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- PDB-1ud0: CRYSTAL STRUCTURE OF THE C-TERMINAL 10-kDA SUBDOMAIN OF HSC70 -

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Basic information

Entry
Database: PDB / ID: 1ud0
TitleCRYSTAL STRUCTURE OF THE C-TERMINAL 10-kDA SUBDOMAIN OF HSC70
Components70 kDa heat-shock-like protein
KeywordsCHAPERONE / HSC70
Function / homology
Function and homology information


Attenuation phase / PKR-mediated signaling / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / Protein methylation / A1 adenosine receptor binding / HSF1-dependent transactivation / mRNA Splicing - Major Pathway ...Attenuation phase / PKR-mediated signaling / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / Protein methylation / A1 adenosine receptor binding / HSF1-dependent transactivation / mRNA Splicing - Major Pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / response to nickel cation / protein transmembrane import into intracellular organelle / negative regulation of supramolecular fiber organization / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to odorant / Lysosome Vesicle Biogenesis / positive regulation by host of viral genome replication / synaptic vesicle uncoating / protein-containing complex disassembly / GABA synthesis, release, reuptake and degradation / Golgi Associated Vesicle Biogenesis / messenger ribonucleoprotein complex / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / Regulation of HSF1-mediated heat shock response / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / modulation by host of viral process / C3HC4-type RING finger domain binding / photoreceptor ribbon synapse / negative regulation of NLRP3 inflammasome complex assembly / clathrin coat disassembly / ATP-dependent protein disaggregase activity / maintenance of postsynaptic specialization structure / regulation of protein complex stability / Clathrin-mediated endocytosis / neuron spine / glycinergic synapse / Prp19 complex / postsynaptic specialization membrane / presynaptic cytosol / positive regulation of mRNA splicing, via spliceosome / protein folding chaperone complex / axo-dendritic transport / intermediate filament / regulation of postsynapse organization / negative regulation of cardiac muscle cell apoptotic process / postsynaptic cytosol / Neutrophil degranulation / chaperone-mediated autophagy / phosphatidylserine binding / response to starvation / non-chaperonin molecular chaperone ATPase / positive regulation of proteolysis / chaperone cofactor-dependent protein refolding / estrous cycle / asymmetric synapse / autophagosome / positive regulation of phagocytosis / chaperone-mediated protein folding / skeletal muscle tissue development / ATP metabolic process / protein folding chaperone / forebrain development / cellular response to cadmium ion / heat shock protein binding / photoreceptor inner segment / cerebellum development / lysosomal lumen / RNA splicing / dendritic shaft / response to progesterone / response to activity / kidney development / G protein-coupled receptor binding / ADP binding / peptide binding / ATP-dependent protein folding chaperone / spliceosomal complex / G1/S transition of mitotic cell cycle / regulation of protein stability / terminal bouton / cellular response to hydrogen peroxide / mRNA processing / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / melanosome / unfolded protein binding / synaptic vesicle / protein-macromolecule adaptor activity / protein folding / late endosome / presynapse / response to estradiol / cellular response to heat / protein-folding chaperone binding / perikaryon / protein refolding
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 cognate 71 kDa protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.45 Å
AuthorsChou, C.C. / Forouhar, F. / Yeh, Y.H. / Wang, C. / Hsiao, C.D.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Crystal structure of the C-terminal 10-kDa subdomain of Hsc70
Authors: Chou, C.C. / Forouhar, F. / Yeh, Y.H. / Shr, H.L. / Wang, C. / Hsiao, C.D.
History
DepositionApr 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: 70 kDa heat-shock-like protein
B: 70 kDa heat-shock-like protein
C: 70 kDa heat-shock-like protein
D: 70 kDa heat-shock-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8707
Polymers49,8014
Non-polymers693
Water41423
1
A: 70 kDa heat-shock-like protein
B: 70 kDa heat-shock-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9243
Polymers24,9012
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-27 kcal/mol
Surface area11230 Å2
MethodPISA
2
C: 70 kDa heat-shock-like protein
D: 70 kDa heat-shock-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9474
Polymers24,9012
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-45 kcal/mol
Surface area10840 Å2
MethodPISA
3
C: 70 kDa heat-shock-like protein
D: 70 kDa heat-shock-like protein
hetero molecules

A: 70 kDa heat-shock-like protein
B: 70 kDa heat-shock-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8707
Polymers49,8014
Non-polymers693
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area9500 Å2
ΔGint-86 kcal/mol
Surface area19890 Å2
MethodPISA
4
C: 70 kDa heat-shock-like protein
D: 70 kDa heat-shock-like protein
hetero molecules

A: 70 kDa heat-shock-like protein
B: 70 kDa heat-shock-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8707
Polymers49,8014
Non-polymers693
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666x-y+1,-y+1,-z+11
Buried area9260 Å2
ΔGint-82 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.479, 117.479, 163.777
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-701-

NA

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Components

#1: Protein
70 kDa heat-shock-like protein / HSC70


Mass: 12450.306 Da / Num. of mol.: 4 / Fragment: C-TERMINAL SUBDOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63018
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.14 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: ammonium sulfate, 2-propanol, sodium acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9795, 0.9793, 0.940, 0.9802
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.941
40.98021
ReflectionResolution: 3.45→15 Å / Num. all: 62784 / Num. obs: 62784 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.4
Reflection shellResolution: 3.45→3.58 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 5.4 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 3.45→14.93 Å / Rfactor Rfree error: 0.012 / Data cutoff high rms absF: 4127813.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.309 718 4.8 %RANDOM
Rwork0.249 ---
obs0.249 9139 90.3 %-
all-14845 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.18201 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.4 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 3.45→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 3 23 2705
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it1.262
X-RAY DIFFRACTIONc_scangle_it2.172.5
LS refinement shellResolution: 3.45→3.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 87 3.9 %
Rwork0.237 2150 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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