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- PDB-2qxl: Crystal Structure Analysis of Sse1, a yeast Hsp110 -

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Basic information

Entry
Database: PDB / ID: 2qxl
TitleCrystal Structure Analysis of Sse1, a yeast Hsp110
ComponentsHeat shock protein homolog SSE1Heat shock response
KeywordsCHAPERONE / Hsp110 / Hsp70 / molecular chaperone / ATP state / ATP-binding / Calmodulin-binding / Nucleotide-binding / Phosphorylation / Stress response
Function / homology
Function and homology information


adenyl-nucleotide exchange factor activity / proteasomal ubiquitin-independent protein catabolic process / peptide binding / ATP-dependent protein folding chaperone / autophagy / protein folding / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / calmodulin binding / ATP binding ...adenyl-nucleotide exchange factor activity / proteasomal ubiquitin-independent protein catabolic process / peptide binding / ATP-dependent protein folding chaperone / autophagy / protein folding / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / calmodulin binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Heat shock protein homolog SSE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å
AuthorsHendrickson, W.A. / Liu, Q.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Insights into hsp70 chaperone activity from a crystal structure of the yeast hsp110 Sse1.
Authors: Liu, Q. / Hendrickson, W.A.
History
DepositionAug 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein homolog SSE1
B: Heat shock protein homolog SSE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,2738
Polymers147,1322
Non-polymers1,1416
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.045, 125.331, 74.708
Angle α, β, γ (deg.)90.000, 98.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Heat shock protein homolog SSE1 / Heat shock response / Chaperone protein MSI3


Mass: 73565.859 Da / Num. of mol.: 2 / Fragment: residues 2 to 659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSE1, MSI3 / Plasmid: pSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32589
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 6000, 0.1M cacodylate, pH 6.5, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.97923
SYNCHROTRONNSLS X4A20.97917, 0.97948, 0.96791
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 3, 2005
ADSC QUANTUM 42CCDJun 3, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1KOHZU double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2KOHZU double crystal monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979171
30.979481
40.967911
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 12.7 / Number: 285550 / Rmerge(I) obs: 0.064 / Χ2: 1.09 / D res high: 3 Å / D res low: 50 Å / Num. obs: 76284 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465097.710.0271.1243.5
5.136.4699.910.0441.063.7
4.485.1399.910.0411.0633.7
4.074.4810010.0461.1063.7
3.784.0710010.0591.0643.8
3.563.7810010.0711.0783.8
3.383.5610010.0951.1073.8
3.233.3810010.1281.0983.8
3.113.2310010.1731.0993.8
33.1110010.2231.0673.8
ReflectionResolution: 2.4→30 Å / Num. obs: 75393 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Χ2: 1.422 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.493.30.27974770.9571,299.7
2.49-2.593.50.21575271.0171,299.8
2.59-2.73.60.17575271.071,299.9
2.7-2.853.70.13675471.1571,299.9
2.85-3.023.80.10175231.3421,299.9
3.02-3.263.80.07575191.4471,299.7
3.26-3.583.70.05775431.6891,299.6
3.58-4.13.60.04775421.8641,299.7
4.1-5.163.50.04175581.831,299.5
5.16-303.30.03975561.8321,298.2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.81 Å / D res low: 20 Å / FOM : 0.37 / Reflection: 46944
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97953.26-9.5
13 wavelength20.97925.09-6.95
13 wavelength30.96793.45-3.17
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se41.1050.2520.4970.0820.273
2Se42.3620.410.3070.4370.294
3Se44.3750.660.3110.0540.285
4Se47.8930.2570.0490.0820.285
5Se46.5860.3410.3240.0050.286
6Se57.6160.8380.2260.0040.292
7Se600.1360.2440.4260.304
8Se600.3720.0720.290.288
9Se600.8430.2390.060.329
10Se600.1620.4780.2820.255
11Se600.3780.0780.4190.221
12Se600.9480.0560.4290.265
13Se600.1670.4720.410.23
14Se600.0930.0040.410.228
Phasing MAD shell
Resolution (Å)FOM Reflection
9.39-200.752507
6.18-9.390.73990
4.9-6.180.65060
4.19-4.90.495869
3.71-4.190.386661
3.37-3.710.277254
3.11-3.370.197759
2.9-3.110.117844

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.06phasing
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.41→29.49 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.993 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3795 5 %RANDOM
Rwork0.195 ---
obs0.197 75392 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.618 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20.26 Å2
2--3.11 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.41→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9639 0 66 355 10060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229879
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.97113385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47151235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86325.192443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16151725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5221546
X-RAY DIFFRACTIONr_chiral_restr0.0790.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027390
X-RAY DIFFRACTIONr_nbd_refined0.1940.24019
X-RAY DIFFRACTIONr_nbtor_refined0.2950.26733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2435
X-RAY DIFFRACTIONr_metal_ion_refined0.050.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0670.212
X-RAY DIFFRACTIONr_mcbond_it0.4311.56190
X-RAY DIFFRACTIONr_mcangle_it0.8829963
X-RAY DIFFRACTIONr_scbond_it1.50333729
X-RAY DIFFRACTIONr_scangle_it2.6084.53422
LS refinement shellResolution: 2.41→2.476 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 272 -
Rwork0.245 4740 -
all-5012 -
obs--100 %
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)
11.1357-0.19560.20722.7263-0.03581.43010.0450.19010.2766-0.3661-0.0642-0.5652-0.14260.01720.0192-0.1840.1130.0543-0.07940.1511-0.057774.551385.2326-18.2924
21.0829-0.24990.14371.2519-0.46161.7672-0.0048-0.033-0.05520.04250.0746-0.01320.0192-0.1617-0.0698-0.1503-0.04220.0158-0.07610.0347-0.193875.420446.509118.7372
32.61160.5242-0.91296.6618-1.22213.89330.17530.32181.1418-0.2901-0.1388-0.7681-0.78590.1999-0.03650.0480.04210.1283-0.16250.32660.597576.944118.4385-22.4183
42.5859-0.120.1564.535-0.70095.22730.0537-0.1804-1.0175-0.18970.009-0.23821.26180.0983-0.06270.1663-0.0655-0.0068-0.23340.1170.189878.772112.538122.5882
54.9858-1.84620.66760.7764-0.03590.5709-0.2947-0.4039-0.44690.09560.0472-0.0159-0.13950.13540.2475-0.17550.0508-0.0622-0.0580.09820.029991.905671.95619.4216
62.39490.4049-0.17053.569-0.4891.24970.02490.30830.60660.07370.0034-0.3133-0.16190.011-0.0283-0.13620.0028-0.0021-0.03120.0114-0.112291.242159.5971-18.5958
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 3942 - 393
2X-RAY DIFFRACTION2BB3 - 3942 - 393
3X-RAY DIFFRACTION3AA395 - 545394 - 544
4X-RAY DIFFRACTION4BB395 - 545394 - 544
5X-RAY DIFFRACTION5AA546 - 656545 - 655
6X-RAY DIFFRACTION6BB546 - 652545 - 651

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