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- PDB-8yvb: Crystal structure of Caenorhabditis elegans ZIM-1 ZF1-2-CTD domai... -

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Basic information

Entry
Database: PDB / ID: 8yvb
TitleCrystal structure of Caenorhabditis elegans ZIM-1 ZF1-2-CTD domain in complex with Chromosome II/III pairing center
Components
  • C2H2-type domain-containing protein
  • DNA (5'-D(*TP*TP*GP*GP*TP*CP*TP*GP*CP*TP*A)-3')
  • DNA (5'-D(P*AP*GP*CP*AP*GP*AP*CP*CP*AP*A)-3')
KeywordsDNA BINDING PROTEIN / double 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: 1.9 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*TP*GP*CP*TP*A)-3')
C: DNA (5'-D(P*AP*GP*CP*AP*GP*AP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5475
Polymers21,4163
Non-polymers1312
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-18 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.767, 62.464, 101.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-118-

HOH

21C-120-

HOH

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Components

#1: Protein C2H2-type domain-containing protein


Mass: 15013.706 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zim-1, CELE_T07G12.6, T07G12.6 / Production host: Escherichia coli (E. coli) / References: UniProt: B2MZC6
#2: DNA chain DNA (5'-D(*TP*TP*GP*GP*TP*CP*TP*GP*CP*TP*A)-3')


Mass: 3355.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: DNA chain DNA (5'-D(P*AP*GP*CP*AP*GP*AP*CP*CP*AP*A)-3')


Mass: 3047.033 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.: 110 / 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: 2.06 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG 600 and 0.1 M HEPES, pH 7.4

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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: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 14363 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.028 / Rrim(I) all: 0.101 / Χ2: 0.956 / Net I/σ(I): 6.5 / Num. measured all: 183804
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9311.90.9726960.8530.960.2891.0150.947100
1.93-1.9712.50.9216990.870.9650.2690.9610.939100
1.97-2.0112.30.787170.8870.9690.2290.8140.954100
2.01-2.05130.6656910.9080.9750.190.6920.944100
2.05-2.0912.70.5717300.940.9840.1650.5950.967100
2.09-2.1412.70.4546890.960.990.1320.4730.997100
2.14-2.1911.30.3647160.9640.9910.1110.3810.982100
2.19-2.2513.40.3366980.9770.9940.0950.3490.971100
2.25-2.3213.60.2927300.9830.9960.0820.3031.006100
2.32-2.3913.50.2517050.9830.9960.070.2610.986100
2.39-2.4813.30.2247260.9890.9970.0640.2330.96100
2.48-2.5813.30.1766960.9910.9980.050.1830.979100
2.58-2.6913.20.1497150.9940.9990.0430.1550.985100
2.69-2.8411.60.1237250.9930.9980.0370.1290.95899.7
2.84-3.0113.70.1087120.9960.9990.030.1121.028100
3.01-3.2513.60.0847270.9980.9990.0240.0870.989100
3.25-3.5713.20.0737290.99910.0210.0760.971100
3.57-4.0812.20.0687360.9980.9990.020.0710.91699.7
4.08-5.13130.0657390.9960.9990.0190.0680.872100
5.13-2012.10.0617870.9980.9990.0180.0640.75999.4

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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: 1.9→19.7 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 692 4.9 %
Rwork0.1896 --
obs0.192 14122 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 428 2 110 1404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031365
X-RAY DIFFRACTIONf_angle_d0.5851917
X-RAY DIFFRACTIONf_dihedral_angle_d26.111538
X-RAY DIFFRACTIONf_chiral_restr0.04204
X-RAY DIFFRACTIONf_plane_restr0.003167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.26151310.22462492X-RAY DIFFRACTION95
2.05-2.250.27831420.20692677X-RAY DIFFRACTION100
2.25-2.580.25861410.19882705X-RAY DIFFRACTION100
2.58-3.240.22571260.1982739X-RAY DIFFRACTION100
3.25-19.70.22081520.16842817X-RAY DIFFRACTION100
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)
11.4199-0.2372-0.18880.69160.00940.82030.06210.4871-0.0364-0.5493-0.0711-0.2203-0.18340.04260.01750.175-0.04270.0850.1679-0.01730.11598.5443-19.38079.4904
22.42020.5326-0.20992.3141-0.56871.92690.001-0.1489-0.5209-0.252-0.2203-0.31490.20960.28240.11550.0983-0.00620.00840.16320.01690.18690.5877-36.690815.3719
30.25450.44070.39741.07880.55410.6604-0.0797-0.3176-0.19140.234-0.14940.19290.3728-0.1519-0.1110.2205-0.05390.05740.1810.07330.24781.8367-31.773923.8883
41.0233-0.4165-0.97092.72930.36111.7628-0.21410.0059-0.08230.0730.244-0.5462-0.13860.53920.17730.1647-0.07590.05630.1853-0.03840.221714.1314-16.855116.7125
50.6279-0.17420.24411.5545-0.15821.3280.01490.1168-0.0271-0.27190.03510.0782-0.085-0.1866-0.08870.14330.0227-0.02070.1596-0.00960.1415-6.4339-18.978413.1304
60.4876-0.04130.45810.04520.09531.69990.09540.1202-0.0553-0.4114-0.08560.0462-0.0707-0.32890.05380.20680.0054-0.04410.1651-0.02760.1162-6.3212-21.150611.9505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 454 through 493 )
2X-RAY DIFFRACTION2chain 'A' and (resid 494 through 516 )
3X-RAY DIFFRACTION3chain 'A' and (resid 517 through 536 )
4X-RAY DIFFRACTION4chain 'A' and (resid 537 through 558 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 11 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 11 )

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