[English] 日本語
Yorodumi
- PDB-4wv7: HEAT SHOCK PROTEIN 70 SUBSTRATE BINDING DOMAIN WITH COVALENTLY LI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wv7
TitleHEAT SHOCK PROTEIN 70 SUBSTRATE BINDING DOMAIN WITH COVALENTLY LINKED NOVOLACTONE
ComponentsHeat shock 70 kDa protein 1A/1B
Keywordschaperone/chaperone inhibitor / Allosteric Inhibitor / chaperone-chaperone inhibitor complex
Function / homology
Function and homology information


: / positive regulation of endoribonuclease activity / : / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / death receptor agonist activity / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway ...: / positive regulation of endoribonuclease activity / : / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / death receptor agonist activity / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitotic spindle assembly / transcription regulator inhibitor activity / lysosomal transport / aggresome / 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 / chaperone-mediated protein complex assembly / cellular response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / vesicle-mediated transport / inclusion body / heat shock protein binding / negative regulation of protein ubiquitination / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cell growth / PKR-mediated signaling / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / vesicle / blood microparticle / ficolin-1-rich granule lumen / protein stabilization / receptor ligand activity / 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 / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 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 / ATPase, nucleotide binding domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-3UM / Heat shock 70 kDa protein 1B / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsKirby, C.A. / Baird, J. / Stams, T.
CitationJournal: Chem.Biol. / Year: 2015
Title: The novolactone natural product disrupts the allosteric regulation of hsp70.
Authors: Hassan, A.Q. / Kirby, C.A. / Zhou, W. / Schuhmann, T. / Kityk, R. / Kipp, D.R. / Baird, J. / Chen, J. / Chen, Y. / Chung, F. / Hoepfner, D. / Movva, N.R. / Pagliarini, R. / Petersen, F. / ...Authors: Hassan, A.Q. / Kirby, C.A. / Zhou, W. / Schuhmann, T. / Kityk, R. / Kipp, D.R. / Baird, J. / Chen, J. / Chen, Y. / Chung, F. / Hoepfner, D. / Movva, N.R. / Pagliarini, R. / Petersen, F. / Quinn, C. / Quinn, D. / Riedl, R. / Schmitt, E.K. / Schitter, A. / Stams, T. / Studer, C. / Fortin, P.D. / Mayer, M.P. / Sadlish, H.
History
DepositionNov 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock 70 kDa protein 1A/1B
B: Heat shock 70 kDa protein 1A/1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6364
Polymers32,9672
Non-polymers6692
Water1,38777
1
A: Heat shock 70 kDa protein 1A/1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8182
Polymers16,4841
Non-polymers3341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock 70 kDa protein 1A/1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8182
Polymers16,4841
Non-polymers3341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.536, 87.779, 52.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

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


Mass: 16483.518 Da / Num. of mol.: 2 / Fragment: unp residues 395-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSPA1, HSX70, HSPA1B / Production host: Escherichia coli (E. coli) / References: UniProt: P08107, UniProt: P0DMV8*PLUS
#2: Chemical ChemComp-3UM / (5beta,6alpha,8alpha,14alpha)-13-ethenyl-5,6-dihydroxy-14-methylpodocarp-12-en-15-oic acid


Mass: 334.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10 mg/ml covalently modified protein in 25 mM Tris-HCl, 50 mM NaCl, 1 mM TCEP was mixed 1:1 with reservior solution containing 0.1 M HEPES, pH 7.0, 70% 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→87.78 Å / Num. obs: 12438 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 40.31 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.3
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUW

1yuw


Resolution: 2.42→53.53 Å / Cor.coef. Fo:Fc: 0.8506 / Cor.coef. Fo:Fc free: 0.7962 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.434 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.281
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 599 4.83 %RANDOM
Rwork0.2004 ---
obs0.2039 12404 99.89 %-
Displacement parametersBiso mean: 38.91 Å2
Baniso -1Baniso -2Baniso -3
1-13.4353 Å20 Å20 Å2
2---31.3582 Å20 Å2
3---17.9229 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 2.42→53.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 48 77 2271
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012220HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.263019HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d787SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes302HARMONIC5
X-RAY DIFFRACTIONt_it2220HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion19.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion323SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2542SEMIHARMONIC4
LS refinement shellResolution: 2.42→2.65 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2685 125 4.32 %
Rwork0.2121 2771 -
all0.2147 2896 -
obs--99.89 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more