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- PDB-7suo: Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1... -

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Basic information

Entry
Database: PDB / ID: 7suo
TitleCrystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein
Components
  • Nucleoprotein
  • Ras GTPase-activating protein-binding protein 1
KeywordsHydrolase/Viral Protein / nucleocapsid protein / G3BP1 / Hydrolase-Viral Protein complex
Function / homology
Function and homology information


positive regulation of stress granule assembly / DNA/RNA helicase activity / ribosomal small subunit binding / positive regulation of type I interferon production / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / perikaryon ...positive regulation of stress granule assembly / DNA/RNA helicase activity / ribosomal small subunit binding / positive regulation of type I interferon production / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / perikaryon / endonuclease activity / defense response to virus / Ras protein signal transduction / DNA helicase / RNA helicase activity / RNA helicase / ribonucleoprotein complex / focal adhesion / mRNA binding / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Ras GTPase-activating protein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBiswal, M. / Lu, J. / Song, J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)1R21AI147057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119721 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI153419 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01HD092431 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01ES032024 United States
CitationJournal: J.Mol.Biol. / Year: 2022
Title: SARS-CoV-2 Nucleocapsid Protein Targets a Conserved Surface Groove of the NTF2-like Domain of G3BP1.
Authors: Biswal, M. / Lu, J. / Song, J.
History
DepositionNov 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras GTPase-activating protein-binding protein 1
B: Ras GTPase-activating protein-binding protein 1
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)33,7724
Polymers33,7724
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-34 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.704, 51.140, 153.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras GTPase-activating protein-binding protein 1 / G3BP-1 / ATP-dependent DNA helicase VIII / hDH VIII / GAP SH3 domain-binding protein 1


Mass: 15767.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G3BP1, G3BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13283, DNA helicase, RNA helicase
#2: Protein/peptide Nucleoprotein /


Mass: 1118.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% propan-2-ol, 0.1 M MES monohydrate (pH 6.0), 20% PEG MME 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 14524 / % possible obs: 98.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 32.38 Å2 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.056 / Rrim(I) all: 0.16 / Χ2: 0.727 / Net I/σ(I): 4.6 / Num. measured all: 114088
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.436.10.65913180.7440.2810.720.4692.4
2.43-2.537.10.59513910.8510.2360.6420.46696.9
2.53-2.657.80.51814250.9170.1950.5550.49898.9
2.65-2.798.30.39914410.9510.1460.4260.527100
2.79-2.968.40.31614220.9660.1140.3360.599100
2.96-3.198.40.21614770.9830.0790.230.694100
3.19-3.518.40.14614620.9920.0530.1560.8100
3.51-4.028.30.10514700.9940.0380.1120.901100
4.02-5.068.10.09515020.9950.0350.1011.148100
5.06-507.50.06516160.9980.0250.0691.006100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000v721.3data scaling
PDB_EXTRACT3.27data extraction
HKL-3000v721.3data reduction
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FW5

5fw5


Resolution: 2.35→48.51 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1446 9.99 %
Rwork0.1968 --
obs0.2017 14470 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 87 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042437
X-RAY DIFFRACTIONf_angle_d0.6993316
X-RAY DIFFRACTIONf_dihedral_angle_d5.087343
X-RAY DIFFRACTIONf_chiral_restr0.049351
X-RAY DIFFRACTIONf_plane_restr0.007446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.32031300.26121180X-RAY DIFFRACTION92
2.43-2.530.31861400.24161250X-RAY DIFFRACTION97
2.53-2.650.28741400.23371284X-RAY DIFFRACTION99
2.65-2.790.27481450.21021296X-RAY DIFFRACTION100
2.79-2.960.26381420.21261276X-RAY DIFFRACTION100
2.96-3.190.23691480.20421326X-RAY DIFFRACTION100
3.19-3.510.24581450.18431311X-RAY DIFFRACTION100
3.51-4.020.23121460.18161320X-RAY DIFFRACTION100
4.02-5.060.2061500.1561346X-RAY DIFFRACTION100
5.06-48.510.25121600.21091435X-RAY DIFFRACTION100
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)
12.39970.93210.41955.44671.256.02860.1507-0.41080.0473-0.24470.0755-0.7955-0.3920.5701-0.11530.1882-0.04720.03430.3778-0.16770.3884-5.1769.259-9.438
27.94840.2756-4.00914.7842.24948.60570.33671.50350.7674-2.1937-0.51170.0009-1.7041-0.37670.17531.02070.02910.07680.4996-0.04020.6111-10.82622.903-17.994
35.2996-0.962-1.25662.78441.56853.41830.0783-0.09560.0512-0.0292-0.05650.0677-0.2289-0.11530.0140.1905-0.0049-0.01550.288-0.07510.1975-12.8459.124-12.811
42.4291-0.2784-1.77031.1771-2.25946.4918-0.62451.56730.1831-1.40570.214-1.5362-0.17720.88040.32720.7026-0.34720.22180.7442-0.04890.8256-3.87413.357-41.078
55.93442.4281.78297.1828-0.01684.51140.14350.3836-0.1529-0.4322-0.05290.31160.03860.0652-0.07630.22830.04060.01290.2415-0.01450.1199-18.854-0.83-33.417
68.9186-5.014-3.50168.43135.67233.8182-0.2048-2.1485-0.90742.01830.4658-0.13661.67420.6934-0.12810.822-0.0908-0.15480.73630.22380.7671-19.77-10.468-16.47
74.80622.47962.91197.5945-0.41967.1547-0.0201-0.6409-0.3961-0.11960.01110.33420.5942-0.84610.03410.4155-0.013-0.03760.3307-0.09820.2644-24.179-11.049-30.114
87.13260.9276-1.70664.55820.66954.8015-0.2812-0.07090.7739-0.28180.0430.325-0.68030.00170.13260.36090.0705-0.05880.2366-0.07410.1795-19.2138.302-26.684
95.53540.9536-0.93333.86640.72834.00650.09690.22810.1732-0.4446-0.02630.1893-0.0963-0.13120.02970.24050.0126-0.01910.2665-0.00240.1809-19.8871.04-29.231
106.2985-0.7419-5.4962.89370.78246.5631-0.1994-0.45680.29020.19060.2917-0.11330.57360.4795-0.24980.1943-0.0106-0.03730.3201-0.09450.2143-19.269-0.555-21.862
114.49232.14330.2944.0096-2.73387.53720.1031-0.38470.4087-0.1916-0.5608-1.69650.35681.39410.52840.26930.00480.04850.8764-0.13930.5953.4664.608-9.208
126.97380.18080.99785.4849-6.3089.01410.59251.13240.449-1.5247-1.5667-1.86830.82280.89240.88320.7895-0.0120.31540.7460.0070.4492-10.481.651-42.534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:42 )A3 - 42
2X-RAY DIFFRACTION2( CHAIN A AND RESID 43:67 )A43 - 67
3X-RAY DIFFRACTION3( CHAIN A AND RESID 68:138 )A68 - 138
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:7 )B2 - 7
5X-RAY DIFFRACTION5( CHAIN B AND RESID 8:42 )B8 - 42
6X-RAY DIFFRACTION6( CHAIN B AND RESID 43:57 )B43 - 57
7X-RAY DIFFRACTION7( CHAIN B AND RESID 58:73 )B58 - 73
8X-RAY DIFFRACTION8( CHAIN B AND RESID 74:99 )B74 - 99
9X-RAY DIFFRACTION9( CHAIN B AND RESID 100:123 )B100 - 123
10X-RAY DIFFRACTION10( CHAIN B AND RESID 124:139 )B124 - 139
11X-RAY DIFFRACTION11( CHAIN C AND RESID 13:21 )C13 - 21
12X-RAY DIFFRACTION12( CHAIN D AND RESID 12:22 )D12 - 22

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