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- PDB-2g1l: Crystal structure of the FHA domain of human kinesin family member C -

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Basic information

Entry
Database: PDB / ID: 2g1l
TitleCrystal structure of the FHA domain of human kinesin family member C
ComponentsKinesin-like protein KIF1C
KeywordsTRANSPORT PROTEIN / transport / FHA domain / structural genomics consortium / kinesin / SGC
Function / homology
Function and homology information


anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / cytoskeleton-dependent intracellular transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement ...anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / cytoskeleton-dependent intracellular transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement / cytoskeletal motor activity / vesicle-mediated transport / axon cytoplasm / microtubule binding / microtubule / neuron projection / axon / dendrite / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
Tumour Suppressor Smad4 - #20 / Kinesin-associated / Kinesin-associated / Kinesin-like protein / Tumour Suppressor Smad4 / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain ...Tumour Suppressor Smad4 - #20 / Kinesin-associated / Kinesin-associated / Kinesin-like protein / Tumour Suppressor Smad4 / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Kinesin-like protein KIF1C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.602 Å
AuthorsWang, J. / Tempel, W. / Shen, Y. / Shen, L. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the FHA domain of human kinesin family member C
Authors: Wang, J. / Tempel, W. / Shen, Y. / Shen, L. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionFeb 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 42MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 11.67 (3.26 B<40) BAD ROTAMERS : 1.1% 1/94 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.0% 0/101 (TARGET 0.2%) RAMACHANDRAN FAVORED : 96.0% 97/101 (TARGET 98.0%)
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7814
Polymers11,6861
Non-polymers943
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Kinesin-like protein KIF1C
hetero molecules

A: Kinesin-like protein KIF1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5618
Polymers23,3732
Non-polymers1886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area1880 Å2
ΔGint-65 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.620, 107.620, 82.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Detailsnot known

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Components

#1: Protein Kinesin-like protein KIF1C


Mass: 11686.424 Da / Num. of mol.: 1 / Fragment: FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF1C, KIAA0706 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: O43896
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
1679.3
2679.3
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.4M malonate, pH 7, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 9139 / % possible obs: 99.8 % / Redundancy: 20.9 % / Rmerge(I) obs: 0.121 / Χ2: 0.974 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2.6-2.6999.421.30.948770.7321
2.69-2.899.521.40.728810.7281
2.8-2.9399.721.30.5548840.7551
2.93-3.0899.621.30.3899090.791
3.08-3.2899.921.20.2498820.8341
3.28-3.5399.821.20.159061.0521
3.53-3.8899.9210.1159181.2221
3.88-4.4410020.90.0739221.2631
4.44-5.5910020.60.0539361.2231
5.59-30100190.03910241.121

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å29.08 Å
Translation3 Å29.08 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1wln

1wln


Resolution: 2.602→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.181 / SU B: 6.996 / SU ML: 0.144 / ESU R: 0.222 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2433 423 4.639 %
Rwork0.2147 --
all0.216 --
obs0.216 9119 99.781 %
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: 40.806 Å2
Baniso -1Baniso -2Baniso -3
1-2.394 Å21.197 Å20 Å2
2--2.394 Å20 Å2
3----3.591 Å2
Refinement stepCycle: LAST / Resolution: 2.602→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 3 8 825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022830
X-RAY DIFFRACTIONr_bond_other_d0.0030.02560
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.971125
X-RAY DIFFRACTIONr_angle_other_deg0.83931375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27924.61539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14415147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.117155
X-RAY DIFFRACTIONr_chiral_restr0.0780.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02154
X-RAY DIFFRACTIONr_nbd_refined0.2080.2146
X-RAY DIFFRACTIONr_nbd_other0.1950.2537
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2378
X-RAY DIFFRACTIONr_nbtor_other0.0880.2492
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.420.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0950.21
X-RAY DIFFRACTIONr_mcbond_it3.4272653
X-RAY DIFFRACTIONr_mcbond_other0.4672207
X-RAY DIFFRACTIONr_mcangle_it4.1453839
X-RAY DIFFRACTIONr_scbond_it2.6672349
X-RAY DIFFRACTIONr_scangle_it3.6973286
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 all% reflection obs (%)
2.602-2.6690.452280.3316200.33665299.387
2.669-2.7410.315270.315990.3163099.365
2.741-2.820.375320.2845880.28862499.359
2.82-2.9060.344370.2815700.28560999.672
2.906-3.0010.295220.2365610.23958499.829
3.001-3.1050.195240.2525390.2556499.823
3.105-3.2210.289250.2325170.234542100
3.221-3.3510.243180.235200.231538100
3.351-3.4980.288290.2184870.22251799.807
3.498-3.6660.248270.214670.212494100
3.666-3.8610.256200.1994440.20246599.785
3.861-4.0910.2190.1894200.18944199.546
4.091-4.3680.192170.1784120.179429100
4.368-4.7090.141190.1753830.174402100
4.709-5.1460.152120.163500.16362100
5.146-5.7320.266180.1813180.185336100
5.732-6.5790.304100.2253020.227312100
6.579-7.9630.134170.222510.214268100
7.963-10.8840.219100.1722090.174219100
10.884-300.245120.2611390.26151100

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