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- PDB-3q6m: Crystal Structure of Human MC-HSP90 in C2221 Space Group -

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Basic information

Entry
Database: PDB / ID: 3q6m
TitleCrystal Structure of Human MC-HSP90 in C2221 Space Group
ComponentsHeat shock protein HSP 90-alphaHeat shock response
KeywordsCHAPERONE / three domains / trimer of dimer / hexamer
Function / homology
Function and homology information


sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity ...sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / skeletal muscle contraction / regulation of protein ubiquitination / positive regulation of cell size / protein unfolding / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / DNA polymerase binding / axonal growth cone / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle contraction / Signaling by ERBB2 / cardiac muscle cell apoptotic process / Recruitment of mitotic centrosome proteins and complexes / positive regulation of telomerase activity / response to salt stress / positive regulation of defense response to virus by host / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / protein tyrosine kinase binding / response to cold / activation of innate immune response / positive regulation of interferon-beta production / nitric-oxide synthase regulator activity / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / cellular response to virus / VEGFA-VEGFR2 Pathway / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus / response to estrogen / histone deacetylase binding / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / melanosome
Similarity search - Function
Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein ...Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, C.C. / Lin, T.W. / Ko, T.P. / Wang, A.H.-J.
CitationJournal: Plos One / Year: 2011
Title: The hexameric structures of human heat shock protein 90
Authors: Lee, C.C. / Lin, T.W. / Ko, T.P. / Wang, A.H.-J.
History
DepositionJan 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,4036
Polymers157,1153
Non-polymers2883
Water2,396133
1
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
hetero molecules

A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,80612
Polymers314,2296
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)162.702, 304.553, 87.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock response / HSP90 / Heat shock 86 kDa / HSP 86 / HSP86 / Renal carcinoma antigen NY-REN-38


Mass: 52371.547 Da / Num. of mol.: 3
Fragment: Middle and C-terminal domain, UNP residues 293-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07900
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.5M ammonium sulfate, 0.1M Tris-sodium citrate, 0.1mM cis-dichloro(ethylenediamine)platinum (II), pH 5.4-5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
PH range: 5.4-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 43809 / Num. obs: 43634 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CGE

2cge


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 35.924 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.985 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25163 2185 5 %RANDOM
Rwork0.2086 ---
obs0.21094 41365 99.18 %-
all-41749 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---2.4 Å20 Å2
3---2.91 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9197 0 15 133 9345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.98212592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33251103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16124.923455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.599151895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2241554
X-RAY DIFFRACTIONr_chiral_restr0.1040.21392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5641.55568
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10929051
X-RAY DIFFRACTIONr_scbond_it1.47833805
X-RAY DIFFRACTIONr_scangle_it2.6454.53541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.003→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 139 -
Rwork0.261 2909 -
obs--95.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.3260.5494-2.4375100.5495.67670.16480.9210.2407-0.4142-0.1621-0.2853-0.321-0.0257-0.00270.0310.01020.05420.3560.00170.3251-15.084-39.835-4.187
223.16775.4715-8.38297.18411.60426.71080.6541-2.13930.78110.9372-0.76530.2337-0.22490.72480.11110.2883-0.1618-0.04310.4277-0.01710.5445-12.269-35.9727.668
35.15933.1607-2.05664.4504-2.1261.08890.4054-0.05720.52930.50990.0050.222-0.28460.0747-0.41040.2281-0.07920.11380.4714-0.16530.5403-44.844-51.81112.989
45.9518-1.51-2.21945.19240.68015.2518-0.0836-0.2864-0.05810.57550.16120.2360.36170.2685-0.07760.2712-0.0336-0.09720.36080.00940.2198-56.027-75.00127.422
59.3786-0.4757-0.05736.92471.17577.3289-0.2826-0.19240.6370.1678-0.0436-0.1147-0.04030.12790.32630.156-0.0344-0.01280.19370.08630.34662.213-65.74548.035
621.30613.7397-0.111813.43062.7465.3572-0.82681.5437-0.0262-0.87760.482-0.3054-0.30650.21460.34480.2061-0.02460.0190.42130.22580.31076.491-64.70236.124
76.41032.17453.35262.11531.32682.79270.0860.5818-0.4817-0.08960.1611-0.10470.06420.2588-0.24710.1552-0.00360.10.409-0.09880.4213-21.766-87.20431.042
88.357-3.97931.95536.94040.36214.30830.46971.0533-0.4549-0.6739-0.19390.44530.025-0.5865-0.27590.1976-0.0023-0.06380.6694-0.07540.2374-48.189-87.36117.041
910.76872.86081.046313.5197-0.94585.7409-0.2391-0.7859-0.48740.65580.3175-0.06680.24210.0432-0.07850.10260.1010.07130.23970.0540.4063-13.605-41.84148.786
103.6085-1.1441.685625.5556-3.83376.3676-0.17790.5778-0.7514-2.08590.2151-0.01950.44080.2462-0.03720.30360.05560.02790.2439-0.0640.4858-15.878-46.73637.222
111.2313-0.00550.230412.9539-1.66461.5243-0.13590.13450.0888-1.81380.31970.9352-0.154-0.0801-0.18380.5624-0.0284-0.09130.19030.09120.4477-20.175-10.43831.296
1212.78232.6852-0.56693.4851-0.46650.5569-0.71870.63950.8918-1.4590.70460.19530.4844-0.09880.01411.9844-0.01390.26580.4290.18010.3202-7.28711.48316.586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A294 - 349
2X-RAY DIFFRACTION2A359 - 395
3X-RAY DIFFRACTION3A405 - 615
4X-RAY DIFFRACTION4A630 - 697
5X-RAY DIFFRACTION5B294 - 349
6X-RAY DIFFRACTION6B359 - 395
7X-RAY DIFFRACTION7B405 - 615
8X-RAY DIFFRACTION8B630 - 699
9X-RAY DIFFRACTION9C294 - 349
10X-RAY DIFFRACTION10C360 - 395
11X-RAY DIFFRACTION11C406 - 614
12X-RAY DIFFRACTION12C630 - 697

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