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- PDB-4akg: Dynein Motor Domain - ATP complex -

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Basic information

Entry
Database: PDB / ID: 4akg
TitleDynein Motor Domain - ATP complex
ComponentsGLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC
KeywordsMOTOR PROTEIN / AAA+ PROTEIN / ASCE PROTEIN / P-LOOP NTPASE / CYTOSKELETAL MOTOR / ATPASE
Function / homology
Function and homology information


karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / spindle pole body / nuclear migration / dynein intermediate chain binding ...karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / spindle pole body / nuclear migration / dynein intermediate chain binding / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / glutathione transferase / glutathione transferase activity / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #740 / Monooxygenase - #160 / Dynein motor, AAA2 domain, small subdomain / Dynein motor, AAA1 domain, small subdomain / Region D6 of dynein motor / Dynein motor heavy chain, linker domain, N-terminal subdomain / Dynein motor heavy chain, linker domain, subdomain 4 / Histone Acetyltransferase; Chain A - #20 / Histone Acetyltransferase; Chain A - #30 / Dynein motor heavy chain, linker domain, subdomain 3 ...Helicase, Ruva Protein; domain 3 - #740 / Monooxygenase - #160 / Dynein motor, AAA2 domain, small subdomain / Dynein motor, AAA1 domain, small subdomain / Region D6 of dynein motor / Dynein motor heavy chain, linker domain, N-terminal subdomain / Dynein motor heavy chain, linker domain, subdomain 4 / Histone Acetyltransferase; Chain A - #20 / Histone Acetyltransferase; Chain A - #30 / Dynein motor heavy chain, linker domain, subdomain 3 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / Split barrel-like / : / DYN1, AAA+ ATPase lid domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid 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 / Monooxygenase / Glutathione S-transferase, C-terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Cyclin A; domain 1 / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Helicase, Ruva Protein; domain 3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histone Acetyltransferase; Chain A / Thioredoxin-like superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Alpha-Beta Barrel / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Glutathione S-transferase class-mu 26 kDa isozyme / Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesSCHISTOSOMA JAPONICUM (invertebrata)
SACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSchmidt, H. / Gleave, E.S. / Carter, A.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Insights Into Dynein Motor Domain Function from a 3.3 Angstrom Crystal Structure
Authors: Schmidt, H. / Gleave, E.S. / Carter, A.P.
History
DepositionFeb 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Other
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC
B: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)622,71212
Polymers620,4102
Non-polymers2,30210
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.326, 117.918, 202.762
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC / GST 26 / SJ26 ANTIGEN / SJGST / DYHC


Mass: 310205.125 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-218,1364-3038,3292-4092
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA JAPONICUM (invertebrata), (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P08515, UniProt: P36022, glutathione transferase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 3.38 Å3/Da / Density % sol: 63.59 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→87.7 Å / Num. obs: 113780 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.1
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.7 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMACNULLrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AI6

4ai6


Resolution: 3.3→50 Å / SU B: 36.109 / SU ML: 0.581 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.629 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30548 5981 5 %RANDOM
Rwork0.23878 ---
obs0.24217 113780 95.89 %-
Displacement parametersBiso mean: 164.076 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å2-0.44 Å2
2---5.27 Å20 Å2
3---6.84 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41496 0 138 0 41634
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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