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- PDB-7ckf: The N-terminus of interferon-inducible antiviral protein-dimer -

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Basic information

Entry
Database: PDB / ID: 7ckf
TitleThe N-terminus of interferon-inducible antiviral protein-dimer
ComponentsGuanylate-binding protein 5
KeywordsHYDROLASE / antiviral
Function / homology
Function and homology information


positive regulation of AIM2 inflammasome complex assembly / positive regulation of interleukin-18 production / symbiont cell surface / protein localization to Golgi apparatus / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / positive regulation of innate immune response / positive regulation of cytokine production involved in inflammatory response / endopeptidase inhibitor activity / positive regulation of NLRP3 inflammasome complex assembly ...positive regulation of AIM2 inflammasome complex assembly / positive regulation of interleukin-18 production / symbiont cell surface / protein localization to Golgi apparatus / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / positive regulation of innate immune response / positive regulation of cytokine production involved in inflammatory response / endopeptidase inhibitor activity / positive regulation of NLRP3 inflammasome complex assembly / molecular function inhibitor activity / protein targeting / activation of innate immune response / side of membrane / positive regulation of interleukin-1 beta production / cytoplasmic vesicle membrane / cellular response to type II interferon / Interferon gamma signaling / cytoplasmic vesicle / cellular response to lipopolysaccharide / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response to virus / protein homotetramerization / defense response to bacterium / inflammatory response / Golgi membrane / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / identical protein binding / membrane / cytoplasm
Similarity search - Function
Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Guanylate-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.284 Å
AuthorsCui, W. / Yang, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81772204 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis for GTP-induced dimerization and antiviral function of guanylate-binding proteins.
Authors: Cui, W. / Braun, E. / Wang, W. / Tang, J. / Zheng, Y. / Slater, B. / Li, N. / Chen, C. / Liu, Q. / Wang, B. / Li, X. / Duan, Y. / Xiao, Y. / Ti, R. / Hotter, D. / Ji, X. / Zhang, L. / Cui, J. ...Authors: Cui, W. / Braun, E. / Wang, W. / Tang, J. / Zheng, Y. / Slater, B. / Li, N. / Chen, C. / Liu, Q. / Wang, B. / Li, X. / Duan, Y. / Xiao, Y. / Ti, R. / Hotter, D. / Ji, X. / Zhang, L. / Cui, J. / Xiong, Y. / Sauter, D. / Wang, Z. / Kirchhoff, F. / Yang, H.
History
DepositionJul 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate-binding protein 5
B: Guanylate-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9568
Polymers70,8532
Non-polymers1,1036
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-48 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.326, 79.329, 140.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Guanylate-binding protein 5 / interferon-induced antiviral protein / GBP-TA antigen / GTP-binding protein 5 / GBP-5 / Guanine ...interferon-induced antiviral protein / GBP-TA antigen / GTP-binding protein 5 / GBP-5 / Guanine nucleotide-binding protein 5


Mass: 35426.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP5, UNQ2427/PRO4987 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: Q96PP8, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 286 K / Method: microbatch / Details: sodium formate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97879 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 33591 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 36.63 Å2 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.087 / Rrim(I) all: 0.219 / Χ2: 0.583 / Net I/σ(I): 2.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.28-2.3412.616540.6340.7810.448100
2.34-2.3812.316260.6990.6640.441100
2.38-2.4311.916660.640.540.439100
2.43-2.4811.316370.7720.5530.449100
2.48-2.5311.816610.8320.4010.456100
2.53-2.591316560.8850.3720.453100
2.59-2.6613.316610.8950.3470.456100
2.66-2.7313.516650.9290.2780.4691000.989
2.73-2.8113.416390.9650.2520.451000.90.935
2.81-2.913.516640.9570.2110.4581000.750.78
2.9-313.316670.9740.1750.4681000.6180.643
3-3.1212.916870.9850.1280.4791000.4430.461
3.12-3.261216690.9860.1070.4981000.3530.369
3.26-3.4413.216760.9930.0810.6141000.2880.299
3.44-3.6513.416780.9860.0951.0991000.3360.35
3.65-3.9312.716770.970.0981.5781000.3350.349
3.93-4.3313.117070.9970.0450.5941000.1570.164
4.33-4.9511.817220.9970.0330.5791000.110.115
4.95-6.2413.417340.9970.0330.5241000.1180.122
6.24-501218450.9990.0210.64999.90.0710.074

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b92

2b92


Resolution: 2.284→47.79 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 1624 4.84 %
Rwork0.2121 31897 -
obs0.2144 33521 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.17 Å2 / Biso mean: 45.671 Å2 / Biso min: 26.04 Å2
Refinement stepCycle: final / Resolution: 2.284→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 66 230 4329
Biso mean--39.65 47.82 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074182
X-RAY DIFFRACTIONf_angle_d1.0395697
X-RAY DIFFRACTIONf_chiral_restr0.058671
X-RAY DIFFRACTIONf_plane_restr0.005709
X-RAY DIFFRACTIONf_dihedral_angle_d7.0692495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2841-2.35130.3451920.2879241791
2.3513-2.42720.3181380.2732620100
2.4272-2.5140.26821260.25472661100
2.514-2.61460.3331300.24142625100
2.6146-2.73360.2921570.2372649100
2.7336-2.87770.28761290.21932640100
2.8777-3.0580.29391290.21472672100
3.058-3.2940.28061520.212660100
3.294-3.62540.23561280.19162687100
3.6254-4.14980.24431510.19162681100
4.1498-5.22730.19021370.17042724100
5.2273-47.790.26451550.22882861100

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