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- PDB-5lef: Rab6A:Kif20A complex -

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Basic information

Entry
Database: PDB / ID: 5lef
TitleRab6A:Kif20A complex
Components
  • Kinesin-like protein KIF20A
  • Ras-related protein Rab-6A
KeywordsPROTEIN TRANSPORT / Rab GTPase / kinesin / motor / protein complex
Function / homology
Function and homology information


peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / endosome to plasma membrane transport vesicle / Mitotic Telophase/Cytokinesis / protein localization to Golgi membrane / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / Kinesins / acrosomal membrane / COPI-dependent Golgi-to-ER retrograde traffic ...peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / endosome to plasma membrane transport vesicle / Mitotic Telophase/Cytokinesis / protein localization to Golgi membrane / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / Kinesins / acrosomal membrane / COPI-dependent Golgi-to-ER retrograde traffic / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / midbody abscission / intra-Golgi vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / RAB GEFs exchange GTP for GDP on RABs / microtubule bundle formation / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TBC/RABGAPs / retrograde transport, endosome to Golgi / microtubule motor activity / kinesin complex / intercellular bridge / microtubule-based movement / antigen processing and presentation / mitotic cytokinesis / endomembrane system / secretory granule membrane / regulation of cytokinesis / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / spindle / neuron projection development / protein transport / midbody / cytoplasmic vesicle / microtubule binding / microtubule / protein domain specific binding / Golgi membrane / GTPase activity / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Kinesin-like protein / small GTPase Rab1 family profile. / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...: / Kinesin-like protein / small GTPase Rab1 family profile. / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Kinesin motor domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / ISOPROPYL ALCOHOL / Ras-related protein Rab-6A / Kinesin-like protein KIF20A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.088 Å
AuthorsBressanelli, G. / Pylypenko, O. / Houdusse, A.
CitationJournal: Nat Commun / Year: 2017
Title: Coupling fission and exit of RAB6 vesicles at Golgi hotspots through kinesin-myosin interactions.
Authors: Miserey-Lenkei, S. / Bousquet, H. / Pylypenko, O. / Bardin, S. / Dimitrov, A. / Bressanelli, G. / Bonifay, R. / Fraisier, V. / Guillou, C. / Bougeret, C. / Houdusse, A. / Echard, A. / Goud, B.
History
DepositionJun 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / 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_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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-6A
B: Ras-related protein Rab-6A
C: Kinesin-like protein KIF20A
D: Kinesin-like protein KIF20A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,20713
Polymers59,6724
Non-polymers1,5359
Water4,522251
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-94 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.250, 128.190, 36.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Rab-6A / Rab-6


Mass: 21866.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB6A, RAB6 / Production host: Escherichia coli (E. coli) / References: UniProt: P20340
#2: Protein Kinesin-like protein KIF20A / Kinesin-like protein 174 / Rab6-interacting kinesin-like protein / Rabkinesin-6


Mass: 7968.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif20a, Rab6kifl / Production host: Escherichia coli (E. coli) / References: UniProt: P97329

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Non-polymers , 6 types, 260 molecules

#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Hepes 0.1M, Ammonium Sulfate 0.2M, PEG 8K 24%, Isopropanol 2%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976273 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976273 Å / Relative weight: 1
ReflectionResolution: 2.088→44.8 Å / Num. obs: 34406 / % possible obs: 96.9 % / Redundancy: 3.6 % / Net I/σ(I): 14.11
Reflection shellResolution: 2.088→2.21 Å / Rmerge(I) obs: 0.733

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIL

2gil


Resolution: 2.088→44.793 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.54
RfactorNum. reflection% reflection
Rfree0.2042 1721 5 %
Rwork0.1764 --
obs0.1778 34405 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.088→44.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 91 251 3696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033545
X-RAY DIFFRACTIONf_angle_d0.7334801
X-RAY DIFFRACTIONf_dihedral_angle_d15.9071336
X-RAY DIFFRACTIONf_chiral_restr0.027546
X-RAY DIFFRACTIONf_plane_restr0.002594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0883-2.14970.27041360.25662572X-RAY DIFFRACTION93
2.1497-2.21910.24841420.22972713X-RAY DIFFRACTION99
2.2191-2.29840.23211440.20512727X-RAY DIFFRACTION99
2.2984-2.39050.24041440.1962729X-RAY DIFFRACTION99
2.3905-2.49920.20081410.19142680X-RAY DIFFRACTION97
2.4992-2.6310.19681440.18242745X-RAY DIFFRACTION98
2.631-2.79580.21341450.18542748X-RAY DIFFRACTION98
2.7958-3.01160.1941450.1682752X-RAY DIFFRACTION98
3.0116-3.31460.19291410.16932689X-RAY DIFFRACTION96
3.3146-3.7940.17341450.15182753X-RAY DIFFRACTION98
3.794-4.77920.1831440.14342735X-RAY DIFFRACTION95
4.7792-44.80350.22951500.19662841X-RAY DIFFRACTION94
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)
10.4059-0.1103-0.45170.60540.18950.49070.13540.11760.4803-0.0808-0.0512-0.0682-0.3461-0.15590.00010.34670.0259-0.00120.33240.04520.327443.483912.9677-0.9194
20.22920.0495-0.19150.3334-0.21541.14120.00280.66710.0490.16880.00360.44580.4964-0.56190.02270.50940.0201-0.04180.71-0.03720.556931.98038.3291-5.6236
30.268-0.4459-0.00950.6651-0.16070.59370.0012-0.00420.1630.06620.00820.011-0.2024-0.0859-00.25530.03870.01870.2974-0.03060.290739.197610.67847.508
40.3916-0.3706-0.15230.9472-0.23240.3230.0398-0.13890.13010.1680.00150.0332-0.0426-0.0202-00.2359-0.02210.01620.2974-0.01630.199447.8262.86618.9251
50.2911-0.1684-0.01830.4754-0.2670.1620.0233-0.0108-0.1202-0.0444-0.1178-0.14170.10830.0425-00.2762-0.04870.0010.3131-0.00490.239449.4913-2.85272.8694
60.07130.10380.1140.14820.16580.1744-0.05550.0643-0.0489-0.15140.03280.13370.0327-0.030900.2635-0.02970.0140.3621-0.00780.247337.9232-0.2686-4.2963
70.5025-0.0848-0.97250.50270.40522.28580.51750.0367-0.49060.00410.19530.3120.46450.31250.47060.49410.1147-0.15760.27950.03650.410421.293839.415616.6463
80.095-0.0963-0.00880.155-0.02950.02940.0759-0.4249-0.06340.60220.2367-0.59030.84460.6226-0.00220.54630.2286-0.06780.5096-0.05210.499530.359742.303318.9355
90.10190.1027-0.2441.89712.10843.74460.8461-0.1151-0.6341-0.38270.31170.56610.179-0.25441.14930.59760.158-0.13060.46610.32090.835816.43530.535222.4908
101.8494-0.0485-0.81780.4971-0.63172.32941.00820.3883-0.7136-0.6194-0.27630.330.03950.30990.57510.91370.3075-0.20040.4143-0.13030.505424.299233.67468.8975
111.2336-0.22240.0391.0283-0.12160.99420.45320.3963-0.5559-0.6260.02560.20730.56030.44381.11490.58220.1472-0.27620.2578-0.08980.457316.28340.10915.2035
120.4977-0.60180.2170.7263-0.47380.68150.17940.0592-0.07440.07290.10840.37080.13840.11130.09320.31360.0358-0.03110.30230.0580.345413.290950.109812.3343
130.7357-0.7677-1.19060.81311.25161.93690.0776-0.16-0.07060.06680.71570.73540.0297-0.13190.52740.4904-0.0412-0.00710.32180.25740.59938.514539.921621.0216
140.23130.36050.1450.23580.23290.51490.3050.1712-0.2425-0.3525-0.27760.0293-0.291-0.2578-0.01090.46490.1026-0.00470.4423-0.00840.753427.909121.16664.4092
150.4152-0.2697-0.02490.1948-0.05050.18150.2163-0.20940.02330.4272-0.03960.0941-0.1645-0.09550.00010.48110.02470.0470.3854-0.01980.721327.648821.70313.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 162 )
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 176 )
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 35 )
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 47 )
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 78 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 115 )
12X-RAY DIFFRACTION12chain 'B' and (resid 116 through 162 )
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 175 )
14X-RAY DIFFRACTION14chain 'C' and (resid 600 through 648 )
15X-RAY DIFFRACTION15chain 'D' and (resid 600 through 646 )

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