[English] 日本語
Yorodumi
- PDB-4lew: Structure of human cGAS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lew
TitleStructure of human cGAS
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / NTase / DNA sensor
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway ...2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway / cGMP-mediated signaling / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / positive regulation of type I interferon production / nucleosome binding / negative regulation of double-strand break repair via homologous recombination / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / cAMP-mediated signaling / determination of adult lifespan / molecular condensate scaffold activity / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / innate immune response / DNA repair / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Beta Polymerase; domain 2 ...Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsLi, P.
CitationJournal: Immunity / Year: 2013
Title: Cyclic GMP-AMP Synthase Is Activated by Double-Stranded DNA-Induced Oligomerization.
Authors: Li, X. / Shu, C. / Yi, G. / Chaton, C.T. / Shelton, C.L. / Diao, J. / Zuo, X. / Kao, C.C. / Herr, A.B. / Li, P.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Cyclic GMP-AMP synthase
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1184
Polymers85,9872
Non-polymers1312
Water6,539363
1
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0592
Polymers42,9941
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0592
Polymers42,9941
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.815, 111.480, 76.414
Angle α, β, γ (deg.)90.00, 92.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 42993.742 Da / Num. of mol.: 2 / Fragment: Catalytic domain, UNP residues 157-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MB21D1, C6orf150 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N884, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-20% PEG 3350, 0.2 M A.S., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.04→43.1 Å / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 31.2
Reflection shellResolution: 2.04→2.08 Å / % possible all: 99.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.04→40.747 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 3973 4.06 %Random
Rwork0.1787 ---
obs0.1805 97840 99.57 %-
all-98377 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→40.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5913 0 2 363 6278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096030
X-RAY DIFFRACTIONf_angle_d1.1228089
X-RAY DIFFRACTIONf_dihedral_angle_d14.8092331
X-RAY DIFFRACTIONf_chiral_restr0.078876
X-RAY DIFFRACTIONf_plane_restr0.0061029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0398-2.06470.28741400.26073159X-RAY DIFFRACTION95
2.0647-2.09080.28791580.24253346X-RAY DIFFRACTION100
2.0908-2.11830.29951250.22873428X-RAY DIFFRACTION100
2.1183-2.14730.23471400.22453297X-RAY DIFFRACTION100
2.1473-2.1780.24291600.21363358X-RAY DIFFRACTION100
2.178-2.21050.27091350.2083384X-RAY DIFFRACTION100
2.2105-2.2450.20621430.19713371X-RAY DIFFRACTION100
2.245-2.28180.25181480.19763332X-RAY DIFFRACTION100
2.2818-2.32120.21721260.1893417X-RAY DIFFRACTION100
2.3212-2.36340.24921590.18253342X-RAY DIFFRACTION100
2.3634-2.40880.26341260.19053325X-RAY DIFFRACTION100
2.4088-2.4580.22361540.18343413X-RAY DIFFRACTION100
2.458-2.51140.23631260.17383312X-RAY DIFFRACTION100
2.5114-2.56990.17741470.16743396X-RAY DIFFRACTION100
2.5699-2.63410.25291430.18433366X-RAY DIFFRACTION100
2.6341-2.70530.2131500.17593328X-RAY DIFFRACTION100
2.7053-2.78490.22661190.18183394X-RAY DIFFRACTION100
2.7849-2.87480.2841520.19873358X-RAY DIFFRACTION100
2.8748-2.97750.31111420.1933329X-RAY DIFFRACTION100
2.9775-3.09670.24231350.19633437X-RAY DIFFRACTION100
3.0967-3.23750.25511430.18743316X-RAY DIFFRACTION100
3.2375-3.40820.2111510.17463377X-RAY DIFFRACTION100
3.4082-3.62160.20961320.16553402X-RAY DIFFRACTION100
3.6216-3.9010.20331440.16213346X-RAY DIFFRACTION100
3.901-4.29320.19441380.15063364X-RAY DIFFRACTION99
4.2932-4.91350.1751510.14943322X-RAY DIFFRACTION100
4.9135-6.1870.191450.17373345X-RAY DIFFRACTION99
6.187-40.75520.23091410.17943303X-RAY DIFFRACTION98
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)
1-0.33491.6196-0.684.2775-1.33910.27250.05150.36790.3033-0.16880.20011.09870.0079-0.5895-0.13270.5272-0.09460.00950.62440.16150.8515-22.168378.267762.044
22.2824-1.71730.97173.0337-1.11993.09730.0076-0.24670.49860.65380.2304-0.4263-1.0320.3256-0.26240.8-0.16430.11790.4165-0.0910.4472-5.841495.096369.8216
31.6426-0.1797-0.49822.40840.57712.83710.0709-0.29010.34710.24320.1090.2722-0.4152-0.0432-0.13380.2411-0.04940.06970.3303-0.0190.2583-10.07580.085366.8447
41.2869-0.2065-1.22681.750.83574.0756-0.1723-0.1474-0.07210.46770.00870.19040.5935-0.17090.10030.3381-0.03830.0290.34180.06230.194-12.928864.787577.9333
52.55661.22260.05658.15251.22972.99310.3084-0.1272-0.37830.3818-0.0344-0.62560.02350.3017-0.15870.25130.0109-0.03060.24980.07720.404122.669856.228341.2551
61.93991.79020.84793.02031.02331.60070.0692-0.04720.0178-0.15430.0027-0.4532-0.1820.0090.00050.19190.00440.00980.1761-0.02150.38227.773386.172733.5728
71.30810.3895-0.45643.1624-0.19250.9591-0.0935-0.01170.1758-0.31810.188-0.51-0.09220.0606-0.1030.1523-0.01080.03630.1901-0.05530.25178.536777.283535.0272
82.1401-0.4061-0.35791.70680.27893.00360.03890.1727-0.197-0.4038-0.1146-0.1080.18560.14770.03550.23870.03830.02120.0986-0.00350.173510.028257.491129.2675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 162 through 224 )
2X-RAY DIFFRACTION2chain 'B' and (resid 225 through 286 )
3X-RAY DIFFRACTION3chain 'B' and (resid 287 through 405 )
4X-RAY DIFFRACTION4chain 'B' and (resid 406 through 520 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 272 )
7X-RAY DIFFRACTION7chain 'A' and (resid 273 through 405 )
8X-RAY DIFFRACTION8chain 'A' and (resid 406 through 520 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more