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- PDB-4j8f: Crystal structure of a fusion protein containing the NBD of Hsp70... -

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Basic information

Entry
Database: PDB / ID: 4j8f
TitleCrystal structure of a fusion protein containing the NBD of Hsp70 and the middle domain of Hip
ComponentsHeat shock 70 kDa protein 1A/1B, Hsc70-interacting protein
KeywordsCHAPERONE / actin-like fold / nucleotide binding domain / tetratricopeptide repeat / solenoid / Molecular chaperone complex / cytosol
Function / homology
Function and homology information


negative regulation of protein refolding / : / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / Regulation of HSF1-mediated heat shock response / death receptor agonist activity / 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 ...negative regulation of protein refolding / : / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / Regulation of HSF1-mediated heat shock response / death receptor agonist activity / 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 / : / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / transcription regulator inhibitor activity / aggresome / dATP binding / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / histone deacetylase complex / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / protein folding chaperone / vesicle-mediated transport / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / Hsp70 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / response to bacterium / 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 / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein-folding chaperone binding / protein refolding / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / blood microparticle / protein dimerization activity / nuclear speck / ribonucleoprotein complex / cadherin binding / negative regulation of cell population proliferation / protein domain specific binding / focal adhesion / signaling receptor binding / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Hsp70-interacting protein, N-terminal / Hsp70-interacting protein N N-terminal domain / STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / 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 ...Hsp70-interacting protein, N-terminal / Hsp70-interacting protein N N-terminal domain / STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / 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 / Tetratricopeptide repeat domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Tetratricopeptide repeat / ATPase, nucleotide binding domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / ATPase, nucleotide binding domain / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IODIDE ION / PHOSPHATE ION / Heat shock 70 kDa protein 1B / Heat shock 70 kDa protein 1A / Hsc70-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsLi, Z. / Bracher, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure and function of Hip, an attenuator of the Hsp70 chaperone cycle.
Authors: Li, Z. / Hartl, F.U. / Bracher, A.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_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, Hsc70-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,12221
Polymers62,4181
Non-polymers2,70420
Water81145
1
A: Heat shock 70 kDa protein 1A/1B, Hsc70-interacting protein
hetero molecules

A: Heat shock 70 kDa protein 1A/1B, Hsc70-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,24542
Polymers124,8372
Non-polymers5,40840
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z+1/41
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.596, 65.596, 141.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Heat shock 70 kDa protein 1A/1B, Hsc70-interacting protein


Mass: 62418.480 Da / Num. of mol.: 1 / Fragment: P08107 residues 1-382, P50503 residues 77-247
Source method: isolated from a genetically manipulated source
Details: Hsp70(1-382)-Hip(77-247) fusion protein
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: HSPA1, HSPA1A, HSPA1B, ST13, Fam10a1, Hip, HSPA1A, St13
Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) cod+ RIL
References: UniProt: P08107, UniProt: P50503, UniProt: P0DMV8*PLUS

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Non-polymers , 5 types, 65 molecules

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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 17 % PEG-3350 and 0.2 M NH4I, pH 7.4, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.65→65.596 Å / Num. all: 17407 / Num. obs: 17407 / % possible obs: 99.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 5.1 % / Rsym value: 0.068 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.65-2.795.10.4911.61285325280.49199.8
2.79-2.965.10.3282.41235224030.32899.9
2.96-3.165.10.1973.91156122460.197100
3.16-3.425.10.1186.41085321140.118100
3.42-3.745.10.06711987719220.06799.9
3.74-4.195.10.04914.8908317700.049100
4.19-4.835.10.04216790815450.04299.9
4.83-5.925.10.04116.6665513050.04199.9
5.92-8.375.10.03220513310160.03299.7
8.37-48.09850.02523.227705580.02598.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å48.1 Å
Translation3 Å48.1 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.2397 / WRfactor Rwork: 0.1794 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.812 / SU B: 34.174 / SU ML: 0.308 / SU R Cruickshank DPI: 0.3247 / SU Rfree: 0.3794 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUEs: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 824 5 %RANDOM
Rwork0.1937 ---
all0.197 15540 --
obs0.197 15540 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 134.75 Å2 / Biso mean: 55.019 Å2 / Biso min: 21.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4243 0 50 45 4338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224344
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9675883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1955550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78424.423208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68415738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.571534
X-RAY DIFFRACTIONr_chiral_restr0.0830.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213307
X-RAY DIFFRACTIONr_mcbond_it0.3991.52737
X-RAY DIFFRACTIONr_mcangle_it0.77324371
X-RAY DIFFRACTIONr_scbond_it1.19631607
X-RAY DIFFRACTIONr_scangle_it2.0624.51512
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 50 -
Rwork0.308 1133 -
all-1183 -
obs--100 %
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)
13.84380.2387-0.44391.7082-0.23732.37950.0551-0.41740.11750.1486-0.16420.0427-0.08480.31420.10910.0814-0.0301-0.03070.2069-0.00060.09399.99876.68473.0311
24.18541.2507-1.49643.5783-2.12796.5444-0.1462-0.4468-0.5073-0.1127-0.0759-0.06380.48920.93790.22210.09230.1506-0.03760.45940.13160.242628.5639-5.5659-4.5194
33.44630.34881.12775.1564-0.58845.4894-0.10880.02610.44710.0519-0.13340.1903-0.789-0.24020.24220.12050.0583-0.05490.0977-0.09860.1742-10.484318.16645.2253
40000000000000000.2379-0.0146-0.05110.32710.12730.467321.88123.25-13.7207
50000000000000000.27790.0179-0.06310.44470.04750.346416.455215.3022-13.7367
60000000000000000.5526-0.01550.28270.80080.04420.8646-19.7372-0.815.1258
70000000000000000.470.102-0.18141.0106-0.14410.665729.710315.6222-6.4523
80000000000000000.97620.41060.18820.58210.49041.051225.8663-26.18634.1402
90000000000000000.62450.0856-0.18130.657-0.00370.94542.816-7.342113.1837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 189
2X-RAY DIFFRACTION1A361 - 408
3X-RAY DIFFRACTION1A603
4X-RAY DIFFRACTION1A610 - 613
5X-RAY DIFFRACTION1A701 - 721
6X-RAY DIFFRACTION2A190 - 360
7X-RAY DIFFRACTION2A601
8X-RAY DIFFRACTION2A602
9X-RAY DIFFRACTION2A614 - 617
10X-RAY DIFFRACTION2A722 - 737
11X-RAY DIFFRACTION3A409 - 550
12X-RAY DIFFRACTION3A618 - 620
13X-RAY DIFFRACTION3A738 - 745
14X-RAY DIFFRACTION4A604
15X-RAY DIFFRACTION5A605
16X-RAY DIFFRACTION6A606
17X-RAY DIFFRACTION7A607
18X-RAY DIFFRACTION8A608
19X-RAY DIFFRACTION9A609

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