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- PDB-3lof: C-terminal domain of human heat shock 70kDa protein 1B. -

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Basic information

Entry
Database: PDB / ID: 3lof
TitleC-terminal domain of human heat shock 70kDa protein 1B.
ComponentsHeat shock 70 kDa protein 1
KeywordsCHAPERONE / structural genomics / heat shock / HSPA1B / HSP70 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Nucleotide-binding / Phosphoprotein / Stress response
Function / homology
Function and homology information


: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / 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 ...: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / 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 / 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 / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / cellular response to heat / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / protein refolding / blood microparticle / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / 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 / 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 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / 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, nucleotide binding domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock 70 kDa protein 1B / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsOsipiuk, J. / Gu, M. / Mihelic, M. / Orton, K. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of C-terminal domain of human heat shock 70kDa protein 1B.
Authors: Osipiuk, J. / Gu, M. / Mihelic, M. / Orton, K. / Morimoto, R.I. / Joachimiak, A.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock 70 kDa protein 1
B: Heat shock 70 kDa protein 1
C: Heat shock 70 kDa protein 1
D: Heat shock 70 kDa protein 1
E: Heat shock 70 kDa protein 1
F: Heat shock 70 kDa protein 1


Theoretical massNumber of molelcules
Total (without water)71,6646
Polymers71,6646
Non-polymers00
Water2,414134
1
A: Heat shock 70 kDa protein 1
B: Heat shock 70 kDa protein 1


Theoretical massNumber of molelcules
Total (without water)23,8882
Polymers23,8882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-5 kcal/mol
Surface area9600 Å2
MethodPISA
2
C: Heat shock 70 kDa protein 1
D: Heat shock 70 kDa protein 1


Theoretical massNumber of molelcules
Total (without water)23,8882
Polymers23,8882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-7 kcal/mol
Surface area9290 Å2
MethodPISA
3
E: Heat shock 70 kDa protein 1
F: Heat shock 70 kDa protein 1


Theoretical massNumber of molelcules
Total (without water)23,8882
Polymers23,8882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-7 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.702, 71.880, 143.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein
Heat shock 70 kDa protein 1 / HSP70.1 / HSP70-1/HSP70-2


Mass: 11944.070 Da / Num. of mol.: 6 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1, HSPA1A, HSPA1B / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08107, UniProt: P0DMV8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.4 M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→32 Å / Num. all: 29050 / Num. obs: 29050 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.119 / Χ2: 2.691 / Net I/σ(I): 13.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 2.88 / Num. unique all: 1385 / Χ2: 1.419 / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→32 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.528 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.272 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1475 5.1 %RANDOM
Rwork0.192 ---
all0.194 29019 --
obs0.194 29019 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.88 Å2 / Biso mean: 29.015 Å2 / Biso min: 7.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 0 134 3915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223841
X-RAY DIFFRACTIONr_bond_other_d0.0010.022638
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9625145
X-RAY DIFFRACTIONr_angle_other_deg0.97136509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0365482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93726.809188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.26815757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.271512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
X-RAY DIFFRACTIONr_mcbond_it0.8771.52413
X-RAY DIFFRACTIONr_mcbond_other0.1981.5981
X-RAY DIFFRACTIONr_mcangle_it1.7723828
X-RAY DIFFRACTIONr_scbond_it3.21831428
X-RAY DIFFRACTIONr_scangle_it5.684.51313
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 98 -
Rwork0.254 1973 -
all-2071 -
obs-2071 97.55 %
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)
12.27390.2879-0.26055.11060.85113.7127-0.06080.0843-0.1583-0.11030.02590.25320.1844-0.12860.03490.04670.01420.00330.0933-0.02290.044659.117936.925349.3137
21.1655-0.729-1.18722.54232.48524.34720.042-0.05440.0405-0.01660.0544-0.1437-0.15860.1806-0.09640.0715-0.0106-0.02470.0671-0.03460.038559.208934.534228.6569
35.5635-0.7428-2.77320.201-0.06233.50880.0778-0.37220.2060.02720.0550.0119-0.1020.115-0.13280.0984-0.05180.04140.0527-0.03560.089743.359349.440371.4753
41.91590.0169-1.09061.8253-0.76632.67850.05440.01790.035-0.07230.0002-0.0142-0.0111-0.0373-0.05460.0777-0.01510.01060.0351-0.01540.066923.645745.606874.2473
53.3432.5243-0.3545.3235-1.29661.65120.09130.0598-0.0476-0.036-0.0166-0.2521-0.07780.1616-0.07470.1065-0.06550.01680.1002-0.06010.077967.600664.844459.7931
64.88730.6407-0.35183.6772-0.22462.2212-0.0950.3149-0.20950.01990.09510.34320.2376-0.41800.0516-0.05490.03460.12070.00850.100169.529184.925759.2215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A530 - 613
2X-RAY DIFFRACTION1A1 - 134
3X-RAY DIFFRACTION2B530 - 615
4X-RAY DIFFRACTION2B8 - 132
5X-RAY DIFFRACTION3C530 - 615
6X-RAY DIFFRACTION3C5 - 112
7X-RAY DIFFRACTION4D530 - 613
8X-RAY DIFFRACTION4D79 - 111
9X-RAY DIFFRACTION5E530 - 616
10X-RAY DIFFRACTION5E3 - 110
11X-RAY DIFFRACTION6F530 - 614
12X-RAY DIFFRACTION6F122 - 133

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