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- PDB-3d2f: Crystal structure of a complex of Sse1p and Hsp70 -

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Basic information

Entry
Database: PDB / ID: 3d2f
TitleCrystal structure of a complex of Sse1p and Hsp70
Components
  • Heat shock 70 kDa protein 1
  • Heat shock protein homolog SSE1Heat shock response
KeywordsCHAPERONE / nucleotide exchange factor / protein folding / ATP-binding / Calmodulin-binding / Nucleotide-binding / Phosphoprotein / Stress response
Function / homology
Function and homology information


: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / adenyl-nucleotide exchange factor activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / death receptor agonist activity / : ...: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / adenyl-nucleotide exchange factor activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / death receptor agonist activity / : / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation / misfolded protein binding / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / proteasomal ubiquitin-independent protein catabolic process / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein complex assembly / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / inclusion body / ATP metabolic process / protein folding chaperone / negative regulation of protein ubiquitination / vesicle-mediated transport / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / peptide binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / autophagy / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / virus receptor activity / cellular response to heat / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / blood microparticle / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / calmodulin binding / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / 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 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily ...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 1. / 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 70 kDa protein 1B / Heat shock 70 kDa protein 1A / Heat shock protein homolog SSE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsPolier, S. / Bracher, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural basis for the cooperation of Hsp70 and Hsp110 chaperones in protein folding.
Authors: Polier, S. / Dragovic, Z. / Hartl, F.U. / Bracher, A.
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein homolog SSE1
B: Heat shock 70 kDa protein 1
C: Heat shock protein homolog SSE1
D: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,11215
Polymers234,7814
Non-polymers1,33011
Water11,908661
1
A: Heat shock protein homolog SSE1
B: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1028
Polymers117,3912
Non-polymers7116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heat shock protein homolog SSE1
D: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0107
Polymers117,3912
Non-polymers6195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.500, 141.902, 151.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 75305.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSE1, MSI3, YPL106C, LPG3C / Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) cod+ RLI / References: UniProt: P32589
#2: Protein Heat shock 70 kDa protein 1 / HSP70.1 / HSP70-1/HSP70-2


Mass: 42084.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSPA1, HSPA1B / Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) cod+ RLI / References: UniProt: P08107, UniProt: P0DMV8*PLUS

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Non-polymers , 5 types, 672 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: 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
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE AGSD LINKER WAS INTRODUCED ON PURPOSE BY PCR TO REPLACE THE LOOP RESIDUES ...AUTHORS STATE THAT THE AGSD LINKER WAS INTRODUCED ON PURPOSE BY PCR TO REPLACE THE LOOP RESIDUES VEEPIPLPEDAPEDAEQEFKKV OF UNP ENTRY P32589 AND WAS FOUND DISORDERED IN COORDINATE DEPOSITED.

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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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 15 % (w/v) polyethyleneglycol-6000, 100 mM Tris-HCl pH 8.0, 10 mM DTT, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→103.695 Å / Num. obs: 124395 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 45.99 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.423.50.5061.562222179800.506100
2.42-2.573.80.3542.164477170510.354100
2.57-2.753.80.2233.360689160410.223100
2.75-2.973.80.1425.156530149390.142100
2.97-3.253.80.0927.552199137900.092100
3.25-3.643.80.06210.247212124870.062100
3.64-4.23.80.0511.941794110830.05100
4.2-5.143.80.052113537594250.052100
5.14-7.273.70.05111.52738073890.051100
7.27-75.843.50.0318.81477842100.0399.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementStarting model: PDB ENTRY 3D2E

3d2e


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.764 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.244 6248 5 %RANDOM
Rwork0.197 ---
obs0.2 124106 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---2.12 Å20 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15391 0 76 661 16128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215816
X-RAY DIFFRACTIONr_angle_refined_deg1.431.96621480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10652022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30124.986706
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.073152636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3951580
X-RAY DIFFRACTIONr_chiral_restr0.1030.22466
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211962
X-RAY DIFFRACTIONr_nbd_refined0.1980.26812
X-RAY DIFFRACTIONr_nbtor_refined0.2970.210726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2806
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.213
X-RAY DIFFRACTIONr_mcbond_it0.4941.510058
X-RAY DIFFRACTIONr_mcangle_it0.941216162
X-RAY DIFFRACTIONr_scbond_it1.56335819
X-RAY DIFFRACTIONr_scangle_it2.5964.55318
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 465 -
Rwork0.254 8558 -
all-9023 -
obs--99.98 %
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)
11.4115-0.04240.181.4252-0.37571.3101-0.01690.0485-0.0391-0.09950.02850.0870.0383-0.005-0.0116-0.2070.0027-0.0104-0.281-0.0134-0.176888.412677.2727184.4403
23.67141.33640.94054.9912-1.42613.06350.293-0.4241-0.61120.1634-0.2054-0.18990.6208-0.048-0.08760.023-0.0244-0.0207-0.21610.06830.053786.096645.2496199.5129
30.38950.7177-0.10016.20411.66640.72740.1031-0.32450.14150.29260.06450.14640.02460.1369-0.1676-0.0753-0.0183-0.0277-0.0298-0.1041-0.035699.0023105.3524211.6609
41.7037-0.88850.12882.07930.4342.7368-0.04240.05590.2452-0.00880.14890.0268-0.4072-0.1187-0.1064-0.16570.0321-0.0017-0.22470.0959-0.102871.0065106.4295185.0321
54.6633-0.6191-3.89378.06320.71824.91950.2220.1990.334-1.91530.0761-1.0356-0.27060.2516-0.29810.29-0.06730.1436-0.1394-0.08340.1086103.7181107.4079187.6851
62.0926-0.14590.2831.9128-0.51141.3852-0.1670.2929-0.1256-0.0102-0.0658-0.34120.03160.19620.2327-0.1831-0.06790.0232-0.08130.0107-0.174474.5664137.0228120.6138
74.3046-1.0415-1.51415.0117-1.56784.8808-0.00531.24420.6555-1.053-0.0305-0.3426-0.2227-0.07610.03580.1809-0.20380.05670.70940.2926-0.04576.4199155.615990.9756
80.50940.2664-0.33490.68091.96528.67810.134-0.03620.18480.0343-0.1080.1225-0.34570.0818-0.0260.1063-0.0106-0.0518-0.1342-0.0455-0.075662.9627161.1703151.38
91.72230.25940.52333.30960.51151.7161-0.0045-0.2258-0.2820.5388-0.2855-0.70510.03480.19490.29-0.1305-0.0986-0.1602-0.00630.27750.15191.2819134.2805149.996
104.29123.90851.43865.79191.809310.01430.3752-0.3146-0.41710.7446-0.1837-0.00952.1195-0.9898-0.19150.4188-0.2115-0.08220.0204-0.0395-0.13958.5293136.7958150.8969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 396
2X-RAY DIFFRACTION1A1001
3X-RAY DIFFRACTION1A2001 - 2002
4X-RAY DIFFRACTION1A3001
5X-RAY DIFFRACTION1A3002
6X-RAY DIFFRACTION1A3003 - 3122
7X-RAY DIFFRACTION1B2002 - 2003
8X-RAY DIFFRACTION1A3151 - 3222
9X-RAY DIFFRACTION1B2061 - 2062
10X-RAY DIFFRACTION2A397 - 500
11X-RAY DIFFRACTION2A525 - 540
12X-RAY DIFFRACTION2A3123 - 3130
13X-RAY DIFFRACTION2A3223 - 3249
14X-RAY DIFFRACTION3A541 - 654
15X-RAY DIFFRACTION3A3131 - 3146
16X-RAY DIFFRACTION3B2004 - 2005
17X-RAY DIFFRACTION3A3250 - 3272
18X-RAY DIFFRACTION3C3002
19X-RAY DIFFRACTION3B2063
20X-RAY DIFFRACTION4B4 - 229
21X-RAY DIFFRACTION4B308 - 382
22X-RAY DIFFRACTION4B2001
23X-RAY DIFFRACTION4A3147 - 3150
24X-RAY DIFFRACTION4B2006 - 2052
25X-RAY DIFFRACTION4A3273 - 3274
26X-RAY DIFFRACTION4B2064 - 2095
27X-RAY DIFFRACTION5B230 - 307
28X-RAY DIFFRACTION5B2053 - 2060
29X-RAY DIFFRACTION5B2096 - 2101
30X-RAY DIFFRACTION6C2 - 396
31X-RAY DIFFRACTION6C1001
32X-RAY DIFFRACTION6C2001 - 2002
33X-RAY DIFFRACTION6C3001
34X-RAY DIFFRACTION6C3003 - 3122
35X-RAY DIFFRACTION6D1063 - 1069
36X-RAY DIFFRACTION6C3152 - 3195
37X-RAY DIFFRACTION6D1227 - 1250
38X-RAY DIFFRACTION7C397 - 498
39X-RAY DIFFRACTION7C526 - 540
40X-RAY DIFFRACTION7C3123 - 3130
41X-RAY DIFFRACTION7C3196 - 3197
42X-RAY DIFFRACTION8C541 - 655
43X-RAY DIFFRACTION8C3131 - 3147
44X-RAY DIFFRACTION8D1145
45X-RAY DIFFRACTION8C3198 - 3207
46X-RAY DIFFRACTION9D4 - 229
47X-RAY DIFFRACTION9D308 - 382
48X-RAY DIFFRACTION9D2001
49X-RAY DIFFRACTION9C3148 - 3151
50X-RAY DIFFRACTION9D1149 - 1198
51X-RAY DIFFRACTION9C3208 - 3209
52X-RAY DIFFRACTION9B2102
53X-RAY DIFFRACTION9D1269 - 1285
54X-RAY DIFFRACTION10D230 - 307
55X-RAY DIFFRACTION10D1200 - 1207
56X-RAY DIFFRACTION10D1286 - 1288

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