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- PDB-2xqq: Human dynein light chain (DYNLL2) in complex with an in vitro evo... -

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Basic information

Entry
Database: PDB / ID: 2xqq
TitleHuman dynein light chain (DYNLL2) in complex with an in vitro evolved peptide (Ac-SRGTQTE).
Components
  • DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
  • SAC-ARG-GLY-THR-GLN-THR-GLU
KeywordsPROTEIN TRANSPORT / DIMER INTERFACE
Function / homology
Function and homology information


myosin V complex / Activation of BMF and translocation to mitochondria / 9+0 non-motile cilium / ciliary tip / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / dynein intermediate chain binding / Macroautophagy / microtubule-based process ...myosin V complex / Activation of BMF and translocation to mitochondria / 9+0 non-motile cilium / ciliary tip / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / dynein intermediate chain binding / Macroautophagy / microtubule-based process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / RHO GTPases Activate Formins / cilium / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / postsynapse / microtubule / cytoskeleton / centrosome / glutamatergic synapse / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Dynein light chain 2, cytoplasmic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsRapali, P. / Radnai, L. / Suveges, D. / Hetenyi, C. / Harmat, V. / Tolgyesi, F. / Wahlgren, W.Y. / Katona, G. / Nyitray, L. / Pal, G.
CitationJournal: Plos One / Year: 2011
Title: Directed Evolution Reveals the Binding Motif Preference of the Lc8/Dynll Hub Protein and Predicts Large Numbers of Novel Binders in the Human Proteome
Authors: Rapali, P. / Radnai, L. / Suveges, D. / Harmat, V. / Tolgyesi, F. / Wahlgren, W.Y. / Katona, G. / Nyitray, L. / Pal, G.
History
DepositionSep 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Version format compliance
Revision 1.2Nov 20, 2013Group: Derived calculations / Refinement description
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
B: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
C: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
D: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
E: SAC-ARG-GLY-THR-GLN-THR-GLU
F: SAC-ARG-GLY-THR-GLN-THR-GLU
G: SAC-ARG-GLY-THR-GLN-THR-GLU
H: SAC-ARG-GLY-THR-GLN-THR-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8029
Polymers44,7438
Non-polymers591
Water6,503361
1
A: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
C: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
E: SAC-ARG-GLY-THR-GLN-THR-GLU
G: SAC-ARG-GLY-THR-GLN-THR-GLU


Theoretical massNumber of molelcules
Total (without water)22,3714
Polymers22,3714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-8.4 kcal/mol
Surface area8280 Å2
MethodPISA
2
B: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
F: SAC-ARG-GLY-THR-GLN-THR-GLU
hetero molecules

D: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
H: SAC-ARG-GLY-THR-GLN-THR-GLU


Theoretical massNumber of molelcules
Total (without water)22,4305
Polymers22,3714
Non-polymers591
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area4680 Å2
ΔGint-10.1 kcal/mol
Surface area8600 Å2
MethodPISA
3
D: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
H: SAC-ARG-GLY-THR-GLN-THR-GLU

B: DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
F: SAC-ARG-GLY-THR-GLN-THR-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4305
Polymers22,3714
Non-polymers591
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area4680 Å2
ΔGint-10.1 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.600, 64.000, 151.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.717, 0.3174, -0.6207), (-0.3216, -0.9405, -0.1096), (-0.6185, 0.121, 0.7764)48.24, 53.32, 28.93
2given(0.9454, -0.3202, 0.06079), (-0.32, -0.9473, -0.01308), (0.06178, -0.007088, -0.9981)12.75, 87.97, 53.75
3given(-0.6269, -0.6106, 0.4839), (0.5456, -0.7874, -0.2869), (0.5562, 0.08418, 0.8268)73.72, 37.13, 14.9

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Components

#1: Protein
DYNEIN LIGHT CHAIN 2, CYTOPLASMIC / DYNEIN LIGHT CHAIN LC8-TYPE 2 / 8 KDA DYNEIN LIGHT CHAIN B


Mass: 10364.847 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96FJ2
#2: Protein/peptide
SAC-ARG-GLY-THR-GLN-THR-GLU


Mass: 820.825 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 1.7 Å3/Da / Density % sol: 27.2 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: HANGING DROP VAPOR DIFFUSION AT 293K WITH A RESERVOIR SOLUTION 31% PEG 4000, 0.4 M NH4AC, 0.1 M NAAC PH 4.6, 2UL RESERVOIR SOLUTION AND 2UL PROTEIN SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.31→151.84 Å / Num. obs: 81872 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.66
Reflection shellResolution: 1.31→1.34 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.93 / % possible all: 67.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CMI

1cmi


Resolution: 1.31→151.84 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.17 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15636 4096 5 %RANDOM
Rwork0.12276 ---
obs0.12447 77776 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.471 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.31→151.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 4 361 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223332
X-RAY DIFFRACTIONr_bond_other_d0.0010.022305
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9444519
X-RAY DIFFRACTIONr_angle_other_deg1.06535652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09524.756164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93615639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4271513
X-RAY DIFFRACTIONr_chiral_restr0.1350.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023741
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02692
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4051.51987
X-RAY DIFFRACTIONr_mcbond_other0.9551.5799
X-RAY DIFFRACTIONr_mcangle_it3.4923224
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.09231345
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.4644.51265
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.38215633
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.306→1.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 215 -
Rwork0.185 3930 -
obs--66.87 %

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