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- PDB-7e5a: interferon-inducible anti-viral protein R356A -

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Basic information

Entry
Database: PDB / ID: 7e5a
Titleinterferon-inducible anti-viral protein R356A
ComponentsGuanylate-binding protein 5
KeywordsHYDROLASE / interferon-induced / GTPase / anti-HIV
Function / homology
Function and homology information


positive regulation of AIM2 inflammasome complex assembly / symbiont cell surface / positive regulation of interleukin-18 production / protein localization to Golgi apparatus / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / positive regulation of cytokine production involved in inflammatory response / positive regulation of innate immune response / endopeptidase inhibitor activity / molecular function inhibitor activity ...positive regulation of AIM2 inflammasome complex assembly / symbiont cell surface / positive regulation of interleukin-18 production / protein localization to Golgi apparatus / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / positive regulation of cytokine production involved in inflammatory response / positive regulation of innate immune response / endopeptidase inhibitor activity / molecular function inhibitor activity / positive regulation of NLRP3 inflammasome complex assembly / protein targeting / side of membrane / activation of innate immune response / cytoplasmic vesicle membrane / positive regulation of interleukin-1 beta production / cellular response to type II interferon / Interferon gamma signaling / cellular response to lipopolysaccharide / cytoplasmic vesicle / protein homotetramerization / defense response to virus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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
Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, C-terminal domain superfamily / 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. ...Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, C-terminal domain superfamily / 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. / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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: 2.5 Å
AuthorsCui, W. / Wang, W. / Chen, C. / Slater, B. / Xiong, Y. / Ji, X.Y. / 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
DepositionFeb 18, 2021Deposition 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)110,9568
Polymers109,8532
Non-polymers1,1036
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-61 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.260, 114.260, 168.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 158 or resid 165 through 483 or resid 593 through 595))
21(chain B and (resid 5 through 332 or (resid 333...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 158 or resid 165 through 483 or resid 593 through 595))A5 - 158
121(chain A and (resid 5 through 158 or resid 165 through 483 or resid 593 through 595))A165 - 483
131(chain A and (resid 5 through 158 or resid 165 through 483 or resid 593 through 595))A593 - 595
211(chain B and (resid 5 through 332 or (resid 333...B5 - 332
221(chain B and (resid 5 through 332 or (resid 333...B333
231(chain B and (resid 5 through 332 or (resid 333...B5 - 484
241(chain B and (resid 5 through 332 or (resid 333...B5 - 484
251(chain B and (resid 5 through 332 or (resid 333...B5 - 484
261(chain B and (resid 5 through 332 or (resid 333...B5 - 484

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Components

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


Mass: 54926.523 Da / Num. of mol.: 2 / Mutation: R356A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP5, UNQ2427/PRO4987 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96PP8, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: 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
#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3 / 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 / 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

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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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 289.15 K / Method: microbatch
Details: ammonium sulfate, HEPES pH 7.5, 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: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 44229 / % possible obs: 98.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.041 / Rrim(I) all: 0.131 / Χ2: 1.035 / Net I/σ(I): 5.5 / Num. measured all: 401695
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.547.91.29421990.6390.4551.3760.76698.6
2.54-2.599.41.12321790.7790.3691.1840.783100
2.59-2.649.30.94422090.8160.3120.9970.804100
2.64-2.699.40.79721820.8720.2620.8410.80299.9
2.69-2.759.40.67222440.8910.2210.7090.811100
2.75-2.829.20.57121980.9320.1880.6030.851100
2.82-2.899.40.49221920.9350.1610.5190.84899.5
2.89-2.969.30.38622090.960.1260.4070.90399.1
2.96-3.059.20.32521900.970.1070.3430.9599
3.05-3.158.80.25522330.9810.0850.2691.06799.6
3.15-3.267.80.22221990.9840.0780.2361.09199.3
3.26-3.399.30.18122120.9880.0590.1911.14599.5
3.39-3.559.70.1522000.9920.0480.1581.25799.1
3.55-3.739.50.12822180.9930.0410.1351.2498.9
3.73-3.979.40.11822080.9940.0380.1241.33498.5
3.97-4.279.30.10121900.9950.0330.1061.32997.4
4.27-4.78.40.08721720.9960.0290.0921.22996.1
4.7-5.389.10.08322190.9960.0270.0871.16697.5
5.38-6.789.50.08222660.9960.0270.0871.11298.1
6.78-508.20.07523100.9830.0280.0811.18895.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f5n

1f5n


Resolution: 2.5→49.48 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 2288 5.18 %
Rwork0.2111 41887 -
obs0.2131 44175 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.36 Å2 / Biso mean: 84.6632 Å2 / Biso min: 40.41 Å2
Refinement stepCycle: final / Resolution: 2.5→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7370 0 66 110 7546
Biso mean--52.38 61.23 -
Num. residues----936
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4319X-RAY DIFFRACTION11.585TORSIONAL
12B4319X-RAY DIFFRACTION11.585TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.550.35751340.33762566270097
2.55-2.610.33381410.29726222763100
2.61-2.680.33561690.289926002769100
2.68-2.750.27111290.273226202749100
2.75-2.830.29581460.269526262772100
2.83-2.920.31761440.26982601274599
2.92-3.030.32221470.27042588273599
3.03-3.150.31081200.25292641276199
3.15-3.290.29931250.24922651277699
3.29-3.460.24991620.23032615277799
3.46-3.680.29991460.22362609275599
3.68-3.960.23221690.20752578274799
3.96-4.360.22711510.18272580273197
4.36-4.990.18721300.16782598272897
4.99-6.290.23691220.19552689281198
6.29-49.480.21951530.17292703285695
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)
11.1950.0356-0.18130.95370.02070.9621-0.09290.0139-0.0276-0.01230.06620.0243-0.1038-0.1875-00.5272-0.0298-0.00420.4126-0.00680.416531.16661.10269.527
20.3688-0.21130.56050.16620.16790.16830.02940.0722-0.10320.33960.0056-0.2923-0.40690.2641-0.00021.1153-0.19690.16320.54450.08790.965748.569651.00571.469
30.1177-0.1125-0.29190.01070.07820.3082-0.47930.1153-0.02730.56690.5431-0.21120.3885-0.2263-0.00031.4008-0.2198-0.25290.79930.13181.377541.049991.506810.5443
40.3419-0.06970.17260.0206-0.07520.15140.0425-0.0368-0.12350.18290.2593-0.52720.39830.323600.6463-0.13460.02610.5881-0.05630.717174.24165.8408-3.1855
50.36620.02450.17710.4839-0.17490.2358-0.0478-0.0613-0.02210.10910.1905-0.21040.11480.13820.00010.5766-0.12460.06580.395-0.04690.523162.8613-0.7112-6.3189
60.82780.0651-0.07610.34880.33650.7044-0.08940.07040.1413-0.18420.116-0.1528-0.1976-0.082700.6377-0.10570.02170.44150.03860.482149.463610.6322-11.0317
71.43490.1544-0.25940.2830.21771.0394-0.10760.22190.0924-0.12830.13340.0459-0.0627-0.022500.5847-0.13390.0260.4074-0.00850.51355.8664.9452-11.3782
80.02330.08650.02460.3134-0.22670.23190.08440.1333-0.2756-0.3553-0.10170.0289-0.4336-0.269-0.00020.98140.0992-0.02450.5358-0.06270.645530.564140.263418.202
90.46410.63840.55430.50910.2279-0.2902-0.364-0.0262-0.0075-0.27970.25640.7105-0.156-0.060201.41740.1612-0.09190.5962-0.03580.761828.064775.421519.0849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 312 )A5 - 312
2X-RAY DIFFRACTION2chain 'A' and (resid 313 through 412 )A313 - 412
3X-RAY DIFFRACTION3chain 'A' and (resid 413 through 483 )A413 - 483
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 36 )B5 - 36
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 108 )B37 - 108
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 211 )B109 - 211
7X-RAY DIFFRACTION7chain 'B' and (resid 212 through 312 )B212 - 312
8X-RAY DIFFRACTION8chain 'B' and (resid 313 through 373 )B313 - 373
9X-RAY DIFFRACTION9chain 'B' and (resid 374 through 484 )B374 - 484

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