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- PDB-3p8m: Human dynein light chain (DYNLL2) in complex with an in vitro evo... -

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Basic information

Entry
Database: PDB / ID: 3p8m
TitleHuman dynein light chain (DYNLL2) in complex with an in vitro evolved peptide dimerized by leucine zipper
Components
  • Dynein light chain 2
  • General control protein GCN4
KeywordsPROTEIN BINDING / Phage display / Leucine zipper / Hub protein
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 / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding ...myosin V complex / Activation of BMF and translocation to mitochondria / 9+0 non-motile cilium / ciliary tip / Intraflagellar transport / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / COPI-independent Golgi-to-ER retrograde traffic / nitrogen catabolite activation of transcription from RNA polymerase II promoter / cytoplasmic dynein complex / Oxidative Stress Induced Senescence / dynein intermediate chain binding / Macroautophagy / microtubule-based process / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / amino acid biosynthetic process / 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 / cellular response to amino acid starvation / RHO GTPases Activate Formins / cilium / Aggrephagy / HCMV Early Events / RNA polymerase II transcription regulator complex / Separation of Sister Chromatids / : / postsynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / cytoskeleton / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / centrosome / glutamatergic synapse / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / 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 / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 ...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 / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
General control transcription factor GCN4 / Dynein light chain 2, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionOct 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 2
B: Dynein light chain 2
D: General control protein GCN4
C: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)31,5164
Polymers31,5164
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-42 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.839, 68.415, 101.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C
13D
23C

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSERAA5 - 888 - 91
21LYSLYSSERSERBB5 - 888 - 91
12SERSERTHRTHRDC131 - 1382 - 9
22SERSERTHRTHRCD131 - 1382 - 9
13METMETARGARGDC144 - 16715 - 38
23METMETARGARGCD144 - 16715 - 38

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Dynein light chain 2 / 8 kDa dynein light chain b / DLC8b / Dynein light chain LC8-type 2


Mass: 10647.124 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLL2, DLC2 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q96FJ2
#2: Protein/peptide General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 5110.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCN4, AAS3, ARG9, YEL009C / Plasmid: modified pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P03069
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE IN VITRO EVOLVED BINDING SEQUENCE.

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / pH: 7
Details: 20% PEG8000, 0.2 M MgCl2, 0.1 M TRIS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2010 / Details: OSMIC BLUE
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→56.76 Å / Num. obs: 8273 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 3.23 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.12 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 1.5 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0102refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XQQ

2xqq


Resolution: 2.9→42.31 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.894 / SU B: 46.408 / SU ML: 0.391 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 385 4.7 %RANDOM
Rwork0.248 ---
obs0.25 7886 94.4 %-
all-7886 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å20 Å20 Å2
2--1.47 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 0 41 2016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222037
X-RAY DIFFRACTIONr_bond_other_d0.0050.021315
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9472756
X-RAY DIFFRACTIONr_angle_other_deg2.41633227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69625.32692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.64415344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.12155
X-RAY DIFFRACTIONr_chiral_restr0.0630.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
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_it0.1751.51291
X-RAY DIFFRACTIONr_mcbond_other0.0531.5534
X-RAY DIFFRACTIONr_mcangle_it0.30522050
X-RAY DIFFRACTIONr_scbond_it0.5233746
X-RAY DIFFRACTIONr_scangle_it0.8374.5701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A494tight positional0.030.05
21D46tight positional0.030.05
31D142tight positional0.040.05
12B553loose positional0.035
22C49loose positional0.035
32C146loose positional0.065
11A494tight thermal0.080.5
21D46tight thermal0.080.5
31D142tight thermal0.050.5
12B553loose thermal0.110
22C49loose thermal0.0910
32C146loose thermal0.0710
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 33 -
Rwork0.328 586 -
obs--96.72 %
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)
17.2897-0.35560.71824.08680.76044.33550.0449-0.2660.12380.5119-0.0707-0.0328-0.3797-0.06730.02580.1926-0.07370.02380.267-0.08750.19383.399423.189410.444
28.1608-0.1169-1.91094.18021.84214.3899-0.12170.3255-1.31680.11460.2544-0.31780.86670.0943-0.13270.2118-0.0279-0.07040.3339-0.1880.58724.9485.21670.7907
38.49732.8792-0.65937.69472.0110.79880.24040.3878-0.11910.5806-0.24080.24670.131-0.12190.00040.0784-0.05760.04560.5328-0.13690.501814.296416.1357.7514
414.89930.9239-7.91795.5659-1.959813.28110.817-0.33030.97040.24620.08580.4338-0.76790.3303-0.90280.43070.01310.02510.2847-0.04160.5319-1.26326.121546.013
516.8751-1.39161.34688.45412.91551.20780.54510.6379-2.2845-0.1365-0.42790.84040.0209-0.0052-0.11720.083-0.00950.0180.3819-0.20580.6278-5.596311.81344.8656
62.78041.2551-6.35583.7292.205334.7805-0.45930.27470.31720.0521-0.56251.1145-1.2478-1.00991.02180.8320.00350.09770.58670.07860.7852-5.501212.212843.1662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 89
2X-RAY DIFFRACTION2B3 - 89
3X-RAY DIFFRACTION3D130 - 139
4X-RAY DIFFRACTION4D140 - 172
5X-RAY DIFFRACTION5C131 - 139
6X-RAY DIFFRACTION6C140 - 172

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