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- PDB-5jv3: The neck-linker and alpha 7 helix of Homo sapiens Eg5 fused to EB1 -

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Basic information

Entry
Database: PDB / ID: 5jv3
TitleThe neck-linker and alpha 7 helix of Homo sapiens Eg5 fused to EB1
ComponentsChimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
KeywordsMOTOR PROTEIN / kinesin / coiled-coil
Function / homology
Function and homology information


protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / spindle elongation / protein localization to microtubule / microtubule plus-end / cell projection membrane / mitotic spindle microtubule / attachment of mitotic spindle microtubules to kinetochore ...protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / spindle elongation / protein localization to microtubule / microtubule plus-end / cell projection membrane / mitotic spindle microtubule / attachment of mitotic spindle microtubules to kinetochore / microtubule bundle formation / regulation of mitotic centrosome separation / microtubule plus-end binding / non-motile cilium assembly / plus-end-directed microtubule motor activity / Kinesins / mitotic centrosome separation / protein localization to centrosome / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic spindle pole / negative regulation of microtubule polymerization / spindle midzone / microtubule polymerization / microtubule organizing center / establishment of mitotic spindle orientation / mitotic spindle assembly / regulation of microtubule polymerization or depolymerization / spindle assembly / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / mitotic spindle organization / RHO GTPases Activate Formins / spindle / spindle pole / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / cell migration / mitotic cell cycle / microtubule binding / microtubule / ciliary basal body / cadherin binding / cell division / focal adhesion / intracellular membrane-bounded organelle / centrosome / protein kinase binding / Golgi apparatus / protein-containing complex / RNA binding / ATP binding / identical protein binding / nucleus / membrane / 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-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : ...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-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Calponin homology (CH) 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 / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Kinesin motor domain superfamily / 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 KIF11 / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 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)R37-GM54141 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 10, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
B: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
C: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
D: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8615
Polymers35,8214
Non-polymers401
Water4,684260
1
A: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
B: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)17,9102
Polymers17,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-40 kcal/mol
Surface area9630 Å2
MethodPISA
2
C: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
D: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9503
Polymers17,9102
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-36 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.839, 59.502, 72.664
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1 / Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / ...Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / Thyroid receptor-interacting protein 5 / TRIP-5 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 8955.164 Da / Num. of mol.: 4
Fragment: UNP P52732 residues 366-391,UNP Q15691 residues 210-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52732, UniProt: Q15691
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% (w/v) PEE797, 100 mM CaCl2, 100 mM MOPS pH 7.0, 0.1% (w/v) octylglucoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→30.622 Å / Num. obs: 19131 / % possible obs: 97 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.9
Reflection shellResolution: 2→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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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: 2.006→30.622 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 962 5.03 %
Rwork0.2154 --
obs0.217 19131 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.006→30.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 1 260 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022239
X-RAY DIFFRACTIONf_angle_d0.3242998
X-RAY DIFFRACTIONf_dihedral_angle_d17.4431410
X-RAY DIFFRACTIONf_chiral_restr0.032333
X-RAY DIFFRACTIONf_plane_restr0.002391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0056-2.11140.30541250.26162283X-RAY DIFFRACTION86
2.1114-2.24360.27591380.23352609X-RAY DIFFRACTION99
2.2436-2.41680.26351390.22972685X-RAY DIFFRACTION100
2.4168-2.65990.25091410.23192658X-RAY DIFFRACTION100
2.6599-3.04440.29151420.22552659X-RAY DIFFRACTION100
3.0444-3.83450.23411420.19612694X-RAY DIFFRACTION100
3.8345-30.62560.21061350.20172581X-RAY DIFFRACTION95
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)
11.878-0.1678-2.02472.70892.5348.45930.0757-0.30760.00570.65070.00190.1850.34920.1061-0.00760.2607-0.03780.00630.1286-0.00330.315214.4565-0.556547.9225
24.5895-1.9383-0.66756.1311.92655.04180.53540.5810.1968-1.19240.03270.7843-0.4128-0.9943-0.1220.37660.0254-0.18740.41870.20220.547810.7813-2.194120.6591
33.1223-3.19990.14713.3585-0.12350.01660.526-0.22540.5828-1.0643-0.284-0.0258-0.08370.4116-0.57990.8266-0.02690.25480.7498-0.04090.50030.79717.24968.8619
42.4927-0.8523-2.17354.00932.54258.92440.007-0.0402-0.12740.2324-0.13680.43270.0024-0.43350.19160.0768-0.0337-0.04570.11250.00750.30669.9803-5.583639.1458
58.6341-1.5243.06057.1743-4.80437.7242-0.14790.2176-0.1594-0.11530.0332-0.6178-0.15750.18550.07590.12520.0257-0.00280.1218-0.06090.314625.9687-10.125329.8788
65.587-7.11476.23832.0015-8.0037.01530.96410.4811-0.35270.6970.0972-2.2110.75353.0169-0.89910.50990.0259-0.26330.9206-0.2130.63956.2988-20.63348.1467
70.64830.551-1.13520.7912-0.21224.2057-0.04860.31850.024-0.63260.0607-0.1052-0.4608-0.6691-0.0180.57860.10230.03230.322-0.01230.17650.5088-16.12897.2436
86.5225-5.68946.56945.7707-5.6426.6232-0.7996-1.18060.18440.44390.67840.7173-1.396-2.3992-0.20910.54380.25810.00630.70180.03050.3621-12.9805-14.849442.6131
90.93530.3207-1.42120.6245-0.40596.1973-0.03740.16320.0381-0.70130.1104-0.00350.5075-0.0238-0.03630.56760.06520.05210.2084-0.02030.172.6067-21.199212.348
107.2995-0.1604-4.35792.0749-0.02963.483-0.47170.9510.161-0.09720.1745-0.2253-1.78830.14210.23031.0332-0.150.04070.46360.03040.29417.1455-9.9373-10.0099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 72 )
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 15 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 53 )
5X-RAY DIFFRACTION5chain 'B' and (resid 54 through 76 )
6X-RAY DIFFRACTION6chain 'C' and (resid 3 through 7 )
7X-RAY DIFFRACTION7chain 'C' and (resid 8 through 66 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 7 )
9X-RAY DIFFRACTION9chain 'D' and (resid 8 through 53 )
10X-RAY DIFFRACTION10chain 'D' and (resid 54 through 68 )

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