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- PDB-5wde: Crystal structure of the KIFC3 motor domain in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 5wde
TitleCrystal structure of the KIFC3 motor domain in complex with ADP
ComponentsKinesin-like protein KIFC3
KeywordsMOTOR PROTEIN / kinesin / motor domain / adp / STRUCTURAL GENOMICS / STRUCTUR AL GENOMICS CONSORTIUM / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


zonula adherens maintenance / epithelial cell-cell adhesion / zonula adherens / minus-end-directed microtubule motor activity / kinesin complex / microtubule motor activity / microtubule-based movement / Golgi organization / Association of TriC/CCT with target proteins during biosynthesis / visual perception ...zonula adherens maintenance / epithelial cell-cell adhesion / zonula adherens / minus-end-directed microtubule motor activity / kinesin complex / microtubule motor activity / microtubule-based movement / Golgi organization / Association of TriC/CCT with target proteins during biosynthesis / visual perception / cytoplasmic vesicle membrane / microtubule binding / microtubule / centrosome / Golgi apparatus / extracellular exosome / ATP binding / identical protein binding
Similarity search - Function
Kinesin-like protein KIFC3-like / 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-like protein KIFC3-like / 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-like protein KIFC3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsShen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of small molecule ATPase inhibition of a human mitotic kinesin motor protein.
Authors: Park, H.W. / Ma, Z. / Zhu, H. / Jiang, S. / Robinson, R.C. / Endow, S.A.
History
DepositionJul 5, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 9, 2017ID: 2H58
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIFC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,67349
Polymers36,2221
Non-polymers45248
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.608, 187.608, 151.363
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsAuthor states that there is no direct experimental evidence for biological assembly since this is a fragment of full length protein.

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Components

#1: Protein Kinesin-like protein KIFC3


Mass: 36221.527 Da / Num. of mol.: 1 / Fragment: motor domain (UNP residues 443-770)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIFC3 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: Q9BVG8
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 46 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 7.3 Å3/Da / Density % sol: 83.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.2M sodium citrate, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9176 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9176 Å / Relative weight: 1
ReflectionResolution: 1.85→47.69 Å / Num. obs: 86307 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 22.2 / Num. measured all: 549983 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.886.40.9922941445680.6620.4331.0872100
9.79-47.694.80.02126365540.9990.010.02456.389.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f9t

1f9t


Resolution: 1.85→27.079 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 24.68
Details: This REDO of the KIFC3 structure was in part motivated by the PDB-REDO model of PDB entry 2H58. Diffraction images that formed the basis for PDB entry 2H58 were reprocessed. Merging ...Details: This REDO of the KIFC3 structure was in part motivated by the PDB-REDO model of PDB entry 2H58. Diffraction images that formed the basis for PDB entry 2H58 were reprocessed. Merging statistics indicate significant anisotropy of diffraction. For this round of model refinement, new crossvalidation flags were assigned to the reflections using the CCP4 FREERFLAG command. This reassignment was followed by torsion angle simulated annealing. We note the high solvent content of this crystal form and the presence of many uninterpreted features in the difference maps when contoured at 1.5*rmsd (2FOFCWT) or +/-3*rmsd (FOFCWT). We thank CCP4BB participants who responded to questions related to this structure on the board and off-list.
RfactorNum. reflection% reflection
Rfree0.1992 6755 4.02 %
Rwork0.1854 --
obs0.186 168229 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.04 Å2 / Biso mean: 37.5357 Å2 / Biso min: 20.74 Å2
Refinement stepCycle: final / Resolution: 1.85→27.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 74 126 2605
Biso mean--37.71 40.71 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112566
X-RAY DIFFRACTIONf_angle_d0.7763473
X-RAY DIFFRACTIONf_chiral_restr0.051407
X-RAY DIFFRACTIONf_plane_restr0.004451
X-RAY DIFFRACTIONf_dihedral_angle_d13.0431544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8710.36732310.362954115642100
1.871-1.8930.35622370.343454365673100
1.893-1.91610.35542140.33854105624100
1.9161-1.94040.32172450.319353505595100
1.9404-1.96590.35652410.292454095650100
1.9659-1.99280.30042480.285754355683100
1.9928-2.02130.26262090.261754165625100
2.0213-2.05140.25822160.246553805596100
2.0514-2.08350.25452380.25995403564199
2.0835-2.11760.26332180.237753895607100
2.1176-2.15410.25722090.220854215630100
2.1541-2.19330.22922470.205453785625100
2.1933-2.23540.22222110.213154095620100
2.2354-2.2810.23582420.21895347558999
2.281-2.33060.2262440.20153965640100
2.3306-2.38480.23112480.200154365684100
2.3848-2.44440.20932160.18995414563099
2.4444-2.51040.22240.187653695593100
2.5104-2.58430.21822010.189254115612100
2.5843-2.66760.19652020.19085397559999
2.6676-2.76290.20742330.19635414564799
2.7629-2.87340.2182440.195753755619100
2.8734-3.0040.22362380.1965402564099
3.004-3.16210.18952220.18295378560099
3.1621-3.35990.18381910.16995423561499
3.3599-3.61880.17662250.15595372559799
3.6188-3.98190.13882170.14045384560199
3.9819-4.55570.14782020.13325355555799
4.5557-5.73080.15512380.14815323556198
5.7308-27.08180.17342040.17655031523593
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)
11.1697-0.4150.08322.1183-0.70880.5919-0.04030.09940.2284-0.15570.0333-0.0338-0.02150.04710.09310.3009-0.01170.00710.24870.10470.2418-3.856639.634753.6495
20.1864-0.5322-0.16991.3019-0.04530.8420.06840.06860.0191-0.2018-0.0947-0.3109-0.00140.112-00.26850.01590.07580.28890.08170.33312.066822.832957.1074
30.626-0.0389-0.11661.0264-0.10980.7457-0.0629-0.0822-0.1509-0.02210.0508-0.14550.10590.18510.00010.27850.0086-0.00580.29840.06640.2864-1.19911.914864.7465
40.0736-0.01110.04140.2022-0.03570.0414-0.2310.54060.1559-0.32440.1426-0.28720.05950.19870.0020.5589-0.0576-0.04270.47830.14730.31981.524715.519747.2783
50.0503-0.1481-0.10360.892-0.04070.26430.01770.17590.0614-0.24040.01260.10860.14860.066900.34430.0049-0.00260.29120.06540.2993-2.97816.717957.1467
60.0853-0.0074-0.12310.88410.31820.58030.0595-0.0018-0.3757-0.1180.17710.23330.06940.12320.05010.27130.01120.03270.27470.09830.31431.313224.299562.5902
70.50310.1657-0.03470.5644-0.63120.8970.029-0.14010.020.09160.02470.2132-0.0618-0.010.01950.3050.01190.04250.26160.09340.2908-8.851529.196367.9291
80.25730.0181-0.09210.0638-0.05040.084-0.0543-0.03890.22740.21320.10330.5512-0.2122-0.11440.01470.35940.00930.03240.25070.12220.3777-14.826340.781259.0574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 445 through 546 )A445 - 546
2X-RAY DIFFRACTION2chain 'A' and (resid 547 through 578 )A547 - 578
3X-RAY DIFFRACTION3chain 'A' and (resid 579 through 618 )A579 - 618
4X-RAY DIFFRACTION4chain 'A' and (resid 619 through 634 )A619 - 634
5X-RAY DIFFRACTION5chain 'A' and (resid 635 through 659 )A635 - 659
6X-RAY DIFFRACTION6chain 'A' and (resid 660 through 687 )A660 - 687
7X-RAY DIFFRACTION7chain 'A' and (resid 688 through 748 )A688 - 748
8X-RAY DIFFRACTION8chain 'A' and (resid 749 through 767 )A749 - 767

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