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- PDB-6fhk: Structure of a modified protein containing a genetically encoded ... -

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Basic information

Entry
Database: PDB / ID: 6fhk
TitleStructure of a modified protein containing a genetically encoded phosphoserine
ComponentsHeat shock 70 kDa protein 1A
KeywordsCHAPERONE / phosphoserine / ADP
Function / homology
Function and homology information


: / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity / 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 ...: / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity / 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 / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / : / regulation of protein ubiquitination / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / cellular response to unfolded protein / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / transcription regulator inhibitor activity / inclusion body / heat shock protein binding / negative regulation of protein ubiquitination / centriole / protein folding chaperone / AUF1 (hnRNP D0) binds and destabilizes mRNA / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of interleukin-8 production / negative regulation of transforming growth factor beta receptor signaling pathway / ATP-dependent protein folding chaperone / G protein-coupled receptor binding / positive regulation of NF-kappaB transcription factor activity / negative regulation of cell growth / PKR-mediated signaling / histone deacetylase binding / disordered domain specific binding / transcription corepressor activity / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / virus receptor activity / protein refolding / cellular response to oxidative stress / blood microparticle / vesicle / ficolin-1-rich granule lumen / protein stabilization / nuclear speck / cadherin binding / receptor ligand activity / ribonucleoprotein complex / signaling receptor binding / negative regulation of cell population proliferation / focal adhesion / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Defensin A-like - #30 / 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 ...Defensin A-like - #30 / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / PHOSPHATE ION / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.657 Å
AuthorsMukherjee, M. / Bayliss, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L023113/1 United Kingdom
Cancer Research UKC24461/A12772 United Kingdom
Citation
Journal: Sci Signal / Year: 2018
Title: Mitotic phosphorylation regulates Hsp72 spindle localization by uncoupling ATP binding from substrate release.
Authors: Mukherjee, M. / Sabir, S. / O'Regan, L. / Sampson, J. / Richards, M.W. / Huguenin-Dezot, N. / Ault, J.R. / Chin, J.W. / Zhuravleva, A. / Fry, A.M. / Bayliss, R.
#1: Journal: Sci Signal / Year: 2018
Title: Mitotic phosphorylation regulates Hsp72 spindle localization by uncoupling ATP binding from substrate release.
Authors: Mukherjee, M. / Sabir, S. / O'Regan, L. / Sampson, J. / Richards, M.W. / Huguenin-Dezot, N. / Ault, J.R. / Chin, J.W. / Zhuravleva, A. / Fry, A.M. / Bayliss, R.
History
DepositionJan 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_conn_type
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.conn_type_id / _struct_conn.id / _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_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Heat shock 70 kDa protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,35810
Polymers84,1872
Non-polymers1,1718
Water10,431579
1
A: Heat shock 70 kDa protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6795
Polymers42,0941
Non-polymers5864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock 70 kDa protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6795
Polymers42,0941
Non-polymers5864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.625, 110.876, 63.483
Angle α, β, γ (deg.)90.00, 90.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 42093.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DMV8

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Non-polymers , 5 types, 587 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Succinic acid pH 7.0, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.657→55.09 Å / Num. obs: 83152 / % possible obs: 98.3 % / Redundancy: 6.4 % / Net I/σ(I): 13.2
Reflection shellResolution: 1.657→1.662 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AY9

3ay9


Resolution: 1.657→55.09 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.18
RfactorNum. reflection% reflection
Rfree0.1944 4139 4.98 %
Rwork0.1622 --
obs0.1638 83150 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.657→55.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5874 0 68 579 6521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016036
X-RAY DIFFRACTIONf_angle_d1.3948172
X-RAY DIFFRACTIONf_dihedral_angle_d14.0562240
X-RAY DIFFRACTIONf_chiral_restr0.094924
X-RAY DIFFRACTIONf_plane_restr0.0061060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6569-1.67570.24661140.21282316X-RAY DIFFRACTION85
1.6757-1.69550.26811250.2182403X-RAY DIFFRACTION92
1.6955-1.71610.2661140.2172654X-RAY DIFFRACTION97
1.7161-1.73790.28281390.20892616X-RAY DIFFRACTION99
1.7379-1.76070.21871230.19652680X-RAY DIFFRACTION99
1.7607-1.78480.25351660.1822635X-RAY DIFFRACTION99
1.7848-1.81030.22261430.17422638X-RAY DIFFRACTION99
1.8103-1.83740.21861550.16762625X-RAY DIFFRACTION99
1.8374-1.86610.2261310.16292675X-RAY DIFFRACTION100
1.8661-1.89670.19831310.16622666X-RAY DIFFRACTION100
1.8967-1.92940.22761280.19262199X-RAY DIFFRACTION83
1.9294-1.96450.19511020.16432723X-RAY DIFFRACTION100
1.9645-2.00230.19821480.16872678X-RAY DIFFRACTION100
2.0023-2.04310.22161130.16282664X-RAY DIFFRACTION100
2.0431-2.08760.21131440.1712673X-RAY DIFFRACTION100
2.0876-2.13610.21511530.15792656X-RAY DIFFRACTION100
2.1361-2.18950.19861540.15552651X-RAY DIFFRACTION100
2.1895-2.24870.20921460.15282678X-RAY DIFFRACTION100
2.2487-2.31490.20271490.15842654X-RAY DIFFRACTION100
2.3149-2.38960.20171420.15562658X-RAY DIFFRACTION100
2.3896-2.4750.21961580.16052675X-RAY DIFFRACTION100
2.475-2.57410.20351280.16852689X-RAY DIFFRACTION100
2.5741-2.69130.20951500.16342658X-RAY DIFFRACTION100
2.6913-2.83320.2141220.16742710X-RAY DIFFRACTION100
2.8332-3.01070.19661580.17182653X-RAY DIFFRACTION100
3.0107-3.24310.18561480.16672688X-RAY DIFFRACTION100
3.2431-3.56940.17441560.15512664X-RAY DIFFRACTION100
3.5694-4.08580.15421180.1422711X-RAY DIFFRACTION100
4.0858-5.14710.16011340.14492705X-RAY DIFFRACTION100
5.1471-55.12120.18021470.16592716X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.6467 Å / Origin y: 6.5478 Å / Origin z: 79.3449 Å
111213212223313233
T0.0997 Å2-0.0051 Å2-0.0055 Å2-0.1277 Å20.014 Å2--0.1355 Å2
L0.0894 °2-0.0712 °2-0.071 °2-0.3566 °20.2556 °2--0.4534 °2
S0.0072 Å °-0.001 Å °0.0033 Å °0.0027 Å °0.0054 Å °-0.0139 Å °0.0083 Å °0.0094 Å °-0.0157 Å °
Refinement TLS groupSelection details: all

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