[English] 日本語
Yorodumi
- PDB-6nje: Crystal structure of the motor domain of human kinesin family mem... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nje
TitleCrystal structure of the motor domain of human kinesin family member 22
ComponentsKinesin-like protein KIF22
KeywordsTRANSPORT PROTEIN / limited proteolysis / kinesin / structural genomics consortium / motor domain / adp / SGC
Function / homology
Function and homology information


metaphase chromosome alignment / Kinesins / sister chromatid cohesion / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / MHC class II antigen presentation / mitotic spindle ...metaphase chromosome alignment / Kinesins / sister chromatid cohesion / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / MHC class II antigen presentation / mitotic spindle / kinetochore / mitotic cell cycle / microtubule binding / microtubule / nuclear speck / DNA repair / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
Helix-hairpin-helix motif / Kinesin motor domain / Kinesin / Kinesin-like protein / RuvA domain 2-like / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. ...Helix-hairpin-helix motif / Kinesin motor domain / Kinesin / Kinesin-like protein / RuvA domain 2-like / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein KIF22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWalker, B.C. / Zhu, H. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Park, H. / Cochran, J.C. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of the motor domain of human kinesin family member 22
Authors: Walker, B.C. / Zhu, H. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Park, H. / Structural Genomics Consortium (SGC)
History
DepositionJan 3, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionJan 16, 2019ID: 3BFN
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinesin-like protein KIF22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7147
Polymers42,1331
Non-polymers5816
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.530, 58.730, 116.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Kinesin-like protein KIF22 / Kinesin-like DNA-binding protein / Kinesin-like protein 4


Mass: 42132.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF22, KID, KNSL4 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon(+) RIL / References: UniProt: Q14807

-
Non-polymers , 5 types, 96 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.81 Å3/Da / Density % sol: 31.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 3.2 M NaCl, 0.1 M Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→35.48 Å / Num. obs: 16157 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.049 / Rrim(I) all: 0.13 / Net I/σ(I): 16.1 / Num. measured all: 109199 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.274.40.845812130958120.7680.4260.9462.495
9.06-35.485.80.022161427810.010.02453.898.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data scaling
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: continued refinement of model from PDB entry 3BFN. Previously solved using coordinates from PDB entry 3B6U.

3bfn
PDB Unreleased entry

3b6u


Resolution: 2.2→35.48 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.891 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.276 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.288 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.222
Details: Discontinuous electron density suggests that some residues between positions 55 and 71, which have been omitted from the model, form an additional strand adjacent to the strand that includes ...Details: Discontinuous electron density suggests that some residues between positions 55 and 71, which have been omitted from the model, form an additional strand adjacent to the strand that includes residues 74 through 76.
RfactorNum. reflection% reflection
Rfree0.258 814 5.06 %
Rwork0.2 --
obs0.203 16084 99.6 %
Displacement parametersBiso max: 128.33 Å2 / Biso mean: 39.38 Å2 / Biso min: 15.37 Å2
Baniso -1Baniso -2Baniso -3
1--5.5528 Å20 Å20 Å2
2--7.8393 Å20 Å2
3----2.2866 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.2→35.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 32 90 2455
Biso mean--35.77 36.63 -
Num. residues----297
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d851SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes365HARMONIC5
X-RAY DIFFRACTIONt_it2412HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion306SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2719SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2412HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3269HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion16.36
LS refinement shellResolution: 2.2→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.315 150 5.31 %
Rwork0.246 2674 -
all-2824 -
obs--97.99 %

+
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