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- PDB-7uq2: Vs.4 from T4 phage in complex with cGAMP -

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Basic information

Entry
Database: PDB / ID: 7uq2
TitleVs.4 from T4 phage in complex with cGAMP
ComponentsVs.4
KeywordsVIRAL PROTEIN / Binds 3' / 3'-cGAMP
Function / homologyChem-4BW / Uncharacterized 10.2 kDa protein in regB-denV intergenic region
Function and homology information
Biological speciesTequatrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJenson, J.M. / Chen, Z.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Nature / Year: 2023
Title: Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence.
Authors: Jenson, J.M. / Li, T. / Du, F. / Ea, C.K. / Chen, Z.J.
#1: Journal: Nature / Year: 2021
Title: Highly accurate protein structure prediction with AlphaFold.
Authors: John Jumper / Richard Evans / Alexander Pritzel / Tim Green / Michael Figurnov / Olaf Ronneberger / Kathryn Tunyasuvunakool / Russ Bates / Augustin Žídek / Anna Potapenko / Alex Bridgland ...Authors: John Jumper / Richard Evans / Alexander Pritzel / Tim Green / Michael Figurnov / Olaf Ronneberger / Kathryn Tunyasuvunakool / Russ Bates / Augustin Žídek / Anna Potapenko / Alex Bridgland / Clemens Meyer / Simon A A Kohl / Andrew J Ballard / Andrew Cowie / Bernardino Romera-Paredes / Stanislav Nikolov / Rishub Jain / Jonas Adler / Trevor Back / Stig Petersen / David Reiman / Ellen Clancy / Michal Zielinski / Martin Steinegger / Michalina Pacholska / Tamas Berghammer / Sebastian Bodenstein / David Silver / Oriol Vinyals / Andrew W Senior / Koray Kavukcuoglu / Pushmeet Kohli / Demis Hassabis /
Abstract: Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort, the structures of around ...Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort, the structures of around 100,000 unique proteins have been determined, but this represents a small fraction of the billions of known protein sequences. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence-the structure prediction component of the 'protein folding problem'-has been an important open research problem for more than 50 years. Despite recent progress, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14), demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm.
History
DepositionApr 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Vs.4
B: Vs.4
C: Vs.4
D: Vs.4
E: Vs.4
F: Vs.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,04813
Polymers61,8646
Non-polymers2,1847
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19460 Å2
ΔGint-113 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.694, 81.694, 217.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Vs.4


Mass: 10310.673 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tequatrovirus / Gene: y06G, 62.5, vs.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P13314
#2: Chemical ChemComp-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 7% PEG8000, 0.1 M imidazole, pH 6.3, 0.2 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0448 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0448 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49941 / % possible obs: 98.2 % / Redundancy: 14.4 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 0.984 / Rpim(I) all: 0.026 / Rrim(I) all: 0.101 / Net I/σ(I): 33.6
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 2.17 / Num. unique obs: 2436 / CC1/2: 0.76 / Rpim(I) all: 0.346

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 2→40.85 Å / SU ML: 0.1834 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.7907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2061 1943 4.02 %
Rwork0.1826 46432 -
obs0.1836 48375 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.47 Å2
Refinement stepCycle: LAST / Resolution: 2→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 4 619 4985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01544481
X-RAY DIFFRACTIONf_angle_d1.22896072
X-RAY DIFFRACTIONf_chiral_restr0.0936645
X-RAY DIFFRACTIONf_plane_restr0.0048757
X-RAY DIFFRACTIONf_dihedral_angle_d22.60021656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31741230.24922927X-RAY DIFFRACTION86.3
2.05-2.110.24061330.21483097X-RAY DIFFRACTION90.5
2.11-2.170.2281290.20573113X-RAY DIFFRACTION91.4
2.17-2.240.21431340.19253207X-RAY DIFFRACTION93.48
2.24-2.320.23791360.18483247X-RAY DIFFRACTION94.66
2.32-2.410.22511390.18183292X-RAY DIFFRACTION95.17
2.41-2.520.20361370.19123283X-RAY DIFFRACTION95.83
2.52-2.650.23051390.19113277X-RAY DIFFRACTION95.05
2.65-2.820.22951390.18953393X-RAY DIFFRACTION97.52
2.82-3.040.1971410.18013400X-RAY DIFFRACTION97.84
3.04-3.340.20091430.17713425X-RAY DIFFRACTION98.65
3.34-3.820.19851460.16723494X-RAY DIFFRACTION98.75
3.82-4.820.13931490.14683568X-RAY DIFFRACTION99.33
4.82-40.850.22661550.19943709X-RAY DIFFRACTION98.5

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