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- PDB-5jvm: The neck-linker and alpha 7 helix of Mus musculus KIF3C -

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Basic information

Entry
Database: PDB / ID: 5jvm
TitleThe neck-linker and alpha 7 helix of Mus musculus KIF3C
ComponentsChimera protein of Kinesin-like protein KIF3C and Microtubule-associated protein RP/EB family member 1
KeywordsMOTOR PROTEIN / kinesin / coiled-coil
Function / homology
Function and homology information


microtubule motor activity => GO:0003777 / Intraflagellar transport / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / neuronal ribonucleoprotein granule / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / protein localization to microtubule / organelle transport along microtubule ...microtubule motor activity => GO:0003777 / Intraflagellar transport / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / neuronal ribonucleoprotein granule / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / protein localization to microtubule / organelle transport along microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / kinesin complex / microtubule motor activity / microtubule-based movement / mitotic spindle pole / microtubule polymerization / establishment of mitotic spindle orientation / kinesin binding / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / protein localization / positive regulation of neuron projection development / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / cell migration / synaptic vesicle / growth cone / microtubule binding / microtubule / molecular adaptor activity / cadherin binding / cell division / axon / focal adhesion / centrosome / dendrite / neuronal cell body / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / RNA binding / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Kinesin-like protein / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Kinesin-like protein / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Kinesin motor domain signature. / Calponin homology (CH) domain profile. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Kinesin-like protein KIF3C / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.567 Å
AuthorsPhillips, R.K. / Rayment, I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37-GM54141 United States
National Science Foundation (NSF, United States)DGE-0718123 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil.
Authors: Phillips, R.K. / Peter, L.G. / Gilbert, S.P. / Rayment, I.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera protein of Kinesin-like protein KIF3C and Microtubule-associated protein RP/EB family member 1
B: Chimera protein of Kinesin-like protein KIF3C and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3023
Polymers19,2782
Non-polymers241
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-42 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.074, 71.979, 43.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chimera protein of Kinesin-like protein KIF3C and Microtubule-associated protein RP/EB family member 1 / / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 9638.826 Da / Num. of mol.: 2
Fragment: UNP O35066 residues 374-402,UNP Q15691 residues 207-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Kif3c, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O35066, UniProt: Q15691
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% (w/v) pentaerythritol ethoxylate (PEE) 797, 1.5% (w/v) ethylene glycol monoethylether, 400 mM MgCl2, 100 mM bis-tris propane pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.5667→37.004 Å / Num. obs: 44738 / % possible obs: 98 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.7
Reflection shellResolution: 1.5667→1.62 Å / Redundancy: 3 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.6 / Num. measured obs: 2513

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIB

1yib


Resolution: 1.567→37.004 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 2241 5.01 %
Rwork0.1774 --
obs0.1788 44738 73.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.567→37.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 1 276 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051381
X-RAY DIFFRACTIONf_angle_d0.6441861
X-RAY DIFFRACTIONf_dihedral_angle_d17.2879
X-RAY DIFFRACTIONf_chiral_restr0.043203
X-RAY DIFFRACTIONf_plane_restr0.004253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5667-1.60080.2955740.26321385X-RAY DIFFRACTION38
1.6008-1.6380.2278880.22631702X-RAY DIFFRACTION48
1.638-1.6790.2311990.21051843X-RAY DIFFRACTION50
1.679-1.72440.2269960.20141799X-RAY DIFFRACTION50
1.7244-1.77510.2205970.19811823X-RAY DIFFRACTION51
1.7751-1.83240.22761000.20791926X-RAY DIFFRACTION53
1.8324-1.89790.20551150.20082092X-RAY DIFFRACTION58
1.8979-1.97390.2391230.19682534X-RAY DIFFRACTION70
1.9739-2.06370.20921590.18783005X-RAY DIFFRACTION83
2.0637-2.17250.20771720.17843259X-RAY DIFFRACTION90
2.1725-2.30860.1991740.17553314X-RAY DIFFRACTION92
2.3086-2.48680.2041830.16753444X-RAY DIFFRACTION95
2.4868-2.7370.22721920.17273572X-RAY DIFFRACTION99
2.737-3.13290.17981980.17933610X-RAY DIFFRACTION99
3.1329-3.94640.1921830.15853600X-RAY DIFFRACTION100
3.9464-37.01460.2031880.17243589X-RAY DIFFRACTION99
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)
11.1608-0.7777-0.10376.2224-0.97993.57270.00170.1284-0.4515-0.43390.0504-0.03040.23831.19480.16170.24790.0933-0.00350.3682-0.04930.308182.746813.4093-5.1257
24.6244-4.6631-0.06164.79710.3070.442-0.118-0.05940.00530.07630.1229-0.0293-0.0263-0.02480.00620.06790.00810.03080.12780.02320.092654.494338.83824.4508
34.1538-1.3078-0.9415.1324-0.10684.5699-0.1388-0.1506-0.22880.06730.17570.30080.1708-0.25890.00470.0725-0.0096-0.01770.11330.02540.078228.137957.6141-0.5826
43.6489-0.394-2.25547.20054.35995.2884-0.095-0.0268-0.8168-0.3347-0.45230.37521.3461-0.12410.46030.30130.0519-0.05920.1868-0.0330.409468.48543.226311.2994
54.2376-6.01441.01177.8173-0.98870.29860.0663-0.0302-0.2743-0.04620.00790.32290.01460.0071-0.07060.07350.00880.02420.11640.02570.150450.369835.31740.577
64.9178-3.23083.38634.5065-1.40142.7003-0.2751-0.15780.92780.5714-0.0483-0.5755-0.32120.09250.26330.1559-0.0053-0.03580.1501-0.03940.235736.315368.92031.7938
72.8855-0.826-2.04581.4157-1.33144.76180.1289-0.49310.01920.47340.2338-0.60860.20360.35650.24650.28180.0305-0.17090.33150.01310.437645.376161.48188.7447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 82 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 55 )
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 71 )
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 79 )

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