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- PDB-3n8e: Substrate binding domain of the human Heat Shock 70kDa protein 9 ... -

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Basic information

Entry
Database: PDB / ID: 3n8e
TitleSubstrate binding domain of the human Heat Shock 70kDa protein 9 (mortalin)
ComponentsStress-70 protein, mitochondrial
KeywordsCHAPERONE / beta-sandwich / helix / substrate binding domain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of hemopoiesis / MIB complex / negative regulation of hematopoietic stem cell differentiation / SAM complex / negative regulation of erythrocyte differentiation / TIM23 mitochondrial import inner membrane translocase complex / Cristae formation / inner mitochondrial membrane organization / Mitochondrial protein import / iron-sulfur cluster assembly ...negative regulation of hemopoiesis / MIB complex / negative regulation of hematopoietic stem cell differentiation / SAM complex / negative regulation of erythrocyte differentiation / TIM23 mitochondrial import inner membrane translocase complex / Cristae formation / inner mitochondrial membrane organization / Mitochondrial protein import / iron-sulfur cluster assembly / mitochondrial nucleoid / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / protein folding chaperone / heat shock protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / protein export from nucleus / erythrocyte differentiation / ATP-dependent protein folding chaperone / intracellular protein transport / regulation of erythrocyte differentiation / unfolded protein binding / protein refolding / mitochondrial inner membrane / mitochondrial matrix / focal adhesion / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / 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 ...Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / 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
Stress-70 protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWisniewska, M. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Wisniewska, M. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Substrate binding domain of the human Heat Shock 70kDa protein 9 (mortalin)
Authors: Wisniewska, M. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / ...Authors: Wisniewska, M. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Siponem, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stress-70 protein, mitochondrial
B: Stress-70 protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)40,0692
Polymers40,0692
Non-polymers00
Water84747
1
A: Stress-70 protein, mitochondrial

B: Stress-70 protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)40,0692
Polymers40,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area2340 Å2
ΔGint-16 kcal/mol
Surface area16330 Å2
MethodPISA
2
A: Stress-70 protein, mitochondrial
B: Stress-70 protein, mitochondrial

A: Stress-70 protein, mitochondrial
B: Stress-70 protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)80,1384
Polymers80,1384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area6630 Å2
ΔGint-52 kcal/mol
Surface area30710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.680, 118.680, 159.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-100-

HOH

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Components

#1: Protein Stress-70 protein, mitochondrial / 75 kDa glucose-regulated protein / GRP-75 / Heat shock 70 kDa protein 9 / Peptide-binding protein ...75 kDa glucose-regulated protein / GRP-75 / Heat shock 70 kDa protein 9 / Peptide-binding protein 74 / PBP74 / Mortalin / MOT


Mass: 20034.521 Da / Num. of mol.: 2 / Fragment: substrate binding domain residues 439-597
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRP75, HSPA9, HSPA9B / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) R3 pRARE / References: UniProt: P38646
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.06 Å3/Da / Density % sol: 69.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M sodium chloride, 20% PEG 8000, 0.1 M citric acid, 0.1 M di-sodium hydrogen phosphate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 18, 2010 / Details: mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→35 Å / Num. obs: 16980 / % possible obs: 99.8 % / Redundancy: 41.9 % / Biso Wilson estimate: 74 Å2 / Rsym value: 0.11
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 43.8 % / Mean I/σ(I) obs: 5.82 / Num. unique all: 1219 / Rsym value: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→34.94 Å / Cor.coef. Fo:Fc: 0.9125 / Cor.coef. Fo:Fc free: 0.8842 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 998 5.88 %RANDOM
Rwork0.2063 ---
obs0.2085 16980 --
Displacement parametersBiso mean: 57.67 Å2
Baniso -1Baniso -2Baniso -3
1-10.6526 Å20 Å20 Å2
2--10.6526 Å20 Å2
3----21.3051 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 0 47 2473
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0124502
X-RAY DIFFRACTIONt_angle_deg1.2133002
X-RAY DIFFRACTIONt_dihedral_angle_d11982
X-RAY DIFFRACTIONt_trig_c_planes842
X-RAY DIFFRACTIONt_gen_planes3445
X-RAY DIFFRACTIONt_it245020
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion3.53
X-RAY DIFFRACTIONt_chiral_improper_torsion3425
X-RAY DIFFRACTIONt_ideal_dist_contact26914
LS refinement shellResolution: 2.8→2.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3078 160 5.96 %
Rwork0.2464 2525 -
all0.2499 2685 -

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