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- PDB-4rh7: Crystal structure of human cytoplasmic dynein 2 motor domain in c... -

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Basic information

Entry
Database: PDB / ID: 4rh7
TitleCrystal structure of human cytoplasmic dynein 2 motor domain in complex with ADP.Vi
ComponentsGreen fluorescent protein/Cytoplasmic dynein 2 heavy chain 1
KeywordsMOTOR PROTEIN / AAA+ protein / dynein motor domain
Function / homology
Function and homology information


intraciliary retrograde transport / cilium movement involved in cell motility / 9+2 motile cilium / spinal cord motor neuron differentiation / ciliary tip / Intraflagellar transport / protein localization to cilium / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / non-motile cilium assembly ...intraciliary retrograde transport / cilium movement involved in cell motility / 9+2 motile cilium / spinal cord motor neuron differentiation / ciliary tip / Intraflagellar transport / protein localization to cilium / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / non-motile cilium assembly / coronary vasculature development / dynein light intermediate chain binding / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / determination of left/right symmetry / embryonic limb morphogenesis / dynein intermediate chain binding / Golgi organization / axoneme / cytoskeletal motor activity / Hedgehog 'off' state / forebrain development / kidney development / cilium / protein processing / apical part of cell / microtubule / Golgi apparatus / ATP hydrolysis activity / extracellular exosome / ATP binding / plasma membrane
Similarity search - Function
: / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase 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, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain ...: / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase 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, 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADP ORTHOVANADATE / ADENOSINE-5'-TRIPHOSPHATE / Cytoplasmic dynein 2 heavy chain 1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.41 Å
AuthorsSchmidt, H. / Zalyte, R. / Urnavicius, L. / Carter, A.P.
CitationJournal: Nature / Year: 2015
Title: Structure of human cytoplasmic dynein-2 primed for its power stroke.
Authors: Schmidt, H. / Zalyte, R. / Urnavicius, L. / Carter, A.P.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,9177
Polymers392,9631
Non-polymers1,9546
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.030, 487.150, 276.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1


Mass: 392963.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Homo sapiens (human)
Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NCM8
#2: Chemical ChemComp-AOV / ADP ORTHOVANADATE


Mass: 544.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O14P2V / Comment: energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 5.83 Å3/Da / Density % sol: 78.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: mixing equal volumes of protein (8mg/ml) and reservoir solution (4-6 % PEG 6000 and 0.1 M Tris pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.4→56.5 Å / Num. obs: 78411 / % possible obs: 62.2 % / Redundancy: 4.1 % / Rsym value: 0.101 / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.41→56.6 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.886 / SU B: 35.363 / SU ML: 0.532 / Cross valid method: THROUGHOUT / ESU R Free: 0.643 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28546 3915 5 %RANDOM
Rwork0.23746 ---
obs0.23989 74060 62.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.28 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 3.41→56.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22697 0 119 0 22816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01923272
X-RAY DIFFRACTIONr_bond_other_d0.0060.0221480
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.96631669
X-RAY DIFFRACTIONr_angle_other_deg0.846349143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26953000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23424.481973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.385153715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.715121
X-RAY DIFFRACTIONr_chiral_restr0.0730.23633
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0226721
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025304
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_it8.24112.30712015
X-RAY DIFFRACTIONr_mcbond_other8.24112.30612014
X-RAY DIFFRACTIONr_mcangle_it13.70618.45115010
X-RAY DIFFRACTIONr_mcangle_other13.67718.43915011
X-RAY DIFFRACTIONr_scbond_it8.50811.82811257
X-RAY DIFFRACTIONr_scbond_other8.49311.81211256
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.65617.58516656
X-RAY DIFFRACTIONr_long_range_B_refined25.39101750
X-RAY DIFFRACTIONr_long_range_B_other25.39101751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.406→3.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.541 14 -
Rwork0.345 209 -
obs--2.44 %

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