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- PDB-4po2: Crystal Structure of the Stress-Inducible Human Heat Shock Protei... -

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Basic information

Entry
Database: PDB / ID: 4po2
TitleCrystal Structure of the Stress-Inducible Human Heat Shock Protein HSP70 Substrate-Binding Domain in Complex with Peptide Substrate
Components
  • HSP70 substrate peptide
  • Heat shock 70 kDa protein 1A/1B
KeywordsCHAPERONE / HELICAL BUNDLE / SUBSTRATE BINDING
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 / ATP metabolic process / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / vesicle-mediated transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / heat shock protein binding / 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 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / 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 Å
AuthorsZhang, P. / Leu, J.I. / Murphy, M.E. / George, D.L. / Marmorstein, R.
CitationJournal: Plos One / Year: 2014
Title: Crystal structure of the stress-inducible human heat shock protein 70 substrate-binding domain in complex with Peptide substrate.
Authors: Zhang, P. / Leu, J.I. / Murphy, M.E. / George, D.L. / Marmorstein, R.
History
DepositionFeb 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock 70 kDa protein 1A/1B
B: Heat shock 70 kDa protein 1A/1B
C: HSP70 substrate peptide
D: HSP70 substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4187
Polymers54,1314
Non-polymers2873
Water10,052558
1
A: Heat shock 70 kDa protein 1A/1B
C: HSP70 substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2574
Polymers27,0662
Non-polymers1912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-17 kcal/mol
Surface area12920 Å2
MethodPISA
2
B: Heat shock 70 kDa protein 1A/1B
D: HSP70 substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1623
Polymers27,0662
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-19 kcal/mol
Surface area11820 Å2
MethodPISA
3
A: Heat shock 70 kDa protein 1A/1B
B: Heat shock 70 kDa protein 1A/1B
C: HSP70 substrate peptide
D: HSP70 substrate peptide
hetero molecules

A: Heat shock 70 kDa protein 1A/1B
B: Heat shock 70 kDa protein 1A/1B
C: HSP70 substrate peptide
D: HSP70 substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,83714
Polymers108,2628
Non-polymers5746
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area13120 Å2
ΔGint-117 kcal/mol
Surface area41820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.293, 85.282, 72.199
Angle α, β, γ (deg.)90.00, 126.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-887-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 26278.672 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SUBSTRATE-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1, HSPA1A, HSPA1B, HSX70 / Production host: Escherichia coli (E. coli) / References: UniProt: P08107, UniProt: P0DMV8*PLUS
#2: Protein/peptide HSP70 substrate peptide / Heat shock 70 kDa protein 1/2 / HSP70-1/HSP70-2 / HSP70.1/HSP70.2


Mass: 786.941 Da / Num. of mol.: 2 / Fragment: HSP70 SUBSTRATE PEPTIDE / Source method: obtained synthetically / Details: chemically synthesised
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris (pH 5.5), 0.2M Li2SO4, 28~30% PEG3350 in the reservoir and 0.1M Bis-Tris (pH 5.5), 0.2M Li2SO4, 22~25% PEG3350 in the crystallization drop, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.075
SYNCHROTRONNSLS X29A20.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDSep 15, 2013
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
20.97911
ReflectionResolution: 1.848→50 Å / Num. all: 41518 / Num. obs: 40521 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 20.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.2 / % possible all: 79.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→42.641 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 1633 4.98 %
Rwork0.1746 --
obs0.1769 32790 99.8 %
all-41518 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 15 558 4053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043609
X-RAY DIFFRACTIONf_angle_d0.8274895
X-RAY DIFFRACTIONf_dihedral_angle_d13.8061386
X-RAY DIFFRACTIONf_chiral_restr0.054571
X-RAY DIFFRACTIONf_plane_restr0.002645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05890.23241480.19582570X-RAY DIFFRACTION99
2.0589-2.12530.26741310.19632576X-RAY DIFFRACTION99
2.1253-2.20130.27621420.20132561X-RAY DIFFRACTION100
2.2013-2.28940.2651280.1882563X-RAY DIFFRACTION100
2.2894-2.39360.24061360.19282600X-RAY DIFFRACTION100
2.3936-2.51980.27021490.18572591X-RAY DIFFRACTION100
2.5198-2.67760.26441330.18852604X-RAY DIFFRACTION100
2.6776-2.88430.21221510.18342586X-RAY DIFFRACTION100
2.8843-3.17450.22951160.18562591X-RAY DIFFRACTION100
3.1745-3.63360.22461270.16612635X-RAY DIFFRACTION100
3.6336-4.57710.17761320.14632618X-RAY DIFFRACTION100
4.5771-42.65070.17631400.16212662X-RAY DIFFRACTION100

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