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- PDB-4ap0: The mitotic kinesin Eg5 in complex with Mg-ADP and ispinesib -

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Basic information

Entry
Database: PDB / ID: 4ap0
TitleThe mitotic kinesin Eg5 in complex with Mg-ADP and ispinesib
ComponentsKINESIN-LIKE PROTEIN KIF11
KeywordsMOTOR PROTEIN
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / Kinesins / mitotic centrosome separation / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / Kinesins / mitotic centrosome separation / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle pole / spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / 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 / ISPINESIB MESILATE / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsSchuettelkopf, A.W. / Talapatra, S.K. / Kozielski, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The Structure of the Ternary Eg5-Adp-Ispinesib Complex
Authors: Talapatra, S.K. / Schuettelkopf, A.W. / Kozielski, F.
History
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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 KIF11
B: KINESIN-LIKE PROTEIN KIF11
C: KINESIN-LIKE PROTEIN KIF11
D: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,92622
Polymers164,8394
Non-polymers4,08718
Water59433
1
A: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2496
Polymers41,2101
Non-polymers1,0395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2857
Polymers41,2101
Non-polymers1,0756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1784
Polymers41,2101
Non-polymers9693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2145
Polymers41,2101
Non-polymers1,0044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.723, 112.607, 106.913
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999836, 0.017322, 0.005236), (0.017328, -0.999849, -0.001067), (0.005217, 0.001158, -0.999986)32.1999, -0.0851, 40.8745
2given(0.995714, 0.04425, 0.081214), (-0.04123, 0.998408, -0.038493), (-0.082788, 0.034979, 0.995953)28.3733, 1.8342, 55.1788
3given(0.994926, 0.058629, 0.081758), (0.056537, -0.998017, 0.02767), (0.083218, -0.022907, -0.996268)-3.9612, -1.5086, 92.7185

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
KINESIN-LIKE PROTEIN KIF11 / 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 / EG5 / THYROID RECEPTOR-INTERACTING PROTEIN 5 / TR-INTERACTING PROTEIN 5 / TRIP-5


Mass: 41209.746 Da / Num. of mol.: 4 / Fragment: MOTOR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P52732

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Non-polymers , 5 types, 51 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-G7X / ISPINESIB MESILATE


Mass: 517.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H33ClN4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CRYSTALLIZED CONSTRUCT INCLUDES RESIDUES 1 TO 368 OF HUMAN EG5 PRECEDED BY TWO AMINO ACIDS, GP, ...THE CRYSTALLIZED CONSTRUCT INCLUDES RESIDUES 1 TO 368 OF HUMAN EG5 PRECEDED BY TWO AMINO ACIDS, GP, A REMNANT OF THE CLEAVED AFFINITY TAG.

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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: 2.21 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8.5
Details: 0.1M TRIS, PH 8.5; 0.02M MGCL2; 20%(W/V) POLYETHYLENE GLYCOL 8000; 4DEGC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.452
ReflectionResolution: 2.6→30 Å / Num. obs: 45511 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GM1

2gm1


Resolution: 2.594→29.862 Å / σ(F): 0 / Phase error: 29.04 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2525 2386 5.2 %
Rwork0.2035 --
obs0.2065 45505 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.19 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 57.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.6274 Å20 Å2-4.4209 Å2
2---0.2643 Å20 Å2
3---1.8917 Å2
Refinement stepCycle: LAST / Resolution: 2.594→29.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9553 0 263 33 9849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01610369
X-RAY DIFFRACTIONf_angle_d1.46913527
X-RAY DIFFRACTIONf_dihedral_angle_d17.7713664
X-RAY DIFFRACTIONf_chiral_restr0.0941614
X-RAY DIFFRACTIONf_plane_restr0.0091692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5945-2.64740.44731230.44042207X-RAY DIFFRACTION80
2.6474-2.70480.50511220.36972529X-RAY DIFFRACTION90
2.7048-2.76760.49011550.34712506X-RAY DIFFRACTION90
2.7676-2.83670.39341410.31832532X-RAY DIFFRACTION91
2.8367-2.91320.3541290.28582529X-RAY DIFFRACTION92
2.9132-2.99870.37671200.27012580X-RAY DIFFRACTION93
2.9987-3.09520.34581480.25672584X-RAY DIFFRACTION92
3.0952-3.20550.29041470.2382559X-RAY DIFFRACTION92
3.2055-3.33340.25841300.22252583X-RAY DIFFRACTION93
3.3334-3.48450.2511470.21052593X-RAY DIFFRACTION93
3.4845-3.66730.30621140.23922446X-RAY DIFFRACTION88
3.6673-3.89580.25421390.19922442X-RAY DIFFRACTION87
3.8958-4.19450.18031250.16022590X-RAY DIFFRACTION93
4.1945-4.61280.191190.13422628X-RAY DIFFRACTION94
4.6128-5.27150.19121340.14142590X-RAY DIFFRACTION93
5.2715-6.60890.22331450.17552624X-RAY DIFFRACTION93
6.6089-21.38330.14541600.14842636X-RAY DIFFRACTION92
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)
10.0056-0.0013-0.00540.0011-0.00210.0144-0.0127-0.0021-0.0152-0.01510.01250.00360.0259-0.0261-0.0149-0.014-0.00260.00450.4230.04290.057715.7072-10.995328.2217
20.03780.0219-0.01790.0162-0.00960.0398-0.0072-0.01370.04370.01320.05650.0258-0.03730.00670.06120.04-0.0144-0.00780.51970.06510.119847.95810.639111.9871
30.0057-0.0014-0.0080.00630.00180.0347-0.00850.0137-0.0243-0.00490.0166-0.0030.03190.00710.01080.00870.0144-0.01980.51920.05340.083345.9648-10.434781.8173
40.01180.00450.01060.00860.00380.0122-0.0020.00080.01550.00330.03790.0021-0.02440.03910.09-0.0103-0.0007-0.00620.47480.04660.095913.418410.827465.9789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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