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- PDB-7e59: interferon-inducible anti-viral protein truncated -

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Basic information

Entry
Database: PDB / ID: 7.0E+59
Titleinterferon-inducible anti-viral protein truncated
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 / protein localization to Golgi apparatus / positive regulation of interleukin-18 production / 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 / molecular function inhibitor activity ...positive regulation of AIM2 inflammasome complex assembly / symbiont cell surface / protein localization to Golgi apparatus / positive regulation of interleukin-18 production / 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 / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homotetramerization / defense response to virus / 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, 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 / Rossmann fold ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Guanylate-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
G: Guanylate-binding protein 5
A: Guanylate-binding protein 5
B: Guanylate-binding protein 5
C: Guanylate-binding protein 5


Theoretical massNumber of molelcules
Total (without water)219,7064
Polymers219,7064
Non-polymers00
Water00
1
G: Guanylate-binding protein 5


Theoretical massNumber of molelcules
Total (without water)54,9271
Polymers54,9271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Guanylate-binding protein 5


Theoretical massNumber of molelcules
Total (without water)54,9271
Polymers54,9271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Guanylate-binding protein 5


Theoretical massNumber of molelcules
Total (without water)54,9271
Polymers54,9271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Guanylate-binding protein 5


Theoretical massNumber of molelcules
Total (without water)54,9271
Polymers54,9271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.874, 137.312, 203.308
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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.: 4 / 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

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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: 57.39 %
Crystal growTemperature: 289.15 K / Method: microbatch / Details: Tacsimate pH 5.0, 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 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 52289 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.045 / Rrim(I) all: 0.135 / Χ2: 1.03 / Net I/σ(I): 5.1 / Num. measured all: 475816
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.0591.88325950.5920.6641.9990.913100
3.05-3.118.51.64225390.6010.5971.750.916100
3.11-3.178.31.24925880.8080.4591.3330.928100
3.17-3.239.21.10925790.8270.3861.1750.941100
3.23-3.39.60.92425590.8750.3140.9770.944100
3.3-3.389.60.75826280.910.2590.8020.948100
3.38-3.469.50.55325490.9380.1880.5850.985100
3.46-3.569.50.49225800.9520.1690.5211.021100
3.56-3.669.50.38325990.9670.1320.4061.021100
3.66-3.789.40.34125900.9730.1170.3611.059100
3.78-3.919.30.26325970.9820.0910.2791.105100
3.91-4.078.50.19725850.990.0710.211.124100
4.07-4.268.70.1626020.9930.0570.1711.184100
4.26-4.489.70.11926220.9970.040.1251.184100
4.48-4.769.60.126330.9970.0340.1061.178100
4.76-5.139.40.09226170.9970.0310.0971.138100
5.13-5.649.20.09226330.9970.0320.0971.091100
5.64-6.468.30.0826660.9980.0290.0850.984100
6.46-8.139.40.0626930.9990.0210.0640.95100
8.13-508.10.04928350.9980.0180.0520.94999.9

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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: 3→48.23 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 2589 5.01 %
Rwork0.2179 49052 -
obs0.22 51641 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 258.18 Å2 / Biso mean: 107.8471 Å2 / Biso min: 46.02 Å2
Refinement stepCycle: final / Resolution: 3→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13005 0 0 0 13005
Num. residues----1633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.060.40921300.354326832813100
3.06-3.120.36611450.334527052850100
3.12-3.190.4181330.329326722805100
3.19-3.260.37171690.304326652834100
3.26-3.340.29931360.279226982834100
3.34-3.430.31671370.250227092846100
3.43-3.540.31911460.260527012847100
3.54-3.650.32671490.259526912840100
3.65-3.780.30551420.258926962838100
3.78-3.930.28431420.235627302872100
3.93-4.110.25361430.217826962839100
4.11-4.330.28041420.205527282870100
4.33-4.60.2531390.17627302869100
4.6-4.950.20271440.168527432887100
4.95-5.450.22151550.193627322887100
5.45-6.240.28571610.219627592920100
6.24-7.850.21621400.2128052945100
7.85-48.230.20091360.18922909304598
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)
14.16621.1458-0.75452.3569-0.70222.7128-0.1136-0.18810.24460.05460.0951-0.1871-0.09510.0026-0.02440.58270.05610.11460.4358-0.10010.6848-2.6447-22.540115.2605
24.67853.8255-3.97972.2758-2.28853.5175-0.09330.0936-0.5659-0.0834-0.0914-0.42010.1674-0.27170.11670.7590.08210.14090.76750.22360.8858-36.7021-68.386539.3271
35.71480.78071.33177.03541.08285.1567-0.263-0.19-0.48-0.24640.5611-0.00860.17480.3509-0.19680.61260.11540.02940.55960.03150.6907-35.0225-44.294816.259
45.08571.92751.12755.22110.76673.3544-0.2352-0.3504-0.3032-0.4420.21561.19180.1731-0.44290.05690.61710.11010.02020.48870.12691.012-50.45-45.905115.4705
52.69032.72680.56213.95891.28071.4977-0.0268-0.18250.0697-0.1868-0.16240.03090.0226-0.04210.2150.67220.17020.06650.7607-0.0850.7532-25.2814-8.851232.0992
63.48831.3621.99471.06270.25131.85290.5892-1.071-0.4163-0.413-0.7083-0.55830.6367-0.4112-0.00220.8552-0.22560.21671.1469-0.01950.87922.333513.330545.7185
79.7310.321-2.41952.2179-1.2552.3080.5493-1.5434-0.53850.3934-0.13370.1875-0.54410.7039-0.42781.1645-0.3501-0.12881.18380.15850.892-45.1145-9.0802-7.0697
85.54110.9622-0.55034.2653-0.10015.50660.10850.2326-0.8903-0.0528-0.1465-0.80590.23760.07380.02690.7064-0.13980.01890.5309-0.04960.9143-37.3278-13.251-25.837
90.418-1.58760.15637.26284.99062.5177-0.1597-0.1173-0.0702-0.1899-0.09020.2496-0.2816-0.39120.26191.13-0.00050.25270.62020.10560.848-54.817220.8953-3.3711
103.8521-1.9717-3.83997.53844.30186.67470.5943-0.38040.2042-1.1323-0.4725-0.6223-0.3048-0.0302-0.16670.7580.2117-0.05031.1201-0.09010.9383-69.414752.480930.6184
117.1117-0.10751.21245.05810.13925.58380.2033-0.86050.0758-0.1929-0.06060.0186-0.1439-0.4288-0.04060.5062-0.0736-0.04180.5491-0.06110.6058-9.8204-57.0663-12.6933
123.3276-0.07960.48523.3928-0.98442.8999-0.09390.50180.4927-0.25620.22760.5189-0.186-0.0257-0.15860.6397-0.205-0.12520.56140.06580.7079-8.8495-57.3897-28.2133
132.5764-3.00423.61313.8022-5.32618.0637-0.2273-0.1732-0.0323-0.0614-0.0120.04890.01670.19340.26410.76230.0916-0.10130.6389-0.0280.863711.2869-105.013312.559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 1 through 309 )G1 - 309
2X-RAY DIFFRACTION2chain 'G' and (resid 310 through 483 )G310 - 483
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 90 )A1 - 90
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 309 )A91 - 309
5X-RAY DIFFRACTION5chain 'A' and (resid 310 through 412 )A310 - 412
6X-RAY DIFFRACTION6chain 'A' and (resid 413 through 470 )A413 - 470
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 36 )B4 - 36
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 287 )B37 - 287
9X-RAY DIFFRACTION9chain 'B' and (resid 288 through 412 )B288 - 412
10X-RAY DIFFRACTION10chain 'B' and (resid 413 through 483 )B413 - 483
11X-RAY DIFFRACTION11chain 'C' and (resid 5 through 108 )C5 - 108
12X-RAY DIFFRACTION12chain 'C' and (resid 109 through 311 )C109 - 311
13X-RAY DIFFRACTION13chain 'C' and (resid 312 through 481 )C312 - 481

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