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- PDB-2rr7: Microtubule Binding Domain of DYNEIN-C -

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Basic information

Entry
Database: PDB / ID: 2rr7
TitleMicrotubule Binding Domain of DYNEIN-C
ComponentsDynein heavy chain 9
KeywordsMOTOR PROTEIN / DYNEIN / MICROTUBULE-Binding / STALK head / MTBD / ANTIPARALLEL coiled coil / DSH
Function / homology
Function and homology information


inner dynein arm / inner dynein arm assembly / dynein light chain binding / cilium movement involved in cell motility / motile cilium / microtubule motor activity / microtubule / 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 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 ...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 / 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 heavy chain 9
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsKato, Y. / Yagi, T. / Ohki, S. / Burgess, S. / Honda, S. / Kamiya, R. / Tanokura, M.
CitationJournal: Structure / Year: 2014
Title: Structure of the microtubule-binding domain of flagellar dynein
Authors: Kato, Y.S. / Yagi, T. / Harris, S.A. / Ohki, S.Y. / Yura, K. / Shimizu, Y. / Honda, S. / Kamiya, R. / Burgess, S.A. / Tanokura, M.
History
DepositionJun 4, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein heavy chain 9


Theoretical massNumber of molelcules
Total (without water)17,3911
Polymers17,3911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Dynein heavy chain 9


Mass: 17391.439 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2791-2942
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: DHC9 / Plasmid: PGEX-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4AC22

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D C(CO)NH
1523D H(CCO)NH
1633D (H)CCH-COSY
1733D (H)CCH-TOCSY
1813D 1H-15N NOESY
1933D 1H-13C NOESY
11023D 1H-13C-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-15N] DYNEIN HEAVY CHAIN 9 stalk head-1, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-13C; U-15N] DYNEIN HEAVY CHAIN 9 stalk head-2, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-13C; U-15N] DYNEIN HEAVY CHAIN 9 stalk head-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMDYNEIN HEAVY CHAIN 9 stalk head-1[U-15N]1
0.4 mMDYNEIN HEAVY CHAIN 9 stalk head-2[U-13C; U-15N]2
0.4 mMDYNEIN HEAVY CHAIN 9 stalk head-3[U-13C; U-15N]3
Sample conditionsIonic strength: 1.42 / pH: 6.4 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
VARIAN INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
CYANAGUNTERT, MUMENTHALER, WUTHRICHrefinement
CYANAGUNTERT, MUMENTHALER, WUTHRICHstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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