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- PDB-6l4p: Crystal structure of the complex between the axonemal outer-arm d... -

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Basic information

Entry
Database: PDB / ID: 6l4p
TitleCrystal structure of the complex between the axonemal outer-arm dynein light chain-1 and microtubule binding domain of gamma heavy chain
Components
  • Dynein light chain 1, axonemal
  • Flagellar outer dynein arm heavy chain gamma
KeywordsCONTRACTILE PROTEIN/MOTOR PROTEIN / Motor protein / Complex / CONTRACTILE PROTEIN-MOTOR PROTEIN complex
Function / homology
Function and homology information


outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / dynein heavy chain binding / axonemal dynein complex / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding ...outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / dynein heavy chain binding / axonemal dynein complex / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / microtubule-based movement / alpha-tubulin binding / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / P-loop containing dynein motor region ...Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Flagellar outer dynein arm heavy chain gamma / Dynein gamma chain, flagellar outer arm / Dynein axonemal light chain 1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsToda, A. / Nishikawa, Y. / Tanaka, H. / Yagi, T. / Kurisu, G.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17J075530 Japan
Japan Society for the Promotion of Science26291014 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The complex of outer-arm dynein light chain-1 and the microtubule-binding domain of the gamma heavy chain shows how axonemal dynein tunes ciliary beating.
Authors: Toda, A. / Nishikawa, Y. / Tanaka, H. / Yagi, T. / Kurisu, G.
History
DepositionOct 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 1, axonemal
B: Flagellar outer dynein arm heavy chain gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7125
Polymers38,4722
Non-polymers2403
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-25 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.550, 73.028, 94.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Dynein light chain 1, axonemal / DNAL1 / Flagellar outer arm dynein light chain 1 / ODA-LC protein LC1


Mass: 22236.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: LC1, CHLREDRAFT_186669 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XHH2
#2: Protein Flagellar outer dynein arm heavy chain gamma


Mass: 16235.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: ODA2, CHLREDRAFT_155136 / Production host: Escherichia coli (E. coli) / References: UniProt: A8JFP1, UniProt: Q39575*PLUS

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Non-polymers , 4 types, 160 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, sodium phosphate monobasic monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→39.69 Å / Num. obs: 31841 / % possible obs: 92.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 31.7
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.766 / Num. unique obs: 174389

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YXM

5yxm


Resolution: 1.703→39.689 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.72
RfactorNum. reflection% reflection
Rfree0.2139 1542 4.85 %
Rwork0.1725 --
obs0.1746 31794 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.86 Å2 / Biso mean: 22.5087 Å2 / Biso min: 6.12 Å2
Refinement stepCycle: final / Resolution: 1.703→39.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 14 157 2792
Biso mean--35.42 25.72 -
Num. residues----333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062737
X-RAY DIFFRACTIONf_angle_d0.7943710
X-RAY DIFFRACTIONf_chiral_restr0.054431
X-RAY DIFFRACTIONf_plane_restr0.005477
X-RAY DIFFRACTIONf_dihedral_angle_d5.7242392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7031-1.75810.32531240.2374260289
1.7581-1.82090.27361430.2194263690
1.8209-1.89380.26151240.2031265991
1.8938-1.980.23841550.1947265991
1.98-2.08440.22741230.1721268990
2.0844-2.2150.21631410.175268690
2.215-2.3860.19431220.1764266489
2.386-2.6260.21991540.1816265690
2.626-3.00590.25781330.1892282994
3.0059-3.78670.1951670.16153005100
3.7867-39.6890.17051560.1429316799

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