[English] 日本語
Yorodumi
- PDB-2y65: Crystal structure of Drosophila melanogaster kinesin-1 motor doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y65
TitleCrystal structure of Drosophila melanogaster kinesin-1 motor domain dimer-tail complex
Components(KINESIN HEAVY CHAIN) x 2
KeywordsMOTOR PROTEIN
Function / homology
Function and homology information


actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde axonal transport of mitochondrion / anterograde dendritic transport / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification ...actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde axonal transport of mitochondrion / anterograde dendritic transport / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification / larval locomotory behavior / pole plasm assembly / dorsal appendage formation / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / larval somatic muscle development / centrosome separation / transport along microtubule / anterograde dendritic transport of neurotransmitter receptor complex / microtubule sliding / actin cap / microtubule plus-end / plus-end-directed microtubule motor activity / axo-dendritic transport / kinesin complex / microtubule motor activity / microtubule-based movement / nuclear migration / stress granule disassembly / dendrite morphogenesis / tropomyosin binding / synaptic vesicle transport / intracellular distribution of mitochondria / microtubule polymerization / cytoskeletal motor activity / axon cytoplasm / dendrite cytoplasm / axonogenesis / axon guidance / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin heavy chain
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKaan, H.Y.K. / Hackney, D.D. / Kozielski, F.
CitationJournal: Science / Year: 2011
Title: The Structure of the Kinesin-1 Motor-Tail Complex Reveals the Mechanism of Autoinhibition.
Authors: Kaan, H.Y.K. / Hackney, D.D. / Kozielski, F.
History
DepositionJan 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Structure summary
Revision 1.2Mar 14, 2012Group: Other
Revision 1.3Sep 30, 2015Group: Derived calculations / Source and taxonomy
Revision 1.4Dec 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_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KINESIN HEAVY CHAIN
B: KINESIN HEAVY CHAIN
C: KINESIN HEAVY CHAIN
D: KINESIN HEAVY CHAIN
W: KINESIN HEAVY CHAIN
X: KINESIN HEAVY CHAIN
Y: KINESIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,08715
Polymers169,2807
Non-polymers1,8068
Water11,818656
1
A: KINESIN HEAVY CHAIN
Y: KINESIN HEAVY CHAIN
hetero molecules

A: KINESIN HEAVY CHAIN
Y: KINESIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5008
Polymers85,5974
Non-polymers9034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
2
B: KINESIN HEAVY CHAIN
X: KINESIN HEAVY CHAIN
hetero molecules

B: KINESIN HEAVY CHAIN
X: KINESIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5008
Polymers85,5974
Non-polymers9034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
3
C: KINESIN HEAVY CHAIN
D: KINESIN HEAVY CHAIN
W: KINESIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5877
Polymers83,6843
Non-polymers9034
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-16.4 kcal/mol
Surface area37290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.765, 190.714, 145.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9805, 0.0458, -0.1911), (0.02055, -0.94324, -0.33148), (-0.19543, -0.32894, 0.92391)
Vector: 37.4737, 21.31671, 7.77144)
DetailsOWING TO ITS AMINO ACID SEQUENCE, CHAINS X AND Y ARE ALMOST SYMMETRICAL, IN TERMS OF SIDE CHAIN PROPERTIES, ABOUT THE LYS 944 RESIDUE. THIS DISTINCTIVE FEATURE OF THE CHAINS X AND Y ALLOWS THEM TO BIND IN TWO DIRECTIONS BETWEEN THE DIMERS A-A' AND B-B', WHICH ALSO EXHIBIT TWO-FOLD SYMMETRY.

-
Components

#1: Protein
KINESIN HEAVY CHAIN / KINESIN


Mass: 40885.301 Da / Num. of mol.: 4 / Fragment: MOTOR DOMAIN, RESIDUES 1-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: P17210
#2: Protein/peptide KINESIN HEAVY CHAIN / KINESIN


Mass: 1913.098 Da / Num. of mol.: 3 / Fragment: TAIL DOMAIN RESIDUES 937-952
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17210
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.87 % / Description: NONE
Crystal growpH: 7.4
Details: 18% POLYETHYLENE GLYCOL-3350, 0.2M POTASSIUM CHLORIDE, 0.1M HEPES SODIUM PH 7.4

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 80517 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 41.383 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.5 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y5W

2y5w


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.611 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. PSEUDOSYMMETRY IN THE CRYSTAL STRUCTURE, WHERE CHAINS X AND Y LIE ON THE TWO-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25192 4044 5 %RANDOM
Rwork0.19503 ---
obs0.19787 76402 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.405 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10784 0 112 656 11552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.96615296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97351435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64524.813509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.417152032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0241564
X-RAY DIFFRACTIONr_chiral_restr0.1340.21750
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218371
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_it1.321.57019
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.406211362
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.54634273
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7334.53909
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
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 279 -
Rwork0.242 5562 -
obs--99.15 %

+
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