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- PDB-9jjv: Truncated RNF112, transition-like state -

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Basic information

Entry
Database: PDB / ID: 9jjv
TitleTruncated RNF112, transition-like state
ComponentsLOC432253 protein
KeywordsHYDROLASE / RNF112 / GTPase / Dynamin / E3 ligase
Function / homology
Function and homology information


GTPase activity / GTP binding / metal ion binding
Similarity search - Function
Guanylate-binding protein, N-terminal / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / zinc finger of C3HC4-type, RING / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type ...Guanylate-binding protein, N-terminal / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / zinc finger of C3HC4-type, RING / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / LOC432253 protein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZhong, Y.T. / Huang, L.L. / Gao, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32320103002 China
National Natural Science Foundation of China (NSFC)82173098 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural and functional characterization of the brain-specific dynamin superfamily member RNF112.
Authors: Zhong, Y.T. / Huang, L.L. / Li, K. / Yang, B. / Ye, X. / Zhong, H.R. / Yu, B. / Ma, M. / Yuan, Y. / Meng, Y. / Pan, R. / Zhang, H. / Shi, L. / Wang, Y. / Tian, R. / Gao, S. / Bian, X.
History
DepositionSep 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LOC432253 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8055
Polymers46,2101
Non-polymers5954
Water5,278293
1
A: LOC432253 protein
hetero molecules

A: LOC432253 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,60910
Polymers92,4202
Non-polymers1,1908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area8970 Å2
ΔGint-62 kcal/mol
Surface area33400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.567, 148.057, 71.315
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
11A-729-

HOH

21A-838-

HOH

31A-889-

HOH

41A-974-

HOH

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Components

#1: Protein LOC432253 protein / Ring finger protein 112 L homeolog


Mass: 46209.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: rnf112.L, LOC432253, rnf112, rnf112.S, znf179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2VPQ0
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tacsimate pH 7.0,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 21, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→77.88 Å / Num. obs: 39475 / % possible obs: 99.2 % / Redundancy: 11.5 % / CC1/2: 0.999 / Net I/σ(I): 14.5
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2689 / CC1/2: 0.609 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: 000)refinement
DIALSdata reduction
DIALSdata scaling
PHENIX(1.19_4092: 000)phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→37.01 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 1954 4.96 %
Rwork0.1863 --
obs0.1882 39404 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 35 293 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093309
X-RAY DIFFRACTIONf_angle_d1.0884467
X-RAY DIFFRACTIONf_dihedral_angle_d10.394434
X-RAY DIFFRACTIONf_chiral_restr0.058482
X-RAY DIFFRACTIONf_plane_restr0.01567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.3591080.3552474X-RAY DIFFRACTION92
1.93-1.980.28841580.25132545X-RAY DIFFRACTION96
1.98-2.040.21561410.2232640X-RAY DIFFRACTION99
2.04-2.10.23481580.2072622X-RAY DIFFRACTION100
2.1-2.180.2661260.19932708X-RAY DIFFRACTION100
2.18-2.270.29731100.23772676X-RAY DIFFRACTION100
2.27-2.370.23481390.21052681X-RAY DIFFRACTION100
2.37-2.490.22421480.19312696X-RAY DIFFRACTION100
2.49-2.650.22151800.20072657X-RAY DIFFRACTION100
2.65-2.850.2511430.22679X-RAY DIFFRACTION100
2.85-3.140.24091410.19942705X-RAY DIFFRACTION100
3.14-3.60.19861220.1742739X-RAY DIFFRACTION100
3.6-4.530.20271370.14962758X-RAY DIFFRACTION100
4.53-37.010.19511430.15962870X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -32.9448 Å / Origin y: -35.3093 Å / Origin z: -17.6977 Å
111213212223313233
T0.1813 Å20.004 Å2-0.0184 Å2-0.2272 Å20.0192 Å2--0.1708 Å2
L0.8798 °20.4644 °20.0292 °2-1.475 °20.097 °2--0.583 °2
S-0.0038 Å °-0.0425 Å °0.0286 Å °-0.0186 Å °-0.0015 Å °-0.1263 Å °-0.0159 Å °0.1153 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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