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- PDB-8shz: Structure of human cGAS -

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Basic information

Entry
Database: PDB / ID: 8shz
TitleStructure of human cGAS
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / IMMUNE SYSTEM
Function / homologyAquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / water channel activity / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / plasma membrane / Probable aquaporin AqpM
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWu, S. / Sohn, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2024
Title: The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS.
Authors: Wu, S. / Gabelli, S.B. / Sohn, J.
History
DepositionApr 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0402
Polymers42,9741
Non-polymers651
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.903, 59.550, 124.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Cyclic GMP-AMP synthase / cGAMP synthase / cGAS / h-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1


Mass: 42974.473 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 157-522)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Plasmid: nHMT hCAT WT
Details (production host): His*6-MBP-Tev-AgeI-hcGAS CAT, Kanamycin resistance
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N884, cyclic GMP-AMP synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 8% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 11, 2020
RadiationMonochromator: double crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→28.96 Å / Num. obs: 26655 / % possible obs: 99.5 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.022 / Rrim(I) all: 0.053 / Χ2: 1.05 / Net I/σ(I): 23.3
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.144 / Num. measured all: 8173 / Num. unique obs: 1475 / CC1/2: 0.986 / Rpim(I) all: 0.066 / Rrim(I) all: 0.159 / Χ2: 0.95 / Net I/σ(I) obs: 10

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KM5

4km5


Resolution: 2.4→28.96 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 2679 10.05 %
Rwork0.2118 --
obs0.2165 26655 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 1 11 2768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.981
X-RAY DIFFRACTIONf_dihedral_angle_d5.645355
X-RAY DIFFRACTIONf_chiral_restr0.05417
X-RAY DIFFRACTIONf_plane_restr0.008470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.34841380.25581226X-RAY DIFFRACTION100
2.44-2.490.30731400.22441291X-RAY DIFFRACTION100
2.49-2.540.28671440.23531270X-RAY DIFFRACTION100
2.54-2.60.3151420.22011268X-RAY DIFFRACTION100
2.6-2.660.28341450.24191287X-RAY DIFFRACTION100
2.66-2.720.33351410.23471263X-RAY DIFFRACTION100
2.72-2.80.31091400.26181275X-RAY DIFFRACTION100
2.8-2.880.26591450.25431264X-RAY DIFFRACTION100
2.88-2.970.35531370.25181288X-RAY DIFFRACTION99
2.97-3.080.26681480.25411244X-RAY DIFFRACTION99
3.08-3.20.29931350.25031266X-RAY DIFFRACTION99
3.2-3.350.28021390.24421257X-RAY DIFFRACTION99
3.35-3.520.26681370.23691268X-RAY DIFFRACTION99
3.52-3.740.33911430.20521272X-RAY DIFFRACTION99
3.74-4.030.25151440.19451237X-RAY DIFFRACTION98
4.03-4.440.22141390.18231237X-RAY DIFFRACTION98
4.44-5.070.18041410.15871267X-RAY DIFFRACTION99
5.08-6.380.22891350.20171266X-RAY DIFFRACTION98
6.38-28.960.1881460.18051230X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 13.644 Å / Origin y: 14.7486 Å / Origin z: 16.8591 Å
111213212223313233
T0.2339 Å20.0393 Å20.035 Å2-0.3056 Å20.0415 Å2--0.2815 Å2
L1.6573 °20.0384 °20.1656 °2-2.0782 °2-0.2774 °2--2.0606 °2
S-0.0762 Å °-0.3169 Å °-0.33 Å °0.2085 Å °0.0348 Å °-0.1469 Å °0.2662 Å °0.0746 Å °0.0234 Å °
Refinement TLS groupSelection details: (chain A and resseq 161:522) or (chain A and resseq 601:601)

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