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- PDB-7e58: interferon-inducible anti-viral protein 2 -

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Basic information

Entry
Database: PDB / ID: 7.0E+58
Titleinterferon-inducible anti-viral protein 2
ComponentsGuanylate-binding protein 2
KeywordsHYDROLASE / interferon-induced / GTPase / anti-HIV
Function / homology
Function and homology information


positive regulation of AIM2 inflammasome complex assembly / cytolysis in another organism / positive regulation of pyroptosis / endopeptidase inhibitor activity / molecular function inhibitor activity / defense response to protozoan / protein localization to nucleus / cellular response to interleukin-1 / activation of innate immune response / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...positive regulation of AIM2 inflammasome complex assembly / cytolysis in another organism / positive regulation of pyroptosis / endopeptidase inhibitor activity / molecular function inhibitor activity / defense response to protozoan / protein localization to nucleus / cellular response to interleukin-1 / activation of innate immune response / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic vesicle membrane / cellular response to type II interferon / Interferon gamma signaling / Interferon alpha/beta signaling / cellular response to tumor necrosis factor / cytoplasmic vesicle / defense response to virus / cellular response to lipopolysaccharide / defense response to Gram-positive bacterium / defense response to bacterium / immune response / Golgi membrane / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / 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
Guanylate-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate-binding protein 2
B: Guanylate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)134,6462
Polymers134,6462
Non-polymers00
Water66737
1
A: Guanylate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)67,3231
Polymers67,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanylate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)67,3231
Polymers67,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.207, 124.161, 355.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 157 or resid 163 through 309 or resid 311 through 583))
21(chain B and (resid 8 through 59 or resid 76...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSER(chain A and (resid 8 through 157 or resid 163 through 309 or resid 311 through 583))AA8 - 1578 - 157
12VALVALCYSCYS(chain A and (resid 8 through 157 or resid 163 through 309 or resid 311 through 583))AA163 - 309163 - 309
13GLUGLUSERSER(chain A and (resid 8 through 157 or resid 163 through 309 or resid 311 through 583))AA311 - 583311 - 583
21PROPROALAALA(chain B and (resid 8 through 59 or resid 76...BB8 - 598 - 59
22LYSLYSGLYGLY(chain B and (resid 8 through 59 or resid 76...BB76 - 10276 - 102
23ASNASNCYSCYS(chain B and (resid 8 through 59 or resid 76...BB109 - 309109 - 309
24GLUGLUSERSER(chain B and (resid 8 through 59 or resid 76...BB311 - 583311 - 583

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Components

#1: Protein Guanylate-binding protein 2 / GTP-binding protein 2 / HuGBP-2 / Guanine nucleotide-binding protein 2 / Interferon-induced ...GTP-binding protein 2 / HuGBP-2 / Guanine nucleotide-binding protein 2 / Interferon-induced guanylate-binding protein 2


Mass: 67322.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP2 / Production host: Escherichia coli (E. coli)
References: UniProt: P32456, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThis sequence corresponds to GenBank AAH73163.

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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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 289.15 K / Method: microbatch
Details: 2-propanol, sodium citrate, tribasic dihydrate pH 5.0, polyethylene glycol 10,000

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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: 2.6→120 Å / Num. obs: 55672 / % possible obs: 92.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.057 / Rrim(I) all: 0.162 / Χ2: 1.041 / Net I/σ(I): 4.3 / Num. measured all: 414059
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.647.21.32521170.5910.4941.4210.8970.8
2.64-2.697.41.22622360.6610.4511.3120.88975.6
2.69-2.747.51.10923880.7130.4061.1860.87281.5
2.74-2.87.51.02624590.7510.3751.0970.89883.4
2.8-2.867.60.88525710.7990.3210.9450.89685.2
2.86-2.937.60.74626020.8520.2710.7980.92490.5
2.93-37.50.65927570.8730.2420.7050.93292.4
3-3.087.30.53328290.9190.1990.5720.93394.3
3.08-3.176.80.44628700.9360.1740.4810.96298.4
3.17-3.286.60.37828950.9360.1530.410.99895.1
3.28-3.397.50.31428890.9610.1180.3371.01598.7
3.39-3.537.70.24729470.9770.0910.2651.06497.6
3.53-3.697.80.19529060.9820.0720.2091.11297.8
3.69-3.887.60.15929310.9870.0590.171.16695.7
3.88-4.137.50.13829380.990.0520.1481.1799.3
4.13-4.457.20.10629300.9930.040.1141.23296.7
4.45-4.896.30.09129780.9950.0370.0991.27997.4
4.89-5.67.50.09130020.9960.0330.0981.06697.8
5.6-7.067.90.09231120.9950.0340.0991.01799.1
7.06-1208.60.05933150.9980.0210.0631.28399.4

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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: 2.6→47.03 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2715 2779 5.04 %
Rwork0.2546 52339 -
obs0.2555 55118 93.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.85 Å2 / Biso mean: 79.2679 Å2 / Biso min: 35.27 Å2
Refinement stepCycle: final / Resolution: 2.6→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8827 0 0 37 8864
Biso mean---56.98 -
Num. residues----1101
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5285X-RAY DIFFRACTION13.133TORSIONAL
12B5285X-RAY DIFFRACTION13.133TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.640.44921240.38931996212071
2.64-2.690.3863990.36022165226480
2.69-2.740.35691230.35712242236582
2.74-2.80.39031150.37042392250784
2.8-2.860.35731410.36772404254589
2.86-2.930.4041470.36122494264191
2.93-30.42141330.35932601273492
3-3.080.37211490.33312644279397
3.08-3.170.40021280.32162736286497
3.17-3.280.3121280.31132721284996
3.28-3.390.3451400.30682702284299
3.39-3.530.2981620.28832725288796
3.53-3.690.26631480.25652731287999
3.69-3.880.2671530.23792706285996
3.88-4.130.26251190.23712792291199
4.13-4.440.20651340.20472755288997
4.45-4.890.18941580.18632755291397
4.89-5.60.2331660.21932794296098
5.6-7.050.25541540.24972915306999
7.05-47.030.20991580.19573069322799
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)
11.41680.74180.40364.0414-0.88672.69650.2567-0.25650.05130.3383-0.3168-0.0525-0.41860.25550.05990.7538-0.25560.14940.5690.00630.44729.5484-23.5795-45.441
21.5554-0.218-0.8892.4146-1.67023.333-0.0588-0.1737-0.4935-0.6382-0.3596-0.57470.49060.66460.38321.0018-0.14310.22850.6182-0.00490.695332.0572-33.4366-58.8912
32.47951.3478-0.44411.58820.54771.8486-0.5940.63920.0501-0.02220.33210.4240.4715-0.16170.19051.3031-0.41460.20010.8035-0.0490.43728.333-25.9124-75.8549
40.68541.5173-1.18542.539-2.08491.4759-0.09340.04430.0646-0.02870.09620.25430.1158-0.1602-0.03210.9229-0.22710.14380.6128-0.01060.61519.5427-33.479-44.3549
51.31371.0422-1.88860.8088-1.67434.00910.3902-0.28570.26190.2304-0.00480.1105-0.63050.4594-0.35510.8372-0.11080.17930.5421-0.00350.5632-3.1849-63.96084.8417
60.6860.7818-0.51041.6884-1.08260.6734-0.3410.2086-0.0001-0.58610.37930.00120.4686-0.29690.1270.9562-0.18560.09550.5353-0.04860.64438.8999-59.1556-37.1444
71.64530.34330.54913.12070.79013.8690.02980.070.156-0.56240.2166-0.1561-0.86270.1627-0.13150.4388-0.0390.12060.35060.03120.30711.673941.2285-45.6834
81.62380.48140.05583.34360.57522.88570.1661-0.23070.20140.5644-0.0789-0.0541-0.4131-0.094-0.08520.4615-0.0140.09790.40.05840.3185-3.881336.7787-28.6146
90.22910.1150.15592.081.26881.50750.01930.0164-0.01720.00630.0896-0.1754-0.14510.0176-0.08450.4098-0.05480.0560.41830.02630.36442.141422.8767-50.3614
100.056-0.3864-0.39842.64532.44823.81370.24890.08840.1924-0.2248-0.1928-0.1779-0.44220.1677-0.19380.58720.03050.04420.6223-0.06250.44937.8623-20.019-104.14
110.2423-0.1828-0.05211.96491.71092.5798-0.0760.0013-0.05740.73490.06450.01810.95130.00150.24790.6212-0.16070.08690.47180.04760.4195-3.4835-0.2208-53.7384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 122 )A8 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 181 )A123 - 181
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 211 )A182 - 211
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 373 )A212 - 373
5X-RAY DIFFRACTION5chain 'A' and (resid 374 through 481 )A374 - 481
6X-RAY DIFFRACTION6chain 'A' and (resid 482 through 583 )A482 - 583
7X-RAY DIFFRACTION7chain 'B' and (resid 8 through 122 )B8 - 122
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 195 )B123 - 195
9X-RAY DIFFRACTION9chain 'B' and (resid 196 through 412 )B196 - 412
10X-RAY DIFFRACTION10chain 'B' and (resid 413 through 481 )B413 - 481
11X-RAY DIFFRACTION11chain 'B' and (resid 482 through 583 )B482 - 583

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