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- PDB-7ndx: Crystal structure of the human HSP40 DNAJB1-CTDs in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7ndx
TitleCrystal structure of the human HSP40 DNAJB1-CTDs in complex with a peptide of NudC
Components
  • DnaJ homolog subfamily B member 1
  • Nuclear migration protein nudC
KeywordsCHAPERONE / Chaperones / Protein Complex
Function / homology
Function and homology information


sperm head / negative regulation of inclusion body assembly / positive regulation of ATP-dependent activity / transcription regulator inhibitor activity / nuclear migration / RND2 GTPase cycle / mitotic metaphase chromosome alignment / ATPase activator activity / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation ...sperm head / negative regulation of inclusion body assembly / positive regulation of ATP-dependent activity / transcription regulator inhibitor activity / nuclear migration / RND2 GTPase cycle / mitotic metaphase chromosome alignment / ATPase activator activity / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of cellular response to heat / protein folding chaperone / Mitotic Prometaphase / forebrain development / EML4 and NUDC in mitotic spindle formation / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitotic spindle organization / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / mitotic spindle / spindle / response to peptide hormone / Separation of Sister Chromatids / transcription corepressor activity / unfolded protein binding / protein folding / cellular response to heat / midbody / ATPase binding / protein-folding chaperone binding / microtubule / dendritic spine / postsynaptic density / cadherin binding / cell division / neuronal cell body / glutamatergic synapse / nucleolus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear migration protein nudC / Nuclear distribution C domain / NudC N-terminal domain / N-terminal conserved domain of Nudc. / NudC family / CS domain / CS domain / CS domain profile. / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal ...Nuclear migration protein nudC / Nuclear distribution C domain / NudC N-terminal domain / N-terminal conserved domain of Nudc. / NudC family / CS domain / CS domain / CS domain profile. / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / HSP20-like chaperone / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain
Similarity search - Domain/homology
DnaJ homolog subfamily B member 1 / Nuclear migration protein nudC
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.541 Å
AuthorsDelhommel, F. / Zak, K.M. / Popowicz, G.M. / Sattler, M.
Funding support Germany, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 243-2018 Germany
German Research Foundation (DFG)SFB 1035 - project A03 Germany
Helmholtz AssociationZT-I-0003 Germany
CitationJournal: Mol.Cell / Year: 2022
Title: NudC guides client transfer between the Hsp40/70 and Hsp90 chaperone systems.
Authors: Biebl, M.M. / Delhommel, F. / Faust, O. / Zak, K.M. / Agam, G. / Guo, X. / Muhlhofer, M. / Dahiya, V. / Hillebrand, D. / Popowicz, G.M. / Kampmann, M. / Lamb, D.C. / Rosenzweig, R. / Sattler, M. / Buchner, J.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaJ homolog subfamily B member 1
B: Nuclear migration protein nudC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8116
Polymers25,5622
Non-polymers2484
Water39622
1
A: DnaJ homolog subfamily B member 1
B: Nuclear migration protein nudC
hetero molecules

A: DnaJ homolog subfamily B member 1
B: Nuclear migration protein nudC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,62112
Polymers51,1254
Non-polymers4978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area5090 Å2
ΔGint-42 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.300, 128.264, 135.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein DnaJ homolog subfamily B member 1 / DnaJ protein homolog 1 / Heat shock 40 kDa protein 1 / Heat shock protein 40 / Human DnaJ protein 1 / hDj-1


Mass: 20894.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB1, DNAJ1, HDJ1, HSPF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P25685
#2: Protein/peptide Nuclear migration protein nudC / Nuclear distribution protein C homolog


Mass: 4668.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y266
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M of sodium acetate trihydrate and 15% (v/v) of polyethylene glycol 400

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→46.53 Å / Num. obs: 12295 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.5
Reflection shellResolution: 2.54→2.65 Å / Num. unique obs: 1465 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AGY

3agy


Resolution: 2.541→46.53 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.9 / SU B: 20.166 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / ESU R: 0.302 / ESU R Free: 0.246
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2681 607 4.937 %
Rwork0.2328 11688 -
all0.235 --
obs-12295 99.911 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.028 Å2
Baniso -1Baniso -2Baniso -3
1--3.914 Å2-0 Å20 Å2
2--2.607 Å2-0 Å2
3---1.307 Å2
Refinement stepCycle: LAST / Resolution: 2.541→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 16 22 1468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131466
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171481
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.6721971
X-RAY DIFFRACTIONr_angle_other_deg1.1541.5843429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4675177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.13921.54971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67415276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3741512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined0.2060.2242
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21313
X-RAY DIFFRACTIONr_nbtor_refined0.1580.2657
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2844
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.231
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.215
X-RAY DIFFRACTIONr_nbd_other0.2010.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.23
X-RAY DIFFRACTIONr_mcbond_it2.2474.259720
X-RAY DIFFRACTIONr_mcbond_other2.2434.259719
X-RAY DIFFRACTIONr_mcangle_it3.576.377893
X-RAY DIFFRACTIONr_mcangle_other3.5686.379894
X-RAY DIFFRACTIONr_scbond_it2.44.533746
X-RAY DIFFRACTIONr_scbond_other2.3994.534747
X-RAY DIFFRACTIONr_scangle_it3.8956.6721078
X-RAY DIFFRACTIONr_scangle_other3.8956.6721078
X-RAY DIFFRACTIONr_lrange_it5.91548.4491424
X-RAY DIFFRACTIONr_lrange_other5.91448.4711425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.541-2.6070.401490.321841X-RAY DIFFRACTION99.6641
2.607-2.6780.337340.277815X-RAY DIFFRACTION100
2.678-2.7560.355470.288807X-RAY DIFFRACTION100
2.756-2.8410.257380.264774X-RAY DIFFRACTION100
2.841-2.9340.265340.253782X-RAY DIFFRACTION100
2.934-3.0370.254280.24730X-RAY DIFFRACTION100
3.037-3.1510.241240.245733X-RAY DIFFRACTION100
3.151-3.280.305270.258694X-RAY DIFFRACTION100
3.28-3.4250.274310.237663X-RAY DIFFRACTION100
3.425-3.5920.344460.253609X-RAY DIFFRACTION100
3.592-3.7860.308250.237617X-RAY DIFFRACTION100
3.786-4.0160.188320.194571X-RAY DIFFRACTION100
4.016-4.2920.228450.189517X-RAY DIFFRACTION100
4.292-4.6350.243260.175522X-RAY DIFFRACTION100
4.635-5.0760.158300.17458X-RAY DIFFRACTION100
5.076-5.6740.247310.228412X-RAY DIFFRACTION100
5.674-6.5470.282200.232380X-RAY DIFFRACTION100
6.547-8.0090.241170.258336X-RAY DIFFRACTION100
8.009-11.2840.345110.202265X-RAY DIFFRACTION100
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)
13.06251.789-1.50694.1837-2.28663.2027-0.1038-0.5161-0.41640.06680.05770.08840.46490.16730.0460.13060.05190.02450.13140.10720.09193.597518.785814.828
23.92970.8782-2.44043.07750.0063.561-0.11170.3796-0.2016-0.1647-0.003-0.06590.3196-0.58320.11470.5686-0.03870.04210.4470.30520.4114-19.0963-4.23726.546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA163 - 340
2X-RAY DIFFRACTION1ALLA401 - 404
3X-RAY DIFFRACTION1ALLA501 - 519
4X-RAY DIFFRACTION2ALLB102 - 128

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