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- PDB-5fw5: Crystal structure of human G3BP1 in complex with Semliki Forest V... -

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Basic information

Entry
Database: PDB / ID: 5fw5
TitleCrystal structure of human G3BP1 in complex with Semliki Forest Virus nsP3-25 comprising two FGDF motives
Components
  • NON-STRUCTURAL PROTEIN 3
  • RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1
KeywordsHYDROLASE / TRANSFERASE / NONSTRUCTURAL PROTEIN 3 (NSP3) / RAS-GTPASE ACTIVATING PROTEIN SH3 DOMAIN BINDING PROTEIN G3BP1 / RASPUTIN / STRESS GRANULE ASSOCIATED
Function / homology
Function and homology information


DNA/RNA helicase activity / positive regulation of stress granule assembly / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity ...DNA/RNA helicase activity / positive regulation of stress granule assembly / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / ribosomal small subunit binding / 7-methylguanosine mRNA capping / positive regulation of type I interferon production / stress granule assembly / cysteine-type peptidase activity / DNA helicase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / molecular condensate scaffold activity / host cell cytoplasmic vesicle membrane / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / perikaryon / endonuclease activity / defense response to virus / DNA helicase / Ras protein signal transduction / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / innate immune response / focal adhesion / virus-mediated perturbation of host defense response / DNA-templated transcription / mRNA binding / host cell nucleus / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
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 / : / : / : / Non-structural protein 3, zinc-binding domain ...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 / : / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Polyprotein P1234 / Ras GTPase-activating protein-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SEMLIKI FOREST VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSchulte, T. / Liu, L. / Panas, M.D. / Thaa, B. / Goette, B. / Achour, A. / McInerney, G.M.
CitationJournal: Open Biol / Year: 2016
Title: Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication.
Authors: Schulte, T. / Liu, L. / Panas, M.D. / Thaa, B. / Dickson, N. / Gotte, B. / Achour, A. / McInerney, G.M.
History
DepositionFeb 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Derived calculations / Other
Revision 1.2Mar 22, 2017Group: Database references / Source and taxonomy
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: NON-STRUCTURAL PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,65615
Polymers34,7073
Non-polymers94912
Water4,954275
1
A: RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1
B: RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1
C: NON-STRUCTURAL PROTEIN 3
hetero molecules

A: RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1
B: RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1
C: NON-STRUCTURAL PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,31230
Polymers69,4146
Non-polymers1,89824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x+1/2,-y-1/2,-z-1/41
Buried area20140 Å2
ΔGint-56.2 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.975, 94.975, 107.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein RAS GTPASE-ACTIVATING PROTEIN-BINDING PROTEIN 1 / G3BP-1 / ATP-DEPENDENT DNA HELICASE VIII / HDH VIII / GAP SH3 DOMAIN-BINDING PROTEIN 1 / G3BP1


Mass: 15986.153 Da / Num. of mol.: 2 / Fragment: NTF2-LIKE, RESIDUES 1-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q13283, DNA helicase, RNA helicase
#2: Protein/peptide NON-STRUCTURAL PROTEIN 3


Mass: 2734.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 449-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SEMLIKI FOREST VIRUS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P08411

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Non-polymers , 5 types, 287 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE NUMBERING IN SUBMITTED PDB FILE CORRESPONDS TO PROCESSED NSP3 PROTEIN, THUS NUMBERS ARE ...RESIDUE NUMBERING IN SUBMITTED PDB FILE CORRESPONDS TO PROCESSED NSP3 PROTEIN, THUS NUMBERS ARE FROM 1-482 COVERING RESIDUES 1337-1818 OF THE ENTIRE NSP SEQUENCE

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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: 3.5 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 2 M AMMONIUMSULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 14, 2014 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.92→47.5 Å / Num. obs: 38208 / % possible obs: 100 % / Observed criterion σ(I): 2.1 / Redundancy: 6.9 % / Biso Wilson estimate: 25.64 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.3
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FCM

4fcm


Resolution: 1.92→47.487 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 18.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 1908 5 %
Rwork0.1672 --
obs0.1689 38141 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.2 Å2
Refinement stepCycle: LAST / Resolution: 1.92→47.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 54 275 2680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012506
X-RAY DIFFRACTIONf_angle_d1.0763385
X-RAY DIFFRACTIONf_dihedral_angle_d16.514909
X-RAY DIFFRACTIONf_chiral_restr0.09350
X-RAY DIFFRACTIONf_plane_restr0.007448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.9680.32061320.25422497X-RAY DIFFRACTION99
1.968-2.02120.25441350.2182565X-RAY DIFFRACTION100
2.0212-2.08070.23871330.19052524X-RAY DIFFRACTION100
2.0807-2.14790.21931340.18842554X-RAY DIFFRACTION100
2.1479-2.22460.25021340.18212549X-RAY DIFFRACTION100
2.2246-2.31370.23221360.17152573X-RAY DIFFRACTION100
2.3137-2.4190.19171340.16272549X-RAY DIFFRACTION100
2.419-2.54650.21111340.15662561X-RAY DIFFRACTION100
2.5465-2.70610.20951380.1632608X-RAY DIFFRACTION100
2.7061-2.9150.1931350.16562575X-RAY DIFFRACTION100
2.915-3.20830.19771370.16172605X-RAY DIFFRACTION100
3.2083-3.67240.19051380.15162622X-RAY DIFFRACTION100
3.6724-4.62620.14661400.13532654X-RAY DIFFRACTION100
4.6262-47.5020.21871480.18582797X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.1024 Å / Origin y: -30.9056 Å / Origin z: -11.0175 Å
111213212223313233
T0.121 Å2-0.0143 Å20.0273 Å2-0.1284 Å20.011 Å2--0.1429 Å2
L2.9284 °2-0.8882 °20.4839 °2-1.0396 °20.0605 °2--1.4029 °2
S0.065 Å °0.1228 Å °0.1304 Å °-0.0313 Å °-0.0788 Å °0.0321 Å °-0.0175 Å °0.0148 Å °-0.0009 Å °
Refinement TLS groupSelection details: CHAIN A OR CHAIN B OR CHAIN C

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