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- PDB-9jjw: Truncated RNF112, GDP-bound form 1 -

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Basic information

Entry
Database: PDB / ID: 9jjw
TitleTruncated RNF112, GDP-bound form 1
ComponentsLOC432253 protein
KeywordsHYDROLASE / RNF112 / GTPase / Dynamin / E3 ligase
Function / homology
Function and homology information


endoplasmic reticulum organization / protein homooligomerization / GTPase activity / GTP binding / zinc 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
GUANOSINE-5'-DIPHOSPHATE / LOC432253 protein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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

Downloads & links

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Assembly

Deposited unit
A: LOC432253 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6773
Polymers46,2101
Non-polymers4682
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-8 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.461, 147.377, 71.111
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-781-

HOH

21A-865-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Tacsimate pH 7.0,

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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 PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.09→77.71 Å / Num. obs: 28846 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 16.5
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4143 / CC1/2: 0.819 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: 000)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.19_4092: 000)phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→43.28 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 2000 6.94 %
Rwork0.1839 --
obs0.1865 28817 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 29 221 3453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083301
X-RAY DIFFRACTIONf_angle_d1.0434454
X-RAY DIFFRACTIONf_dihedral_angle_d9.773434
X-RAY DIFFRACTIONf_chiral_restr0.052483
X-RAY DIFFRACTIONf_plane_restr0.007565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.32381270.2591892X-RAY DIFFRACTION100
2.14-2.20.27231560.23791887X-RAY DIFFRACTION100
2.2-2.260.28131270.23151886X-RAY DIFFRACTION100
2.26-2.340.28161470.21231912X-RAY DIFFRACTION100
2.34-2.420.26771520.21391870X-RAY DIFFRACTION100
2.42-2.520.26111310.21011909X-RAY DIFFRACTION100
2.52-2.630.25211520.2151906X-RAY DIFFRACTION100
2.63-2.770.25311350.23131904X-RAY DIFFRACTION100
2.77-2.950.25381420.22361901X-RAY DIFFRACTION100
2.95-3.170.27871440.21171910X-RAY DIFFRACTION100
3.17-3.490.1941420.18451928X-RAY DIFFRACTION100
3.49-40.20781440.15241948X-RAY DIFFRACTION100
4-5.030.1561500.1391934X-RAY DIFFRACTION99
5.03-43.280.20861510.16772030X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -32.9206 Å / Origin y: -35.3908 Å / Origin z: -17.423 Å
111213212223313233
T0.2248 Å20.0056 Å2-0.0139 Å2-0.2627 Å20.0185 Å2--0.2214 Å2
L0.8422 °20.5493 °20.1106 °2-1.347 °20.1405 °2--0.671 °2
S-0.0216 Å °-0.0189 Å °0.0132 Å °-0.0218 Å °0.0253 Å °-0.1301 Å °-0.058 Å °0.1333 Å °-0.0013 Å °
Refinement TLS groupSelection details: all

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