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Basic information

Entry
Database: PDB / ID: 3l9k
TitleInsights into dynein assembly from a dynein intermediate chain-light chain roadblock structure
Components
  • Dynein intermediate chain, cytosolic
  • RE64145p
KeywordsMOTOR PROTEIN / dynein / intermediate chain / IC / LC7 / light chain 7 / km23 / roadblock / Hydrolase / Lysosome / Membrane / Microtubule / Nucleus / WD repeat
Function / homology
Function and homology information


cellularization / axonemal dynein complex / eye photoreceptor cell differentiation / mushroom body development / Aggrephagy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / transport along microtubule / sperm individualization ...cellularization / axonemal dynein complex / eye photoreceptor cell differentiation / mushroom body development / Aggrephagy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / transport along microtubule / sperm individualization / dynein light chain binding / dynein heavy chain binding / cytoplasmic dynein complex / protein localization to kinetochore / axo-dendritic transport / dendrite morphogenesis / centrosome localization / spindle organization / dynein intermediate chain binding / microtubule-based movement / dynactin binding / microtubule cytoskeleton organization / nuclear membrane / microtubule / molecular adaptor activity / neuron projection / lysosomal membrane / centrosome / protein-containing complex / cytoplasm
Similarity search - Function
Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain roadblock-type 1/2 / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / WD domain, G-beta repeat / WD40 repeats ...Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain roadblock-type 1/2 / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cytoplasmic dynein 1 intermediate chain / Dynein light chain roadblock
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHall, J. / Karplus, P.A. / Barbar, E.
CitationJournal: To be Published
Title: Insights into dynein assembly from a dynein intermediate chain-light chain roadblock structure
Authors: Hall, J. / Karplus, P.A. / Barbar, E.
History
DepositionJan 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Sep 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RE64145p
B: RE64145p
C: RE64145p
D: RE64145p
W: Dynein intermediate chain, cytosolic
X: Dynein intermediate chain, cytosolic
Y: Dynein intermediate chain, cytosolic
Z: Dynein intermediate chain, cytosolic


Theoretical massNumber of molelcules
Total (without water)61,3028
Polymers61,3028
Non-polymers00
Water0
1
A: RE64145p
Y: Dynein intermediate chain, cytosolic


Theoretical massNumber of molelcules
Total (without water)15,3262
Polymers15,3262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-20 kcal/mol
Surface area8200 Å2
MethodPISA
2
B: RE64145p
Z: Dynein intermediate chain, cytosolic


Theoretical massNumber of molelcules
Total (without water)15,3262
Polymers15,3262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-20 kcal/mol
Surface area8180 Å2
MethodPISA
3
C: RE64145p
W: Dynein intermediate chain, cytosolic


Theoretical massNumber of molelcules
Total (without water)15,3262
Polymers15,3262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-20 kcal/mol
Surface area8180 Å2
MethodPISA
4
D: RE64145p
X: Dynein intermediate chain, cytosolic


Theoretical massNumber of molelcules
Total (without water)15,3262
Polymers15,3262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-19 kcal/mol
Surface area8150 Å2
MethodPISA
5
A: RE64145p
B: RE64145p
Y: Dynein intermediate chain, cytosolic
Z: Dynein intermediate chain, cytosolic


Theoretical massNumber of molelcules
Total (without water)30,6514
Polymers30,6514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-54 kcal/mol
Surface area13560 Å2
MethodPISA
6
C: RE64145p
D: RE64145p
W: Dynein intermediate chain, cytosolic
X: Dynein intermediate chain, cytosolic


Theoretical massNumber of molelcules
Total (without water)30,6514
Polymers30,6514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-53 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.180, 107.180, 65.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17W
27X
18W
28Y
19W
29Z
110X
210Y
111X
211Z
112Y
212Z

NCS domain segments:

Component-ID: 1 / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA3 - 963 - 96
21GLNGLNBB3 - 963 - 96
12GLNGLNAA3 - 963 - 96
22GLNGLNCC3 - 963 - 96
13GLNGLNAA3 - 963 - 96
23GLNGLNDD3 - 963 - 96
14GLNGLNBB3 - 963 - 96
24GLNGLNCC3 - 963 - 96
15GLNGLNBB3 - 963 - 96
25GLNGLNDD3 - 963 - 96
16GLNGLNCC3 - 963 - 96
26GLNGLNDD3 - 963 - 96
17LEULEUWE221 - 2581 - 38
27LEULEUXF221 - 2581 - 38
18LEULEUWE221 - 2581 - 38
28LEULEUYG221 - 2581 - 38
19LEULEUWE221 - 2581 - 38
29LEULEUZH221 - 2581 - 38
110LEULEUXF221 - 2581 - 38
210LEULEUYG221 - 2581 - 38
111LEULEUXF221 - 2581 - 38
211LEULEUZH221 - 2581 - 38
112LEULEUYG221 - 2581 - 38
212LEULEUZH221 - 2581 - 38

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
RE64145p / Roadblock


Mass: 10837.399 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: robl, CG10751, Dmel_CG10751 / Plasmid: pET15Da / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7KMS3
#2: Protein/peptide
Dynein intermediate chain, cytosolic / DH IC / Cytoplasmic dynein intermediate chain / Protein short wing


Mass: 4488.108 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sw, Cdic, Dic19B, CG18000 / Plasmid: pET15Da / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q24246

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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: 3.54 Å3/Da / Density % sol: 65.24 %
Crystal growTemperature: 277.15 K / pH: 7
Details: 1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 133.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2009
RadiationMonochromator: KOHZU: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→92.82 Å / Num. obs: 16845 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.09 / Rsym value: 0.07 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.15 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.402 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0101refinement
HKL-2000data reduction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HZ5

2hz5


Resolution: 3→92.8 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 30.714 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 1.146 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 923 4.9 %RANDOM
Rwork0.227 ---
obs0.228 16845 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 3→92.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 0 0 4180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224151
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9625614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0624.583192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.54215761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0821536
X-RAY DIFFRACTIONr_chiral_restr0.1320.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213056
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.4861.52631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.07424282
X-RAY DIFFRACTIONr_scbond_it6.82231520
X-RAY DIFFRACTIONr_scangle_it11.7014.51332
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1710tight positional0.030.05
2708tight positional0.040.05
3710tight positional0.030.05
4710tight positional0.030.05
5714tight positional0.010.05
6710tight positional0.030.05
7314tight positional0.040.05
8314tight positional0.040.05
9314tight positional0.040.05
10314tight positional0.010.05
11314tight positional0.010.05
12314tight positional0.010.05
1710tight thermal0.030.5
2708tight thermal0.030.5
3710tight thermal0.030.5
4710tight thermal0.030.5
5714tight thermal0.030.5
6710tight thermal0.030.5
7314tight thermal0.020.5
8314tight thermal0.020.5
9314tight thermal0.020.5
10314tight thermal0.020.5
11314tight thermal0.020.5
12314tight thermal0.020.5
LS refinement shellResolution: 3→3.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.019 2 -
Rwork0.521 82 -
obs--4.86 %
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)
11.8877-0.5382-0.89740.88371.84664.99360.1361-0.15450.05310.06270.126-0.04310.34840.6934-0.26210.17370.0227-0.02730.2859-0.01350.1567-15.3665-27.2472-9.5611
20.57770.3371.2662.4614-2.06176.33510.09960.1087-0.035-0.1350.1890.10570.7188-0.0339-0.28860.2749-0.0442-0.02270.168-0.02120.176-22.2909-31.2351-29.2742
30.41130.12040.61133.60881.85196.16370.0684-0.1173-0.10660.1690.1255-0.22220.76710.1215-0.19390.230.0478-0.02490.1650.02460.197322.3665-31.29411.328
41.54431.1015-0.89611.1493-1.72025.89890.15590.16570.1337-0.0460.08490.16430.2616-0.7191-0.24080.14520.009-0.03650.28080.01130.200715.3422-27.2217-18.3563
51.3659-1.5517-0.93210.5415-1.62721.8541-0.1326-0.45520.0350.67370.0938-0.7007-0.06280.58680.03880.27210.096-0.09880.31690.03920.194630.3877-29.71866.0593
610.18954.25490.77032.77531.63481.52320.00730.7710.5916-0.4301-0.010.2689-0.4897-0.22520.00280.24470.103-0.12460.40720.02240.229912.6832-19.5007-23.1008
710.1909-4.18511.17472.294-1.22152.1915-0.0777-0.72840.61020.37490.0553-0.3415-0.5980.23680.02240.2381-0.1075-0.09270.3543-0.02890.2126-12.6603-19.4728-4.8433
80.96421.1312-0.739611.37992.14572.0385-0.10720.3942-0.0143-0.64670.04930.686-0.0206-0.69620.05790.2554-0.1252-0.07340.3546-0.0230.2142-30.365-29.7113-33.9869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 96
2X-RAY DIFFRACTION2B3 - 96
3X-RAY DIFFRACTION3C3 - 96
4X-RAY DIFFRACTION4D3 - 96
5X-RAY DIFFRACTION5W221 - 258
6X-RAY DIFFRACTION6X221 - 258
7X-RAY DIFFRACTION7Y221 - 258
8X-RAY DIFFRACTION8Z221 - 258

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