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- PDB-8yva: Crystal structure of Caenorhabditis elegans ZIM-2 ZF1-2-CTD domai... -

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Basic information

Entry
Database: PDB / ID: 8yva
TitleCrystal structure of Caenorhabditis elegans ZIM-2 ZF1-2-CTD domain in complex with Chromosome V pairing center
Components
  • C2H2-type domain-containing protein
  • DNA (5'-D(*AP*GP*CP*AP*GP*CP*GP*CP*CP*CP*AP*A)-3')
  • DNA (5'-D(*TP*TP*GP*GP*GP*CP*GP*CP*TP*GP*CP*T)-3')
KeywordsDNA BINDING PROTEIN / doule stranded DNA binding protein
Function / homology: / meiotic chromosome segregation / Zinc finger C2H2 type domain signature. / condensed nuclear chromosome / Zinc finger C2H2-type / DNA / DNA (> 10) / C2H2-type domain-containing protein
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLi, F.D. / Li, M.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371282 China
National Natural Science Foundation of China (NSFC)32171222 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for C. elegans pairing center DNA binding specificity by the ZIM/HIM-8 family proteins.
Authors: Li, M. / Zhu, C. / Xu, Z. / Xu, M. / Kuang, Y. / Hou, X. / Huang, X. / Lv, M. / Liu, Y. / Zhang, Y. / Xu, Z. / Han, X. / Wang, S. / Shi, Y. / Guang, S. / Li, F.
History
DepositionMar 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C2H2-type domain-containing protein
B: C2H2-type domain-containing protein
C: DNA (5'-D(*TP*TP*GP*GP*GP*CP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(*AP*GP*CP*AP*GP*CP*GP*CP*CP*CP*AP*A)-3')
E: DNA (5'-D(*TP*TP*GP*GP*GP*CP*GP*CP*TP*GP*CP*T)-3')
F: DNA (5'-D(*AP*GP*CP*AP*GP*CP*GP*CP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,50410
Polymers44,2426
Non-polymers2624
Water5,368298
1
A: C2H2-type domain-containing protein
C: DNA (5'-D(*TP*TP*GP*GP*GP*CP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(*AP*GP*CP*AP*GP*CP*GP*CP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2525
Polymers22,1213
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-20 kcal/mol
Surface area8630 Å2
MethodPISA
2
B: C2H2-type domain-containing protein
E: DNA (5'-D(*TP*TP*GP*GP*GP*CP*GP*CP*TP*GP*CP*T)-3')
F: DNA (5'-D(*AP*GP*CP*AP*GP*CP*GP*CP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2525
Polymers22,1213
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-19 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.019, 46.351, 59.228
Angle α, β, γ (deg.)79.41, 74.33, 72.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein C2H2-type domain-containing protein


Mass: 14794.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zim-2, CELE_T07G12.10, T07G12.10 / Production host: Escherichia coli (E. coli) / References: UniProt: O18067
#2: DNA chain DNA (5'-D(*TP*TP*GP*GP*GP*CP*GP*CP*TP*GP*CP*T)-3')


Mass: 3685.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: DNA chain DNA (5'-D(*AP*GP*CP*AP*GP*CP*GP*CP*CP*CP*AP*A)-3')


Mass: 3641.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 293 K / Method: vapor diffusion, hanging drop / Details: 30% w/v PEG 4000 and 0.2 M Imidazole malate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 31655 / % possible obs: 96.9 % / Redundancy: 3.4 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.037 / Rrim(I) all: 0.07 / Χ2: 0.873 / Net I/σ(I): 7.5 / Num. measured all: 108350
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.90.34314340.9380.9840.2280.4130.77289.5
1.83-1.863.10.33115390.9520.9880.2160.3970.75293.8
1.86-1.93.30.35715530.9430.9850.2260.4240.8893.8
1.9-1.943.30.37215720.8980.9730.2410.4451.04596.9
1.94-1.983.40.28315640.9430.9850.1780.3350.84696.6
1.98-2.033.30.22815970.9580.9890.1480.2730.86896.6
2.03-2.083.30.23915720.9330.9830.1570.2871.20196.7
2.08-2.133.60.19715960.9720.9930.1220.2330.98896.6
2.13-2.23.60.15315830.9830.9960.0940.180.80198
2.2-2.273.60.15415700.9470.9860.0990.1841.10196.5
2.27-2.353.50.12716210.9840.9960.0810.1510.94598.4
2.35-2.443.40.115940.9910.9980.0640.1190.88897.3
2.44-2.553.30.09515990.9880.9970.0620.1140.91597.8
2.55-2.693.70.08815730.9920.9980.0540.1030.94998.1
2.69-2.863.60.06516210.9940.9990.040.0760.77398.1
2.86-3.083.50.05616110.9940.9990.0350.0670.83298.2
3.08-3.393.30.04715930.9980.9990.030.0560.78598.4
3.39-3.883.70.04116320.9970.9990.0250.0480.76798.7
3.88-4.883.40.0416140.9950.9990.0260.0480.7399
4.88-403.60.03916170.9960.9990.0240.0460.63598.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→32.99 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 1384 4.89 %
Rwork0.176 --
obs0.1781 28318 87.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 952 4 298 2940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082790
X-RAY DIFFRACTIONf_angle_d1.053944
X-RAY DIFFRACTIONf_dihedral_angle_d27.783675
X-RAY DIFFRACTIONf_chiral_restr0.055423
X-RAY DIFFRACTIONf_plane_restr0.011336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.2927910.20841582X-RAY DIFFRACTION52
1.86-1.940.23291150.21611976X-RAY DIFFRACTION64
1.94-2.030.26361220.20332441X-RAY DIFFRACTION79
2.03-2.130.28721440.20882791X-RAY DIFFRACTION90
2.13-2.270.2391630.18182978X-RAY DIFFRACTION97
2.27-2.440.21941350.19093037X-RAY DIFFRACTION98
2.44-2.690.22611460.19423000X-RAY DIFFRACTION98
2.69-3.080.24311520.17953067X-RAY DIFFRACTION98
3.08-3.880.19041600.15253013X-RAY DIFFRACTION98
3.88-32.990.19381560.15833049X-RAY DIFFRACTION99

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