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- PDB-7eqb: Crystal structure of the dimerization domain of ZEN-4 -

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Basic information

Entry
Database: PDB / ID: 7eqb
TitleCrystal structure of the dimerization domain of ZEN-4
ComponentsKinesin-like protein
KeywordsCELL CYCLE / ZEN-4 / Dimerization domain / Coiled-coil
Function / homology
Function and homology information


pronuclear migration / regulation of actomyosin contractile ring contraction / meiotic spindle midzone assembly / polar body extrusion after meiotic divisions / mitotic spindle midzone assembly / mitotic spindle midzone / plus-end-directed microtubule motor activity / microtubule motor activity / kinesin complex / microtubule-based movement ...pronuclear migration / regulation of actomyosin contractile ring contraction / meiotic spindle midzone assembly / polar body extrusion after meiotic divisions / mitotic spindle midzone assembly / mitotic spindle midzone / plus-end-directed microtubule motor activity / microtubule motor activity / kinesin complex / microtubule-based movement / mitotic sister chromatid segregation / cleavage furrow / spindle midzone / midbody / microtubule binding / microtubule / centrosome / protein kinase binding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Kinesin-like protein Kif23, Arf6-interacting domain / Kinesin-like protein Kif23, Arf6-interacting domain superfamily / Arf6-interacting domain of mitotic kinesin-like protein 1 / 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-like protein Kif23, Arf6-interacting domain / Kinesin-like protein Kif23, Arf6-interacting domain superfamily / Arf6-interacting domain of mitotic kinesin-like protein 1 / 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
Similarity search - Domain/homology
Kinesin-like protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.103 Å
AuthorsChen, Z. / Pan, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Mechanistic insights into central spindle assembly mediated by the centralspindlin complex.
Authors: Pan, H. / Guan, R. / Zhao, R. / Ou, G. / Chen, Z.
History
DepositionMay 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein
B: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8376
Polymers18,4532
Non-polymers3844
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-56 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.542, 116.542, 47.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Kinesin-like protein / ZEN-4


Mass: 9226.589 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zen-4, CELE_M03D4.1, M03D4.1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EG83
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.33 Å3/Da / Density % sol: 71.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 16% PEG2K, 200mM MgSO4, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 19067 / % possible obs: 98.2 % / Redundancy: 4.8 % / CC1/2: 0.522 / Net I/σ(I): 16.949
Reflection shellResolution: 2.1→2.17 Å / Num. unique obs: 1695 / CC1/2: 0.552

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.103→34.937 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.59 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 954 5 %
Rwork0.2305 18111 -
obs0.2324 19065 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.53 Å2 / Biso mean: 38.12 Å2 / Biso min: 2.32 Å2
Refinement stepCycle: final / Resolution: 2.103→34.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 20 24 1161
Biso mean--90.92 34.06 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071141
X-RAY DIFFRACTIONf_angle_d1.0371501
X-RAY DIFFRACTIONf_chiral_restr0.076151
X-RAY DIFFRACTIONf_plane_restr0.004196
X-RAY DIFFRACTIONf_dihedral_angle_d15.949489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.103-2.21360.28921230.2592233691
2.2136-2.35230.28251350.25255398
2.3523-2.53380.32221350.24032581100
2.5338-2.78870.24631380.23932610100
2.7887-3.1920.30861370.25832617100
3.192-4.02070.26921400.21362668100
4.0207-34.9370.23921460.2171274698
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)
10.0006-0.0004-0.00010.0018-0-0.00010.00330.00350.00350.00030.0020.00290.00590.0102-00.2911-0.141-0.02270.214-0.02560.3499-7.644232.48053.1246
20.00010.00030.00030.0004-0.0012-0.0001-0.02650.0069-0.00090.02760.005-0.01210.01360.003800.0954-0.42970.00010.0344-0.07260.2526-19.011922.19233.657
30.00150.0008-0.00130.00030.0019-0.0012-0.01680.00630.00820.01430.0009-0.0018-0.0206-0.00310-0.0564-0.329-0.01440.0304-0.06410.141-35.12549.1207-1.2127
40.0021-00.00050.0009-0.00070.00170.00510.0001-0.00420.00290.0107-0.0068-0.00650.0185-00.02330.05150.04540.06490.01950.0492-50.9166-1.6309-7.6388
50.0026-0.0001-0.001100.00050.0009-0.0161-0.0011-0.0025-0-0.00030.00340.00930.00750-0.0008-0.0146-0.01180.0658-0.0536-0.0577-61.2328-6.2746-9.5373
60.00080.0008-0.00070.00060.00020.0016-0.002-0.00180.00250.00780.0062-0.0117-0.0027-0.0087-00.0566-0.0824-0.0030.2183-0.01260.0729-67.9433-10.3742-11.6307
70.0012-0.0005-0.00030.00060.00010.00160.00650.0057-0.0025-0.00320.005-0.00050.0022-0.00590-0.0401-0.202-0.04920.1098-0.04430.0623-75.8334-13.0218-9.9932
80.00150.0014-0.00170.0008-0.00110.00420.0115-0.0111-0.0028-0.00160.00280.0023-0.0016-0.0052-00.3359-0.1777-0.00040.4373-0.05230.3602-83.7449-17.4646-12.0714
90.00030.0015-0.0014-0.0011-0.00190.0022-0.00870.007-0.0050.00060.0124-0.0170.0249-0.0105-00.0402-0.54660.1340.1527-0.07220.2599-15.427723.7711-5.1778
100.00020.0038-0.0001-0.0017-0.0048-0.0050.00190.01090.0186-0.01350.025-0.046-0.06280.0925-0-0.1522-0.33750.1433-0.18420.1391-0.0446-42.255214.1391-5.9055
110.0019-0.0006-0.0017-0.0002-0.0055-0.00080.01350.00390.03530.0197-0.0523-0.02310.0871-0.0548-0-0.2607-0.1930.0946-0.00290.05060.0969-67.7912-4.3441-2.4761
120.00050.0013-0.00020.0001-0.00070.0004-0.0006-0.001-0.00480.00150.00690.00620.0042-0.0003-00.1143-0.25180.00790.1656-0.02650.19-82.7012-20.05440.1065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 532:537)A532 - 537
2X-RAY DIFFRACTION2(chain A and resid 538:551)A538 - 551
3X-RAY DIFFRACTION3(chain A and resid 552:566)A552 - 566
4X-RAY DIFFRACTION4(chain A and resid 567:577)A567 - 577
5X-RAY DIFFRACTION5(chain A and resid 578:582)A578 - 582
6X-RAY DIFFRACTION6(chain A and resid 583:587)A583 - 587
7X-RAY DIFFRACTION7(chain A and resid 588:593)A588 - 593
8X-RAY DIFFRACTION8(chain A and resid 594:599)A594 - 599
9X-RAY DIFFRACTION9(chain B and resid 534:551)B534 - 551
10X-RAY DIFFRACTION10(chain B and resid 552:572)B552 - 572
11X-RAY DIFFRACTION11(chain B and resid 573:593)B573 - 593
12X-RAY DIFFRACTION12(chain B and resid 594:601)B594 - 601

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