), 150 MM NACL, 10 MM KCL, 10 MM MGCL2, 20 MM NA2MOO4, 2MM DTT, 0.085MM DDM；pH 7.5；20MM TRIS-HCL (PH 7.5), 150 MM NACL, 10 MM KCL, 10 MM MGCL2, 20 MM NA2MOO4, 2MM DTT, 0.085MM DDM
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 3.90 Å
5FWL Atomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex Deposited 2016-02-18 Different construct 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 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS-HCL, 150 MM NACL, 10MM KCL, 10MM MGCL2, 20MM NA2MOO4, 2MM DTT, 0.085MM DDM；pH 7.5；20MM TRIS-HCL, 150 MM NACL, 10MM KCL, 10MM MGCL2, 20MM NA2MOO4, 2MM DTT, 0.085MM DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
5FWM Atomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex Deposited 2016-02-18 Different construct 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 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS-HCL (PH 7.5), 150 MM NACL, 10 MM KCL, 10 MM MGCL2, 20 MM NA2MOO4, 2MM DTT, 0.085MM DDM；pH 7.5；20MM TRIS-HCL (PH 7.5), 150 MM NACL, 10 MM KCL, 10 MM MGCL2, 20 MM NA2MOO4, 2MM DTT, 0.085MM DDM
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.00 Å
5FWP Atomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex Deposited 2016-02-18 Different construct 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 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris-HCl (pH 7.5), 150 mM NaCl, 10 mM KCl, 10 mM MgCl2, 20 mM Na2MoO4, 2mM DTT, 0.085mM DDM
cryo-EM vitrification conditions Single blot from 4 to 6 seconds, at 20C；95 K；Cryogen ETHANE；LIQUID ETHANE
Resolution 7.20 Å
5UC4 Hsp90b N-terminal domain with inhibitors Deposited 2016-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–218（218 aa） Fragment：N-terminal domain (UNP residues 1-218)
Not recorded 83S 5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylbenzaldehyde × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.05 Å R-free 0.207
5UC4 Hsp90b N-terminal domain with inhibitors Deposited 2016-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–218（218 aa） Fragment：N-terminal domain (UNP residues 1-218)
Not recorded 83S 5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylbenzaldehyde × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.05 Å R-free 0.207
5UC4 Hsp90b N-terminal domain with inhibitors Deposited 2016-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–218（218 aa） Fragment：N-terminal domain (UNP residues 1-218)
Not recorded 83S 5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylbenzaldehyde × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.05 Å R-free 0.207
5UC4 Hsp90b N-terminal domain with inhibitors Deposited 2016-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–218（218 aa） Fragment：N-terminal domain (UNP residues 1-218)
Not recorded 83S 5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylbenzaldehyde × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.05 Å R-free 0.207
5UCH Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded 871 2-(5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylphenyl)acetonitrile × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.65 Å R-free 0.226
5UCH Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded 871 2-(5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylphenyl)acetonitrile × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.65 Å R-free 0.226
5UCH Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded 871 2-(5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylphenyl)acetonitrile × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.65 Å R-free 0.226
5UCH Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded 871 2-(5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylphenyl)acetonitrile × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.65 Å R-free 0.226
5UCI Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded 874 (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.70 Å R-free 0.238
5UCI Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded 874 (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.70 Å R-free 0.238
5UCI Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded 874 (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.70 Å R-free 0.238
5UCI Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded 874 (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 2.70 Å R-free 0.238
5UCJ Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded KU3 (5-fluoroisoindolin-2-yl)(4-hydroxy-5-isopropylbenzo[d]isoxazol-7-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 1.69 Å R-free 0.197
5UCJ Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded KU3 (5-fluoroisoindolin-2-yl)(4-hydroxy-5-isopropylbenzo[d]isoxazol-7-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 1.69 Å R-free 0.197
5UCJ Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded KU3 (5-fluoroisoindolin-2-yl)(4-hydroxy-5-isopropylbenzo[d]isoxazol-7-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 1.69 Å R-free 0.197
5UCJ Hsp90b N-terminal domain with inhibitors Deposited 2016-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–218（218 aa） Fragment：UNP residues 1-218
Not recorded KU3 (5-fluoroisoindolin-2-yl)(4-hydroxy-5-isopropylbenzo[d]isoxazol-7-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5
Resolution 1.69 Å R-free 0.197
6N8W Structure of Unliganded Hsp90-Beta N-Terminal Domain Deposited 2018-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–231（231 aa）
Not recorded GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；Tris-HCl pH 8.5, MgCl2, PEG 4000, Glycerol
Resolution 3.09 Å R-free 0.286
6N8W Structure of Unliganded Hsp90-Beta N-Terminal Domain Deposited 2018-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–231（231 aa）
Not recorded GOL GLYCEROL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；Tris-HCl pH 8.5, MgCl2, PEG 4000, Glycerol
Resolution 3.09 Å R-free 0.286
6N8W Structure of Unliganded Hsp90-Beta N-Terminal Domain Deposited 2018-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–231（231 aa）
Not recorded GOL GLYCEROL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；Tris-HCl pH 8.5, MgCl2, PEG 4000, Glycerol
Resolution 3.09 Å R-free 0.286
6N8W Structure of Unliganded Hsp90-Beta N-Terminal Domain Deposited 2018-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–231（231 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；Tris-HCl pH 8.5, MgCl2, PEG 4000, Glycerol
Resolution 3.09 Å R-free 0.286
6N8Y Hsp90-beta bound to PU-11-trans Deposited 2018-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–221（221 aa）
Not recorded KFY 9-[(2E)-but-2-en-1-yl]-8-[(3,4,5-trimethoxyphenyl)methyl]-9H-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES pH 6.5, MgCl2, PEG 2000 MME. Incubate with PU-11-trans prior to setup.
Resolution 1.55 Å R-free 0.183
7ULJ Hsp90b N-terminal domain in complex with 42C Deposited 2022-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–218（218 aa）
Not recorded 42C N,N-dimethyl-7H-purin-6-amine × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M Sodium cacodylate pH 6.5, 0.1 M Sodium acetate, 5% MPD and 25% PEG8000
Resolution 1.82 Å R-free 0.219
7ULJ Hsp90b N-terminal domain in complex with 42C Deposited 2022-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–218（218 aa）
Not recorded 42C N,N-dimethyl-7H-purin-6-amine × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M Sodium cacodylate pH 6.5, 0.1 M Sodium acetate, 5% MPD and 25% PEG8000
Resolution 1.82 Å R-free 0.219
7ULJ Hsp90b N-terminal domain in complex with 42C Deposited 2022-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–218（218 aa）
Not recorded 42C N,N-dimethyl-7H-purin-6-amine × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M Sodium cacodylate pH 6.5, 0.1 M Sodium acetate, 5% MPD and 25% PEG8000
Resolution 1.82 Å R-free 0.219
7ULJ Hsp90b N-terminal domain in complex with 42C Deposited 2022-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–218（218 aa）
Not recorded 42C N,N-dimethyl-7H-purin-6-amine × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M Sodium cacodylate pH 6.5, 0.1 M Sodium acetate, 5% MPD and 25% PEG8000
Resolution 1.82 Å R-free 0.219
7Z37 Structure of the RAF1-HSP90-CDC37 complex (RHC-II) Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain AP1 3–724（722 aa）
Chain BP1 3–724（722 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds before plunging
Resolution 3.67 Å
7Z38 Structure of the RAF1-HSP90-CDC37 complex (RHC-I) Deposited 2022-03-01 Different construct 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 3–724（722 aa）
Chain B 3–724（722 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds before plunging
Resolution 3.16 Å
7ZR0 CryoEM structure of HSP90-CDC37-BRAF(V600E) complex. Deposited 2022-05-03 Different construct 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 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ZR5 CryoEM structure of HSP90-CDC37-BRAF(V600E)-PP5(closed) complex Deposited 2022-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ZR6 CryoEM structure of HSP90-CDC37-BRAF(V600E)-PP5(open) complex Deposited 2022-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7ZUB Cryo-EM structure of the indirubin-bound Hsp90-XAP2-AHR complex Deposited 2022-05-12 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 2–724（723 aa）
Chain B 2–724（723 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MOO MOLYBDATE ION × 2 JY6 (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8EOA Cryo-EM structure of human HSP90B-AIPL1 complex Deposited 2022-10-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–724（723 aa）
Chain B 2–724（723 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8GAE Hsp90 provides platform for CRaf dephosphorylation by PP5 Deposited 2023-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded K POTASSIUM ION × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3UL OF SAMPLE 10C 100% HUMIDITY 30S WAIT TIME 3S BLOT TIME -2 BLOT FORCE
Resolution 3.30 Å
8GFT Hsp90 provides platform for CRaf dephosphorylation by PP5 Deposited 2023-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 K POTASSIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3uL OF SAMPLE, 10C, 100% HUMIDITY, 30S WAIT TIME, 3S BLOT TIME, -2 BLOT FORCE
Resolution 3.80 Å
8QMO Cryo-EM structure of the benzo[a]pyrene-bound Hsp90-XAP2-AHR complex Deposited 2023-09-24 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 2–724（723 aa）
Chain B 2–724（723 aa）
Not recorded MOO MOLYBDATE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 W62 benzo[a]pyrene × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
9D9H Human Hsp90b nucleotide binding domain in complex with BRI2311 Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–223（223 aa） Fragment：nucleotide binding domain
Not recorded A1A26 (1P)-3-amino-6-[({1-[(2S)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]piperidin-4-yl}amino)methyl]-1-(4-phenyl-3,4-dihydro-2H-1,4-benzoxazin-6-yl)thieno[2,3-b]pyrazin-2(1H)-one × 1 CL CHLORIDE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；21% PEG8000, 0.1M Hepes pH 7.5,1M LiCl
Resolution 1.96 Å R-free 0.208
9D9I Human Hsp90b nucleotide binding domain in complex with BRI2312 Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–223（223 aa） Fragment：nucleotide binding domain
Not recorded A1A24 (1P)-3-amino-6-[({1-[(2R)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]piperidin-4-yl}amino)methyl]-1-(4-phenyl-3,4-dihydro-2H-1,4-benzoxazin-6-yl)thieno[2,3-b]pyrazin-2(1H)-one × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；21% PEG6000, 0.1M NaCacodylate pH 6.6, 1M Li
Resolution 1.50 Å R-free 0.187
9W5I AGO maturation complex (AMC): AGO2-miRNA duplex in complex with Hsp90 beta and co-chaperone p23 Deposited 2025-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–724（724 aa）
Chain B 1–724（724 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å

29 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HS90B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 34–756； UniProt 2–724 Author chain B； PDBConstruct 34–756； UniProt 2–724

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8eob

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8eob
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8eob
Deposition date deposition_date2022-10-02
Structure title titleCryo-EM structure of human HSP90B in the closed state
Keywords keywordsHSP90B, AIPL1, phosphodiesterase 6, CHAPERONE; CHAPERONE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.02 Å
Radius of gyration Rg (electron density) rg_electron38.49 Å
Forward intensity I(0) i0312106000.00
Molecular weight molecular_weight144390.0 kDa
Excluded volume excluded_volume181130 ų
Envelope volume envelope_volume243140 ų
Hydration-shell volume shell_volume52859 ų
Envelope diameter envelope_diameter131.1 Å
Shell Rg shell_rg44.23 Å
Envelope Rg envelope_rg37.96 Å
Shape Rg shape_rg38.48 Å
Total Rg total_rg38.86 Å
Total atoms total_atoms10141
Residues n_residues1245
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.8 Å
Rg (real space) rg_real39.02 Å
Rg uncertainty (real space) rg_real_error1.14 Å
I(0) (real space) i0_real3.1210e+08
I(0) uncertainty (real space) i0_real_error5.6340e+06
Rg (reciprocal space) rg_reciprocal39.02 Å
I(0) (reciprocal space) i0_reciprocal312100000.0000
Solution quality estimate total_estimate0.8973
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.7 Å
Skewness Skewness skewness0.280
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha82180000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.905
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)