[English] 日本語
Yorodumi
- PDB-4w8f: Crystal structure of the dynein motor domain in the AMPPNP-bound state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w8f
TitleCrystal structure of the dynein motor domain in the AMPPNP-bound state
ComponentsDynein heavy chain lysozyme chimera
KeywordsMOTOR PROTEIN / cytoplasmic dynein / microtubule / ATPase / AAA+ / AMPPNP
Function / homology
Function and homology information


karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / nuclear migration ...karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / nuclear migration / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / viral release from host cell by cytolysis / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / peptidoglycan catabolic process / mitotic spindle organization / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cell cortex / host cell cytoplasm / defense response to bacterium / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Region D6 of dynein motor / Dynein motor heavy chain, linker domain, N-terminal subdomain / AAA+ lid domain / : / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 ...Region D6 of dynein motor / Dynein motor heavy chain, linker domain, N-terminal subdomain / AAA+ lid domain / : / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Helicase, Ruva Protein; domain 3 / Lysozyme-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Endolysin / Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.541 Å
AuthorsCheng, H.-C. / Bhabha, G. / Zhang, N. / Vale, R.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM09731 United States
CitationJournal: Cell / Year: 2014
Title: Allosteric communication in the dynein motor domain.
Authors: Gira Bhabha / Hui-Chun Cheng / Nan Zhang / Arne Moeller / Maofu Liao / Jeffrey A Speir / Yifan Cheng / Ronald D Vale /
Abstract: Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which ...Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which collectively provide insight into the roles of dynein's two major ATPase sites, AAA1 and AAA3, in the conformational change mechanism. ATP binding to AAA1 triggers a cascade of conformational changes that propagate to all six AAA domains and cause a large movement of the "linker," dynein's mechanical element. In contrast to the role of AAA1 in driving motility, nucleotide transitions in AAA3 gate the transmission of conformational changes between AAA1 and the linker, suggesting that AAA3 acts as a regulatory switch. Further structural and mutational studies also uncover a role for the linker in regulating the catalytic cycle of AAA1. Together, these results reveal how dynein's two major ATP-binding sites initiate and modulate conformational changes in the motor domain during motility.
History
DepositionAug 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dynein heavy chain lysozyme chimera
B: Dynein heavy chain lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)613,87812
Polymers609,7802
Non-polymers4,09810
Water00
1
A: Dynein heavy chain lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,9396
Polymers304,8901
Non-polymers2,0495
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dynein heavy chain lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,9396
Polymers304,8901
Non-polymers2,0495
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-26 kcal/mol
Surface area227290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.730, 154.380, 177.550
Angle α, β, γ (deg.)90.00, 96.59, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Dynein heavy chain lysozyme chimera / Dynein heavy chain / cytosolic / DYHC / Lysis protein / Muramidase


Mass: 304889.875 Da / Num. of mol.: 2 / Mutation: E1849Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: ATCC 204508 / S288c / Gene: DYN1, DHC1, YKR054C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36022, UniProt: P00720, lysozyme
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.7 % / Description: thin plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 4-10% PEG 3350 and 200-300 mM NaAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 3.54→49.4 Å / Num. obs: 82983 / % possible obs: 92.2 % / Observed criterion σ(I): 3.3 / Redundancy: 10.9 % / Net I/σ(I): 8.9

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1769) / Classification: refinement
RefinementResolution: 3.541→49.4 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 4187 5.05 %
Rwork0.2282 --
obs0.2299 82942 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.541→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42143 0 250 0 42393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643243
X-RAY DIFFRACTIONf_angle_d1.14958485
X-RAY DIFFRACTIONf_dihedral_angle_d15.21316067
X-RAY DIFFRACTIONf_chiral_restr0.0456632
X-RAY DIFFRACTIONf_plane_restr0.0057352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5411-3.58130.3172440.2683689X-RAY DIFFRACTION25
3.5813-3.62340.3457760.26251283X-RAY DIFFRACTION45
3.6234-3.66760.2808850.27641628X-RAY DIFFRACTION59
3.6676-3.7140.27541030.27131982X-RAY DIFFRACTION69
3.714-3.76280.30821380.27422284X-RAY DIFFRACTION81
3.7628-3.81440.31551270.26062535X-RAY DIFFRACTION90
3.8144-3.86880.31921610.27012788X-RAY DIFFRACTION99
3.8688-3.92660.31921540.25822855X-RAY DIFFRACTION100
3.9266-3.98790.24761350.26272829X-RAY DIFFRACTION100
3.9879-4.05330.30051530.25182854X-RAY DIFFRACTION100
4.0533-4.12310.3121470.24382819X-RAY DIFFRACTION100
4.1231-4.1980.27741520.24472824X-RAY DIFFRACTION100
4.198-4.27870.28541490.22832844X-RAY DIFFRACTION100
4.2787-4.3660.26041520.21592818X-RAY DIFFRACTION100
4.366-4.46090.2241570.22132845X-RAY DIFFRACTION100
4.4609-4.56460.23711380.21852888X-RAY DIFFRACTION100
4.5646-4.67870.24381660.22512805X-RAY DIFFRACTION100
4.6787-4.80510.2441600.222837X-RAY DIFFRACTION100
4.8051-4.94630.2651460.22192852X-RAY DIFFRACTION100
4.9463-5.10580.27831460.21962833X-RAY DIFFRACTION100
5.1058-5.28810.26471560.22672825X-RAY DIFFRACTION100
5.2881-5.49960.28151510.2172862X-RAY DIFFRACTION100
5.4996-5.74950.2521620.23032869X-RAY DIFFRACTION100
5.7495-6.05220.27691400.24482833X-RAY DIFFRACTION100
6.0522-6.43060.28121410.24632872X-RAY DIFFRACTION100
6.4306-6.92590.23581480.21992863X-RAY DIFFRACTION100
6.9259-7.62060.2481530.20792860X-RAY DIFFRACTION100
7.6206-8.71810.19771750.17292842X-RAY DIFFRACTION100
8.7181-10.9640.1691270.15722901X-RAY DIFFRACTION100
10.964-49.40510.25651450.23642936X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2985-0.13010.09410.47530.11240.49090.089-0.04970.01730.1505-0.0077-0.00690.1329-0.0088-0.06580.33580.00580.12830.14260.03160.3363-10.0977-56.016633.154
22.79250.687-1.11451.039-0.39221.34460.0418-0.3843-0.0060.1831-0.0201-0.07210.14720.3193-0.03350.34490.0857-0.04010.3257-0.09020.261840.2601-43.71548.0736
30.2152-0.05860.5490.1533-0.42623.10250.0137-0.0259-0.0407-0.1130.014-0.00340.37490.68090.03270.37360.09360.08680.41-0.02120.543951.0587-39.8656-20.9007
41.19760.0599-0.26370.4951-0.22130.45960.03430.1613-0.03620.00440.04480.12860.0262-0.0804-0.07850.3008-0.01110.00850.1941-0.03010.30228.0678-31.0834-3.4015
51.36370.11740.02420.73850.18070.33770.09610.09720.0056-0.1154-0.1187-0.01250.03130.01780.03390.51840.0702-0.08920.15840.04110.2302-13.344819.219653.6367
62.0378-0.27111.36090.8284-0.5772.2195-0.05830.3780.0035-0.0575-0.0303-0.168-0.10880.46420.04030.39190.01410.07770.3792-0.00290.294538.66276.478149.6171
70.86650.2385-1.06420.4073-1.07722.18410.1755-0.27640.04550.0138-0.03940.043-0.56890.8909-0.11120.4065-0.1709-0.09450.4045-0.05770.447334.79694.0149120.2734
81.10.04910.49120.6248-0.08570.73980.1093-0.11860.09410.0592-0.03880.0108-0.0504-0.0996-0.05940.4460.036-0.01540.1657-0.02510.2873-2.3117-5.534794.4179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1365 through 2066 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2067 through 2824 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2825 through 3387 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3388 through 4092 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1365 through 2066 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2067 through 2818 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2819 through 3355 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3356 through 4092 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more