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- PDB-4akh: Dynein Motor Domain - AMPPNP complex -

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Basic information

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


karyogamy / nuclear migration along microtubule / astral microtubule / establishment of mitotic spindle localization / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / dynein intermediate chain binding ...karyogamy / nuclear migration along microtubule / astral microtubule / establishment of mitotic spindle localization / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / dynein intermediate chain binding / glutathione transferase / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / glutathione transferase activity / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / glutathione metabolic process / 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 / Dynein motor heavy chain, linker domain, subdomain 4 / Histone Acetyltransferase; Chain A - #30 / Dynein motor heavy chain, linker domain, subdomain 3 / Region D6 of dynein motor / Histone Acetyltransferase; Chain A - #20 / Dynein motor heavy chain, linker domain, N-terminal subdomain ...Helicase, Ruva Protein; domain 3 - #740 / Monooxygenase - #160 / Dynein motor, AAA2 domain, small subdomain / Dynein motor, AAA1 domain, small subdomain / Dynein motor heavy chain, linker domain, subdomain 4 / Histone Acetyltransferase; Chain A - #30 / Dynein motor heavy chain, linker domain, subdomain 3 / Region D6 of dynein motor / Histone Acetyltransferase; Chain A - #20 / Dynein motor heavy chain, linker domain, N-terminal subdomain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / Split barrel-like / AAA+ lid domain / : / DYN1, AAA+ ATPase lid domain / Monooxygenase / : / Dynein heavy chain, ATPase lid domain / Glutathione S-transferase, C-terminal domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / 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 / 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 / : / Cyclin A; domain 1 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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: 3.6 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 1.3Jan 1, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 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 / struct_ncs_dom_lim / 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_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_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 / _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)622,87012
Polymers620,4102
Non-polymers2,46010
Water00
1
A: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,4356
Polymers310,2051
Non-polymers1,2305
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,4356
Polymers310,2051
Non-polymers1,2305
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.560, 118.130, 201.020
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 1 - 4092 / Label seq-ID: 1 - 2695

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.36 Å3/Da / Density % sol: 63.39 % / 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: 3.6→80.3 Å / Num. obs: 94930 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 3.6→3.94 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0019refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AI6

4ai6


Resolution: 3.6→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 44.589 / SU ML: 0.67 / Cross valid method: THROUGHOUT / ESU R Free: 0.755 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30215 4767 5 %RANDOM
Rwork0.24097 ---
obs0.24412 90155 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 176.544 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20.4 Å2
2---4.03 Å20 Å2
3---5.94 Å2
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41496 0 146 0 41642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01942440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.96457468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80955290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.62824.6741874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.373157448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1615196
X-RAY DIFFRACTIONr_chiral_restr0.0990.26574
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0231502
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3808 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 343 -
Rwork0.388 6342 -
obs--95.38 %

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