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- PDB-6e8m: Legionella Longbeachae LeSH (Llo2327) bound to the human DnaJ-A1 ... -

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Basic information

Entry
Database: PDB / ID: 6e8m
TitleLegionella Longbeachae LeSH (Llo2327) bound to the human DnaJ-A1 pTyr381 peptide
Components
  • DnaJ-A1 pTyr381 peptide
  • LeSH (Llo2327)
KeywordsPEPTIDE BINDING PROTEIN / Src homology 2 domain
Function / homology
Function and homology information


negative regulation of JUN kinase activity / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / regulation of protein transport / C3HC4-type RING finger domain binding / protein localization to mitochondrion / Tat protein binding / negative regulation of establishment of protein localization to mitochondrion / low-density lipoprotein particle receptor binding / cytoplasmic side of endoplasmic reticulum membrane / ATPase activator activity ...negative regulation of JUN kinase activity / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / regulation of protein transport / C3HC4-type RING finger domain binding / protein localization to mitochondrion / Tat protein binding / negative regulation of establishment of protein localization to mitochondrion / low-density lipoprotein particle receptor binding / cytoplasmic side of endoplasmic reticulum membrane / ATPase activator activity / response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / negative regulation of protein ubiquitination / Hsp70 protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / G protein-coupled receptor binding / unfolded protein binding / protein folding / protein-folding chaperone binding / microtubule cytoskeleton / response to heat / protein refolding / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / zinc ion binding / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. ...DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
SH2 domain-containing protein / DnaJ homolog subfamily A member 1
Similarity search - Component
Biological speciesLegionella longbeachae serogroup 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsKaneko, T. / Li, S.S.C.
CitationJournal: Nat Commun / Year: 2018
Title: Identification and characterization of a large family of superbinding bacterial SH2 domains.
Authors: Kaneko, T. / Stogios, P.J. / Ruan, X. / Voss, C. / Evdokimova, E. / Skarina, T. / Chung, A. / Liu, X. / Li, L. / Savchenko, A. / Ensminger, A.W. / Li, S.S.
History
DepositionJul 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 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: LeSH (Llo2327)
B: DnaJ-A1 pTyr381 peptide


Theoretical massNumber of molelcules
Total (without water)21,4702
Polymers21,4702
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-7 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.900, 64.710, 67.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein LeSH (Llo2327)


Mass: 19771.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella longbeachae serogroup 1 (strain NSW150) (bacteria)
Strain: NSW150 / Gene: LLO_2327 / Production host: Escherichia coli (E. coli) / References: UniProt: D3HJY4
#2: Protein/peptide DnaJ-A1 pTyr381 peptide / DnaJ homolog subfamily A member 1 / DnaJ protein homolog 2 / HSDJ / Heat shock 40 kDa protein 4 / ...DnaJ homolog subfamily A member 1 / DnaJ protein homolog 2 / HSDJ / Heat shock 40 kDa protein 4 / Heat shock protein J2 / HSJ-2 / Human DnaJ protein 2 / hDj-2


Mass: 1698.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P31689
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion / Details: PEG3000, malic acid, Tris-HCl

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Data collection

DiffractionMean temperature: 114 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→33.92 Å / Num. obs: 22071 / % possible obs: 90.3 % / Redundancy: 11 % / Biso Wilson estimate: 22.21 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3192 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E8H

6e8h


Resolution: 1.61→24.21 Å / SU ML: 0.1863 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8337
RfactorNum. reflection% reflection
Rfree0.2123 2092 5.08 %
Rwork0.1986 --
obs0.1992 41196 91.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.04 Å2
Refinement stepCycle: LAST / Resolution: 1.61→24.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 0 146 1469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631354
X-RAY DIFFRACTIONf_angle_d0.84251821
X-RAY DIFFRACTIONf_chiral_restr0.061197
X-RAY DIFFRACTIONf_plane_restr0.0057227
X-RAY DIFFRACTIONf_dihedral_angle_d3.3918831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.33071560.28872747X-RAY DIFFRACTION96.22
1.65-1.690.27351480.24442850X-RAY DIFFRACTION100
1.69-1.730.30461680.25182858X-RAY DIFFRACTION100
1.73-1.780.23421470.2232876X-RAY DIFFRACTION100
1.78-1.840.21371470.20592858X-RAY DIFFRACTION100
1.84-1.910.24751340.23152152X-RAY DIFFRACTION76.15
1.91-1.980.38281010.26441487X-RAY DIFFRACTION53.22
1.98-2.070.20321560.1982748X-RAY DIFFRACTION100
2.07-2.180.2096940.18252521X-RAY DIFFRACTION100
2.18-2.320.22441040.23732336X-RAY DIFFRACTION81.25
2.32-2.50.19521610.20632838X-RAY DIFFRACTION100
2.5-2.750.20791700.20032608X-RAY DIFFRACTION91.83
2.75-3.150.23731580.19832843X-RAY DIFFRACTION100
3.15-3.960.16541420.17752534X-RAY DIFFRACTION88.76
3.96-24.220.17821060.17222848X-RAY DIFFRACTION98.3
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)
13.046546509181.04142645049-1.358826181912.897933952030.9828479946693.039086343520.0124891499677-0.1113512703750.3000675858060.0183978389287-0.02761569727630.00175145240687-0.518864907756-0.133910477564-0.1182880166960.201806823829-0.0006839578840730.01709054060210.170241807589-0.03531933136170.1955018107568.9857054962439.698249291113.720770055
26.23008938616-0.1525577086072.239474643873.312685420580.3056671332517.27537057080.137317147023-0.7306522034680.07248566266190.432963870586-0.03579550284120.1048931610870.198707767576-0.468555839079-0.0408598930650.255125936686-0.038061802045-0.01020323728460.215836430137-0.004545370526110.1430070341412.1670706479530.672743631522.6846570834
33.788415841690.126846979688-0.7798296787372.91172608540.620056546653.128181984970.0283721449940.03613217868480.1542441506850.08802626905830.05620813806290.1317240654590.127086579721-0.131588574438-0.03028014952720.0989826033527-0.00151871889922-0.01012081515390.09606193391840.003998819403180.08142571210694.0477190534928.696309907113.0728059377
42.58161290780.353628914933-1.182398610492.34636165450.2544412493423.15031454871-0.06913885944110.0955958042412-0.0347880899157-0.06557950242770.0704700602490.1166263704260.25418445556-0.07635338252940.02806841533260.137124587209-0.00507209974294-0.01983428078790.115837837299-0.001891718827490.1376276655726.7089837201324.2873944838.5733320889
51.43329131798-0.4405967919171.193437970758.11627111216-6.069178027286.771074809180.078045727632-0.768995308312-0.6858529800741.063660057360.2733643422760.6001206939590.156775886641-0.120551608098-0.6644394444190.4615562125570.06309880706860.0921368393110.4382673257390.1248215298970.42152938042713.36026885539.7262881658515.32329943
62.9009320655-1.476282581731.422054824422.9940994168-3.719326742195.77248855709-0.0182763865751-0.139846379432-0.1493454572540.115001152337-0.114517617103-0.7311172009450.05444295027820.1160991303940.08471061875610.2125060303380.03792484448560.03602629100780.24969463387-0.03937725000610.20583966801721.078976601616.73847784016.27888554633
70.1485001232290.007628742990750.2022018991520.08402360133580.1409639417490.458676500272-0.3380686760870.4801415029650.718832518195-1.06770528830.643097859943-1.19043207003-1.79482571071.55678995779-0.5798219412920.7845565657-0.01979513999670.04673200948670.88580643416-0.1569290311340.6299716856315.995402183341.1446155993-1.87956895313
82.456373835260.7891758285-0.5868239067934.968902306022.773202630225.896812941710.07428388338190.2723102373390.195739665192-0.1648154075440.22048167359-0.100707526966-0.3562554947210.0226175141206-0.2739415938180.1796837192010.0443214812667-0.003590451850130.1767614298510.05140035526690.1903011254226.3634912222436.37616718026.2672226582
91.999926446581.99966912459-7.313180562241.999903337052.000186830852.00017402001-0.786623387504-0.721811126357-0.8744116020352.285003022741.265279146862.04039548921-0.291590359182-0.107225750338-0.5155676161110.603923037847-0.079891760372-0.1521493848030.4957254187220.451325559710.3695787620197.837326308318.761603150815.868284444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 81 )
5X-RAY DIFFRACTION5chain 'A' and (resid 82 through 94 )
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 125 )
7X-RAY DIFFRACTION7chain 'A' and (resid 126 through 131 )
8X-RAY DIFFRACTION8chain 'A' and (resid 132 through 167 )
9X-RAY DIFFRACTION9chain 'B' and (resid 380 through 380 )

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