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- PDB-8i3j: Crystal structure of human inner-arm dynein heavy chain d stalk a... -

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Basic information

Entry
Database: PDB / ID: 8i3j
TitleCrystal structure of human inner-arm dynein heavy chain d stalk and microtubule binding domain
ComponentsDynein axonemal heavy chain 1
KeywordsMOTOR PROTEIN / CONTRACTILE PROTEIN
Function / homology
Function and homology information


inner dynein arm / axonemal dynein complex / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility / epithelial cilium movement involved in extracellular fluid movement / flagellated sperm motility / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / microtubule motor activity ...inner dynein arm / axonemal dynein complex / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility / epithelial cilium movement involved in extracellular fluid movement / flagellated sperm motility / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / microtubule motor activity / dynein intermediate chain binding / axoneme / sperm flagellum / microtubule / extracellular region / ATP binding
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 / P-loop containing dynein motor region / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain ...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 / P-loop containing dynein motor region / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynein axonemal heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsKo, S. / Yu, J. / Toda, A. / Tanaka, H. / Kurisu, G.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02390 Japan
CitationJournal: Febs Lett. / Year: 2023
Title: Crystal structure of the stalk region of axonemal inner-arm dynein-d reveals unique features in the coiled-coil and microtubule-binding domain.
Authors: Ko, S. / Toda, A. / Tanaka, H. / Yu, J. / Kurisu, G.
History
DepositionJan 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type
Revision 1.2Sep 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein axonemal heavy chain 1


Theoretical massNumber of molelcules
Total (without water)31,4881
Polymers31,4881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.468, 147.468, 85.075
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Dynein axonemal heavy chain 1 / Axonemal beta dynein heavy chain 1 / Ciliary dynein heavy chain 1 / Heat shock regulated protein 1 ...Axonemal beta dynein heavy chain 1 / Ciliary dynein heavy chain 1 / Heat shock regulated protein 1 / HSRF-1 / hDHC7


Mass: 31487.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAH1, DHC7, DNAHC1, KIAA1410 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P2D7
Has ligand of interestY

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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: 4.3 Å3/Da / Density % sol: 71.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Potassium sodium tartrate tetrahydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97938 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 28811 / % possible obs: 98.66 % / Redundancy: 20.9 % / Biso Wilson estimate: 83.35 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1231 / Rpim(I) all: 0.02019 / Rrim(I) all: 0.1248 / Net I/σ(I): 24.83
Reflection shellResolution: 2.69→2.85 Å / Redundancy: 19.4 % / Mean I/σ(I) obs: 2.12 / Num. unique obs: 4588 / CC1/2: 0.975 / Rrim(I) all: 2.062 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXCDphasing
AutoSolphasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: SAD / Resolution: 2.69→42.57 Å / SU ML: 0.4326 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.8169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 1450 5.1 %
Rwork0.2577 26987 -
obs0.2582 28437 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.64 Å2
Refinement stepCycle: LAST / Resolution: 2.69→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 0 0 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032201
X-RAY DIFFRACTIONf_angle_d1.42192963
X-RAY DIFFRACTIONf_chiral_restr0.0712334
X-RAY DIFFRACTIONf_plane_restr0.0121391
X-RAY DIFFRACTIONf_dihedral_angle_d21.3423870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.780.45761110.46282663X-RAY DIFFRACTION94.74
2.78-2.890.39951530.42132672X-RAY DIFFRACTION97.78
2.89-3.030.42841530.37722626X-RAY DIFFRACTION97.58
3.03-3.180.39221660.37562646X-RAY DIFFRACTION98.12
3.18-3.380.36381540.35922736X-RAY DIFFRACTION99.18
3.38-3.650.38721230.31492729X-RAY DIFFRACTION98.51
3.65-4.010.29671480.28112696X-RAY DIFFRACTION98.99
4.01-4.590.26441550.2352728X-RAY DIFFRACTION99.62
4.59-5.780.31951580.23342727X-RAY DIFFRACTION99.9
5.78-42.570.1361290.19262764X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 43.3415987532 Å / Origin y: 34.9466311044 Å / Origin z: 84.5638404472 Å
111213212223313233
T1.29501662217 Å20.172091310828 Å20.0396673271483 Å2-0.955822881575 Å20.0218315931764 Å2--1.06649208363 Å2
L1.06830148529 °2-0.928251446196 °2-1.25776412633 °2-1.25679665457 °22.1008395432 °2--3.41999758956 °2
S0.325644872542 Å °0.313612666843 Å °0.0191353214538 Å °-0.249484894968 Å °-0.317902855817 Å °0.00633504951394 Å °-0.3898033474 Å °-0.535423903393 Å °0.0161114784581 Å °
Refinement TLS groupSelection details: all

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