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- PDB-3vhx: The crystal structure of Arf6-MKLP1 (Mitotic kinesin-like protein... -

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Basic information

Entry
Database: PDB / ID: 3vhx
TitleThe crystal structure of Arf6-MKLP1 (Mitotic kinesin-like protein 1) complex
Components
  • ADP-ribosylation factor 6
  • Kinesin-like protein KIF23
KeywordsCELL CYCLE/SIGNALING PROTEIN / Small GTPase / GTP Binding / Flemming body / Cytokinesis / CELL CYCLE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


centralspindlin complex / TBC/RABGAPs / MET receptor recycling / erythrocyte apoptotic process / maintenance of postsynaptic density structure / mitotic spindle elongation / Mitotic Telophase/Cytokinesis / mitotic spindle midzone assembly / regulation of dendritic spine development / establishment of epithelial cell polarity ...centralspindlin complex / TBC/RABGAPs / MET receptor recycling / erythrocyte apoptotic process / maintenance of postsynaptic density structure / mitotic spindle elongation / Mitotic Telophase/Cytokinesis / mitotic spindle midzone assembly / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of protein localization to cell surface / regulation of toll-like receptor 4 signaling pathway / protein localization to endosome / negative regulation of dendrite development / regulation of Rac protein signal transduction / ruffle assembly / positive regulation of keratinocyte migration / Clathrin-mediated endocytosis / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / endocytic recycling / thioesterase binding / Flemming body / Kinesins / filopodium membrane / protein localization to cell surface / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / cortical actin cytoskeleton organization / kinesin complex / positive regulation of actin filament polymerization / microtubule-based movement / positive regulation of cytokinesis / hepatocyte apoptotic process / regulation of neuron projection development / cleavage furrow / mitotic cytokinesis / endocytic vesicle / synaptic vesicle endocytosis / regulation of presynapse assembly / signaling adaptor activity / vesicle-mediated transport / ruffle / MHC class II antigen presentation / liver development / cellular response to nerve growth factor stimulus / small monomeric GTPase / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / recycling endosome / G protein activity / mitotic spindle / positive regulation of neuron projection development / spindle / recycling endosome membrane / GDP binding / protein transport / myelin sheath / presynapse / nervous system development / cell cortex / early endosome membrane / midbody / microtubule binding / postsynapse / microtubule / cell differentiation / early endosome / endosome / cell division / focal adhesion / GTPase activity / centrosome / glutamatergic synapse / GTP binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kinesin-like protein Kif23, Arf6-interacting domain / Kinesin-like protein Kif23, Arf6-interacting domain / Kinesin-like protein Kif23, Arf6-interacting domain superfamily / Arf6-interacting domain of mitotic kinesin-like protein 1 / ADP-ribosylation factor 6 / Small GTPase superfamily, ARF type / small GTPase Arf family profile. / Kinesin-like protein / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type ...Kinesin-like protein Kif23, Arf6-interacting domain / Kinesin-like protein Kif23, Arf6-interacting domain / Kinesin-like protein Kif23, Arf6-interacting domain superfamily / Arf6-interacting domain of mitotic kinesin-like protein 1 / ADP-ribosylation factor 6 / Small GTPase superfamily, ARF type / small GTPase Arf family profile. / Kinesin-like protein / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / ADP-ribosylation factor 6 / Kinesin-like protein KIF23
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsMakyio, H. / Takei, T. / Ohgi, H. / Takahashi, S. / Takatsu, H. / Ueda, T. / Kanaho, Y. / Xie, Y. / Shin, H.W. / Kamikubo, H. ...Makyio, H. / Takei, T. / Ohgi, H. / Takahashi, S. / Takatsu, H. / Ueda, T. / Kanaho, Y. / Xie, Y. / Shin, H.W. / Kamikubo, H. / Kataoka, M. / Kawasaki, M. / Kato, R. / Wakatsuki, S. / Nakayama, K.
CitationJournal: Embo J. / Year: 2012
Title: Structural basis for Arf6-MKLP1 complex formation on the Flemming body responsible for cytokinesis
Authors: Makyio, H. / Ohgi, M. / Takei, T. / Takahashi, S. / Takatsu, H. / Katoh, Y. / Hanai, A. / Ueda, T. / Kanaho, Y. / Xie, Y. / Shin, H.W. / Kamikubo, H. / Kataoka, M. / Kawasaki, M. / Kato, R. ...Authors: Makyio, H. / Ohgi, M. / Takei, T. / Takahashi, S. / Takatsu, H. / Katoh, Y. / Hanai, A. / Ueda, T. / Kanaho, Y. / Xie, Y. / Shin, H.W. / Kamikubo, H. / Kataoka, M. / Kawasaki, M. / Kato, R. / Wakatsuki, S. / Nakayama, K.
History
DepositionSep 12, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor 6
B: Kinesin-like protein KIF23
C: ADP-ribosylation factor 6
D: Kinesin-like protein KIF23
E: ADP-ribosylation factor 6
F: Kinesin-like protein KIF23
G: ADP-ribosylation factor 6
H: Kinesin-like protein KIF23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,30717
Polymers134,0258
Non-polymers2,2829
Water1,892105
1
A: ADP-ribosylation factor 6
B: Kinesin-like protein KIF23
C: ADP-ribosylation factor 6
D: Kinesin-like protein KIF23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1078
Polymers67,0124
Non-polymers1,0954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-54 kcal/mol
Surface area24470 Å2
MethodPISA
2
E: ADP-ribosylation factor 6
F: Kinesin-like protein KIF23
G: ADP-ribosylation factor 6
H: Kinesin-like protein KIF23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1999
Polymers67,0124
Non-polymers1,1875
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-59 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.743, 174.573, 76.814
Angle α, β, γ (deg.)90.000, 98.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
ADP-ribosylation factor 6


Mass: 19990.898 Da / Num. of mol.: 4 / Fragment: UNP residues 13-175 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arf6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62331
#2: Protein
Kinesin-like protein KIF23 / Kinesin-like protein 5 / Mitotic kinesin-like protein 1


Mass: 13515.261 Da / Num. of mol.: 4 / Fragment: UNP residues 794-911
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF23, KNSL5, MKLP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02241

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Non-polymers , 4 types, 114 molecules

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


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 4000, 0.05M ammonium sulfate, 0.005M magnesium chloride, 0.1M sodium cacodylate, 0.25-1.0% v/v ethyl acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.809→87.286 Å / Num. all: 29002 / Num. obs: 28794 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.7
Reflection shellResolution: 2.8→2.85 Å / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J5X

2j5x


Resolution: 2.81→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0 / SU B: 32.573 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1461 5.1 %RANDOM
Rwork0.2012 ---
all0.262 29002 --
obs0.2027 28749 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 143.52 Å2 / Biso mean: 55.8034 Å2 / Biso min: 16.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-2.09 Å2
2---1.47 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8416 0 138 105 8659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228541
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.97411584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39451017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15324.185399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.126151533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0561563
X-RAY DIFFRACTIONr_chiral_restr0.0680.21289
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216323
X-RAY DIFFRACTIONr_mcbond_it0.2851.55099
X-RAY DIFFRACTIONr_mcangle_it0.55828273
X-RAY DIFFRACTIONr_scbond_it0.79233442
X-RAY DIFFRACTIONr_scangle_it1.384.53311
LS refinement shellResolution: 2.809→2.881 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 99 -
Rwork0.311 1855 -
all-1954 -
obs--91.22 %
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)
13.9801-1.4730.53545.72881.03554.01660.0144-0.0317-0.17140.3410.1607-0.28170.45890.0528-0.17510.3755-0.0283-0.02030.1157-0.04380.2476-15.907-26.0405-6.673
23.93473.14233.43587.63635.04877.74450.1872-0.0912-0.0217-0.0477-0.0049-0.2468-0.065-0.0751-0.18230.22110.01530.04620.1678-0.01680.362-21.226-5.37582.4201
36.2509-1.38780.22714.16490.31172.9917-0.06-0.14050.2810.28760.16250.089-0.2545-0.0558-0.10250.0480.00290.01670.11960.02870.03077.29430.79318.428
44.5665-3.14384.63757.2104-4.53589.110.18070.1078-0.65850.18240.02-0.07760.2706-0.0189-0.20070.0790.0240.01060.1778-0.00340.2406-9.65214.60119.921
55.5892-0.51450.49793.6167-0.08113.6113-0.0144-0.05430.40290.23750.20630.4284-0.2037-0.2717-0.19180.10220.00740.02390.21990.12460.1522-21.8023-54.7038-55.6046
63.3559-2.59121.65086.6733-2.13095.52840.16870.2733-0.0784-0.2738-0.1247-0.11570.30440.2583-0.0440.0497-0.0551-0.00040.22650.02070.0684-3.884-71.0509-55.5683
74.8226-1.87120.48386.58551.28935.6065-0.02070.2306-0.8206-0.312-0.40560.38160.4191-0.09460.42630.44530.0284-0.10110.21-0.19340.6862-1.882-113.089-32.909
84.28220.48291.19357.75552.77945.90240.16790.0041-0.5739-0.0815-0.3030.54890.0572-0.49340.13510.2232-0.0062-0.03250.2139-0.04290.3024.597-92.077-44.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 173
2X-RAY DIFFRACTION1A184 - 185
3X-RAY DIFFRACTION1A186 - 193
4X-RAY DIFFRACTION2B695 - 800
5X-RAY DIFFRACTION2B808 - 814
6X-RAY DIFFRACTION3C12 - 173
7X-RAY DIFFRACTION3C184 - 185
8X-RAY DIFFRACTION3C186 - 213
9X-RAY DIFFRACTION4D695 - 800
10X-RAY DIFFRACTION4D808 - 819
11X-RAY DIFFRACTION5E12 - 173
12X-RAY DIFFRACTION5E184 - 185
13X-RAY DIFFRACTION5E186 - 207
14X-RAY DIFFRACTION6F699 - 800
15X-RAY DIFFRACTION6F808 - 824
16X-RAY DIFFRACTION7G12 - 173
17X-RAY DIFFRACTION7G184 - 185
18X-RAY DIFFRACTION7G186 - 188
19X-RAY DIFFRACTION8H713 - 800
20X-RAY DIFFRACTION8H808 - 815

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