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- PDB-8yv9: Crystal structure of Caenorhabditis elegans HIM-8 ZF1-2-CTD domai... -

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Basic information

Entry
Database: PDB / ID: 8yv9
TitleCrystal structure of Caenorhabditis elegans HIM-8 ZF1-2-CTD domain in complex with Chromosome X pairing center
Components
  • C2H2-type domain-containing protein
  • DNA (5'-D(*TP*GP*CP*AP*CP*TP*GP*AP*CP*CP*AP*A)-3')
  • DNA (5'-D(*TP*TP*GP*GP*TP*CP*AP*GP*TP*GP*CP*A)-3')
KeywordsDNA BINDING PROTEIN / double stranded DNA binding protein
Function / homology
Function and homology information


meiotic chromosome segregation / X chromosome / condensed nuclear chromosome / nuclear envelope / nucleus
Similarity search - Function
: / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / C2H2-type domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 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: DNA (5'-D(*TP*TP*GP*GP*TP*CP*AP*GP*TP*GP*CP*A)-3')
C: DNA (5'-D(*TP*GP*CP*AP*CP*TP*GP*AP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1805
Polymers24,0493
Non-polymers1312
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-22 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.021, 54.296, 76.770
Angle α, β, γ (deg.)90.00, 109.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein C2H2-type domain-containing protein


Mass: 16724.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: him-8, CELE_T07G12.12, T07G12.12 / Production host: Escherichia coli (E. coli) / References: UniProt: O18068
#2: DNA chain DNA (5'-D(*TP*TP*GP*GP*TP*CP*AP*GP*TP*GP*CP*A)-3')


Mass: 3693.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: DNA chain DNA (5'-D(*TP*GP*CP*AP*CP*TP*GP*AP*CP*CP*AP*A)-3')


Mass: 3631.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% w/v PEG 3350, 0.1M Bis-Tris pH 5.5, and 0.1 M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 12651 / % possible obs: 98.6 % / Redundancy: 4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.066 / Χ2: 0.803 / Net I/σ(I): 13.6 / Num. measured all: 50982
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.14-2.182.70.3285310.8940.9720.220.3970.92684.3
2.18-2.223.10.2986220.9310.9820.1930.3570.87497.2
2.22-2.263.30.2746240.9150.9780.1710.3251.03498.1
2.26-2.313.50.2455980.9350.9830.1470.2870.94298.7
2.31-2.363.80.2326680.9540.9880.1330.2680.92697.9
2.36-2.414.20.2076050.970.9920.1130.2360.96599.7
2.41-2.474.40.1976490.9690.9920.1050.2240.88899.7
2.47-2.544.40.1686320.9770.9940.0890.1910.893100
2.54-2.614.30.1566250.9780.9950.0830.1770.952100
2.61-2.74.20.1236660.9840.9960.0680.1410.961100
2.7-2.794.40.1066170.9860.9960.0560.120.93399.8
2.79-2.94.40.0966430.9860.9960.0510.1090.909100
2.9-3.044.20.0756510.9920.9980.0420.0860.816100
3.04-3.24.10.0646270.9930.9980.0360.0740.82899.1
3.2-3.44.30.0556480.9920.9980.0330.0650.76899.7
3.4-3.664.20.0476520.9940.9990.0270.0550.71399.8
3.66-4.034.20.0416340.9950.9990.0230.0480.56999.1
4.03-4.614.20.0356340.9960.9990.0190.040.45499.1
4.61-5.814.20.0336570.9960.9990.0180.0380.38999.4
5.81-5040.046680.9970.9990.0230.0460.50899.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→27.89 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 625 5.01 %
Rwork0.1786 --
obs0.1807 12478 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 486 2 129 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081378
X-RAY DIFFRACTIONf_angle_d1.0091950
X-RAY DIFFRACTIONf_dihedral_angle_d27.433340
X-RAY DIFFRACTIONf_chiral_restr0.056209
X-RAY DIFFRACTIONf_plane_restr0.006164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.360.26021800.20262757X-RAY DIFFRACTION92
2.36-2.70.27271500.20962999X-RAY DIFFRACTION100
2.7-3.40.23641380.18943030X-RAY DIFFRACTION99
3.4-27.890.18271570.15513067X-RAY DIFFRACTION99

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