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- PDB-9ymg: Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin -

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Basic information

Entry
Database: PDB / ID: 9ymg
TitleHuman KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin
Components
  • Kinesin-like protein KIF18A, DARPin fusion protein
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsMOTOR PROTEIN / kinesin / microtubule / complex
Function / homology
Function and homology information


tubulin-dependent ATPase activity / mitotic spindle astral microtubule / mitotic spindle midzone / kinetochore microtubule / male meiotic nuclear division / microtubule plus-end binding / plus-end-directed microtubule motor activity / Kinesins / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion ...tubulin-dependent ATPase activity / mitotic spindle astral microtubule / mitotic spindle midzone / kinetochore microtubule / male meiotic nuclear division / microtubule plus-end binding / plus-end-directed microtubule motor activity / Kinesins / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / kinesin complex / microtubule depolymerization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic metaphase chromosome alignment / seminiferous tubule development / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ruffle / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / regulation of microtubule cytoskeleton organization / Resolution of Sister Chromatid Cohesion / cellular response to estradiol stimulus / RHO GTPases Activate Formins / caveola / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / Separation of Sister Chromatids / protein transport / mitotic cell cycle / actin binding / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...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 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha-1B chain / Kinesin-like protein KIF18A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å
AuthorsLockbaum, G.J. / Lee, Y.-T. / Boriack-Sjodin, P.A. / Grigoriu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Discovery of kinesin KIF18A inhibitor ATX020: tactical application of silicon atom replacement
Authors: Sparling, B.A. / Lee, H. / Zablocki, M.-M. / Lynes, M.M. / Grigoriu, S. / Shehaj, L. / Lockbaum, G.J. / Khan, S.K. / Holtz, T. / Lee, Y.-T. / Buker, S.M. / Gotur, D. / Lu, C. / Ribich, S. / ...Authors: Sparling, B.A. / Lee, H. / Zablocki, M.-M. / Lynes, M.M. / Grigoriu, S. / Shehaj, L. / Lockbaum, G.J. / Khan, S.K. / Holtz, T. / Lee, Y.-T. / Buker, S.M. / Gotur, D. / Lu, C. / Ribich, S. / Blakemore, S.J. / Boriack-Sjodin, P.A. / Silver, S.J. / Copeland, R.A. / Duncan, K.W.
History
DepositionOct 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Kinesin-like protein KIF18A, DARPin fusion protein
D: Tubulin alpha-1B chain
E: Tubulin beta chain
F: Kinesin-like protein KIF18A, DARPin fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,68819
Polymers319,5356
Non-polymers3,15313
Water8,197455
1
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Kinesin-like protein KIF18A, DARPin fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,37510
Polymers159,7673
Non-polymers1,6087
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-62 kcal/mol
Surface area50130 Å2
MethodPISA
2
D: Tubulin alpha-1B chain
E: Tubulin beta chain
F: Kinesin-like protein KIF18A, DARPin fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3139
Polymers159,7673
Non-polymers1,5456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-64 kcal/mol
Surface area49980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.38, 135.47, 117.67
Angle α, β, γ (deg.)90, 107.673, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111METMETVALVAL1 - 4351 - 435
211METMETVALVAL1 - 4351 - 435
322METMETASPASP1 - 4311 - 431
422METMETASPASP1 - 4311 - 431
533GLNGLNVALVAL11 - 36311 - 363
633GLNGLNVALVAL11 - 36311 - 363
744GLYGLYLYSLYS13 - 16613 - 166
844GLYGLYLYSLYS13 - 16613 - 166

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49793.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Protein Kinesin-like protein KIF18A, DARPin fusion protein / Marrow stromal KIF18A / MS-KIF18A


Mass: 59769.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DARPin fused to the C-terminus of KIF18A via a flexible linker
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: KIF18A, OK/SW-cl.108 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NI77

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Non-polymers , 6 types, 468 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium nitrate, 0.1 M sodium acetate pH 5.6, 20% (w/v) PEG Smear Low (5% PEG 400, 5% PEG 500 MME, 5% PEG 600, 5% PEG 1000), 5% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.406→48.673 Å / Num. obs: 121098 / % possible obs: 99.4 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.3
Reflection shellResolution: 2.41→2.45 Å / Num. unique obs: 5981 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.406→48.673 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 24.172 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R Free: 0.253 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2377 6162 5.088 %
Rwork0.1907 114935 -
all0.193 --
obs-121097 99.265 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.972 Å2
Baniso -1Baniso -2Baniso -3
1-1.022 Å20 Å20.257 Å2
2--2.827 Å2-0 Å2
3----3.336 Å2
Refinement stepCycle: LAST / Resolution: 2.406→48.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20956 0 192 455 21603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01221623
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.82429297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9952688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.4055119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.312103636
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.59110995
X-RAY DIFFRACTIONr_chiral_restr0.0830.23308
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216298
X-RAY DIFFRACTIONr_nbd_refined0.2050.29575
X-RAY DIFFRACTIONr_nbtor_refined0.2980.214605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2797
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1090.213
X-RAY DIFFRACTIONr_mcbond_it6.7396.07210771
X-RAY DIFFRACTIONr_mcangle_it11.15610.91413443
X-RAY DIFFRACTIONr_scbond_it7.2126.29210852
X-RAY DIFFRACTIONr_scangle_it11.6111.46515850
X-RAY DIFFRACTIONr_lrange_it21.17563.51831653
X-RAY DIFFRACTIONr_rigid_bond_restr1.946321623
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.0513961
X-RAY DIFFRACTIONr_ncsr_local_group_20.0920.0513656
X-RAY DIFFRACTIONr_ncsr_local_group_30.1160.059890
X-RAY DIFFRACTIONr_ncsr_local_group_40.080.054798
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.081450.0501
12AX-RAY DIFFRACTIONLocal ncs0.081450.0501
23AX-RAY DIFFRACTIONLocal ncs0.091730.0501
24AX-RAY DIFFRACTIONLocal ncs0.091730.0501
35AX-RAY DIFFRACTIONLocal ncs0.116010.05009
36AX-RAY DIFFRACTIONLocal ncs0.116010.05009
47AX-RAY DIFFRACTIONLocal ncs0.080040.05011
48AX-RAY DIFFRACTIONLocal ncs0.080040.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.406-2.4680.374670.33583920.33789640.9050.9198.82870.296
2.468-2.5350.3674140.3282340.32287510.9070.92798.8230.286
2.535-2.6090.3264110.28280010.28485100.9320.94898.84840.248
2.609-2.6890.3343700.26178030.26482630.930.95998.91080.23
2.689-2.7770.294060.24275460.24480260.950.96699.0780.209
2.777-2.8740.2983970.23372830.23677570.9440.96999.00730.201
2.874-2.9820.2933650.22170410.22574570.9520.97299.31610.19
2.982-3.1030.2863640.20768080.21172390.9490.97499.07450.182
3.103-3.2410.2843420.19864880.20268710.9520.97799.40330.176
3.241-3.3980.2473560.19662550.19866490.9620.97899.42850.178
3.398-3.5810.2343420.18959100.19262900.970.9899.39590.178
3.581-3.7970.23030.16856190.1759470.9780.98599.57960.161
3.797-4.0570.2062740.16453150.16656110.9760.98699.60790.161
4.057-4.380.1842660.1549630.15252450.9830.98999.69490.15
4.38-4.7940.1952380.14245480.14447950.9820.9999.81230.146
4.794-5.3530.2012310.1541370.15343770.980.98999.79440.157
5.353-6.1690.2292210.18136470.18438730.9770.98599.87090.183
6.169-7.5250.2321800.19431070.19632910.9750.98399.87850.202
7.525-10.5170.171360.13824160.1425560.9840.9999.84350.162
10.517-48.6730.194790.18414220.18415040.9780.97999.80050.216

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