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- PDB-9jko: Crystal structure of the RNA- binding domain of human ZAR1 -

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Basic information

Entry
Database: PDB / ID: 9jko
TitleCrystal structure of the RNA- binding domain of human ZAR1
ComponentsZygote arrest protein 1
KeywordsRNA BINDING PROTEIN / RNA / ZAR1
Function / homology
Function and homology information


RNA sequestering activity / membraneless organelle assembly / mRNA stabilization / oocyte maturation / intracellular membraneless organelle / mRNA 3'-UTR binding / molecular condensate scaffold activity / cytoplasmic ribonucleoprotein granule / negative regulation of translation / translation ...RNA sequestering activity / membraneless organelle assembly / mRNA stabilization / oocyte maturation / intracellular membraneless organelle / mRNA 3'-UTR binding / molecular condensate scaffold activity / cytoplasmic ribonucleoprotein granule / negative regulation of translation / translation / zinc ion binding / cytoplasm
Similarity search - Function
Zygote arrest protein 1 / Zinc-binding domain / Zinc-binding domain / Zinc-binding domain
Similarity search - Domain/homology
Zygote arrest protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsLiu, Q.L. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Febs Lett. / Year: 2025
Title: Molecular insights into RNA recognition by the ZAR1 C-terminal domain.
Authors: Liu, Q. / Ma, H. / He, X. / Xu, C. / Zhang, J.
History
DepositionSep 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zygote arrest protein 1
B: Zygote arrest protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0348
Polymers23,6412
Non-polymers3926
Water6,449358
1
A: Zygote arrest protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0174
Polymers11,8211
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zygote arrest protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0174
Polymers11,8211
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.610, 58.450, 81.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zygote arrest protein 1


Mass: 11820.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86SH2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Succinic acid pH 7.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 1.63→27.51 Å / Num. obs: 29055 / % possible obs: 99.95 % / Redundancy: 12.6 % / CC1/2: 0.984 / Net I/σ(I): 10.3
Reflection shellResolution: 1.63→1.69 Å / Rmerge(I) obs: 1.78 / Num. unique obs: 1998 / CC1/2: 0.714

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→27.51 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 2000 6.88 %
Rwork0.188 --
obs0.19 29055 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→27.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 1 358 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.14
X-RAY DIFFRACTIONf_dihedral_angle_d6.35229
X-RAY DIFFRACTIONf_chiral_restr0.07221
X-RAY DIFFRACTIONf_plane_restr0.011291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.31821390.25831892X-RAY DIFFRACTION100
1.67-1.720.26591420.23241903X-RAY DIFFRACTION100
1.72-1.770.26841400.23761910X-RAY DIFFRACTION100
1.77-1.820.30091410.23311898X-RAY DIFFRACTION100
1.82-1.890.25631410.22321904X-RAY DIFFRACTION100
1.89-1.960.23121410.19311899X-RAY DIFFRACTION100
1.96-2.050.2161420.17651926X-RAY DIFFRACTION100
2.05-2.160.22251420.19081918X-RAY DIFFRACTION100
2.16-2.30.23841410.1931913X-RAY DIFFRACTION100
2.3-2.470.19751430.19131931X-RAY DIFFRACTION100
2.47-2.720.21011430.1931944X-RAY DIFFRACTION100
2.72-3.120.23151440.18151953X-RAY DIFFRACTION100
3.12-3.920.16911470.1591984X-RAY DIFFRACTION100
3.93-27.510.17621540.16122080X-RAY DIFFRACTION100

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