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- PDB-5wdh: Motor domain of human kinesin family member C1 -

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Basic information

Entry
Database: PDB / ID: 5wdh
TitleMotor domain of human kinesin family member C1
ComponentsKinesin-like protein KIFC1
KeywordsMOTOR PROTEIN / kinesin / structural genomics consortium / motor domain / adp / SGC
Function / homology
Function and homology information


Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule organizing center / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / mitotic sister chromatid segregation / mitotic spindle assembly / mitotic spindle ...Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule organizing center / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / mitotic sister chromatid segregation / mitotic spindle assembly / mitotic spindle / microtubule binding / spermatogenesis / microtubule / early endosome / cell division / ATP hydrolysis activity / ATP binding / membrane / nucleus
Similarity search - Function
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 ...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 KIFC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å
AuthorsZhu, H. / Tempel, W. / He, H. / Shen, Y. / Wang, J. / Brothers, G. / 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: 2REP
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
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 KIFC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0309
Polymers40,5791
Non-polymers4528
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.713, 63.713, 242.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Kinesin-like protein KIFC1 / Kinesin-like protein 2 / Kinesin-related protein HSET


Mass: 40578.613 Da / Num. of mol.: 1 / Fragment: motor domain (UNP residues 307-663)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIFC1, HSET, KNSL2 / Plasmid: pFBOH-LIC / Cell line (production host): HighFive / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BW19
#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.: 6 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 3.5M sodium chloride, 0.1M bis-tris propane, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→48.49 Å / Num. obs: 24875 / % possible obs: 99.8 % / Redundancy: 14 % / Biso Wilson estimate: 61.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Net I/σ(I): 29.4 / Num. measured all: 349118 / Scaling rejects: 3
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
2.25-2.3213.81.3363038722030.9450.3671.3862.398.4
8.99-48.499.80.02346154690.9990.0080.02569.596.7

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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: pdb entry 2ncd

2ncd


Resolution: 2.248→39.35 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 31.55 / Stereochemistry target values: ML
Details: Merging statistics indicate significant anisotropy of crystal diffraction. Notwithstanding the nominal resolution cut-off, electron density was not clear enough to confirm correctness of the ...Details: Merging statistics indicate significant anisotropy of crystal diffraction. Notwithstanding the nominal resolution cut-off, electron density was not clear enough to confirm correctness of the sequence register outright. The higher resolution PDB entry 1F9T of a yeast kinesin-like protein was used to validate register and conformation of some side chains. Nevertheless, the current model contains segments where the alignment of the amino acid sequence remains uncertain.
RfactorNum. reflection% reflection
Rfree0.2646 2310 5.12 %
Rwork0.224 42835 -
obs0.226 45145 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.39 Å2 / Biso mean: 84.2449 Å2 / Biso min: 46.8 Å2
Refinement stepCycle: final / Resolution: 2.248→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 34 4 2178
Biso mean--63.88 68.43 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092215
X-RAY DIFFRACTIONf_angle_d0.8953010
X-RAY DIFFRACTIONf_chiral_restr0.051349
X-RAY DIFFRACTIONf_plane_restr0.005391
X-RAY DIFFRACTIONf_dihedral_angle_d18.0851314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2478-2.29370.38161390.35592448258796
2.2937-2.34360.32641430.3272511265499
2.3436-2.39810.31281350.29922494262999
2.3981-2.45810.32221520.298625462698100
2.4581-2.52450.28661410.26942474261599
2.5245-2.59880.35061330.263725192652100
2.5988-2.68260.32281330.275525282661100
2.6826-2.77850.26881520.27525302682100
2.7785-2.88970.35851250.274625272652100
2.8897-3.02120.3591480.302425422690100
3.0212-3.18040.38061570.278925092666100
3.1804-3.37960.3081390.250825132652100
3.3796-3.64030.29741360.213225172653100
3.6403-4.00640.23681070.203925572664100
4.0064-4.58530.22291190.174925622681100
4.5853-5.77410.19911230.187925462669100
5.7741-39.35590.22161280.21722512264099
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)
12.1471-0.4821-0.90420.48420.58962.45260.40970.4544-0.1588-0.1161-0.33960.12360.6409-0.91590.00290.55910.0190.02620.952-0.00630.61547.302317.8187107.0414
20.77650.7747-0.09721.05120.4951.37020.22230.42850.4665-0.31920.079-0.37760.0910.3323-00.66570.14150.21950.77870.15990.760768.627.3227103.3423
30.8203-0.10560.8960.4491-0.70641.79280.29080.35120.1374-0.118-0.00250.0302-0.0356-0.0223-0.00040.62560.08050.16050.6870.08190.762763.395926.2454110.3065
40.66370.0469-0.01810.5462-0.23661.70560.56191.16810.3476-0.5706-0.4676-0.03450.0502-0.7660.00030.69040.2980.13451.19430.15960.729451.727725.943695.6297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 309 through 451 )A309 - 451
2X-RAY DIFFRACTION2chain 'A' and (resid 452 through 509 )A452 - 509
3X-RAY DIFFRACTION3chain 'A' and (resid 510 through 550 )A510 - 550
4X-RAY DIFFRACTION4chain 'A' and (resid 551 through 663 )A551 - 663

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