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- PDB-7lt1: Structure of the cGAS-like receptor human MB21D2 -

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Basic information

Entry
Database: PDB / ID: 7lt1
TitleStructure of the cGAS-like receptor human MB21D2
ComponentsProtein MB21D2
KeywordsIMMUNE SYSTEM / cGAS-like receptor / cGLR / nucleotidyltransferase
Function / homology
Function and homology information


nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / cadherin binding / protein-containing complex binding
Similarity search - Function
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
Similarity search - Domain/homology
Nucleotidyltransferase MB21D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMorehouse, B.R. / Slavik, K.M. / Kranzusch, P.J.
CitationJournal: Nature / Year: 2021
Title: cGAS-like receptors sense RNA and control 3'2'-cGAMP signalling in Drosophila.
Authors: Slavik, K.M. / Morehouse, B.R. / Ragucci, A.E. / Zhou, W. / Ai, X. / Chen, Y. / Li, L. / Wei, Z. / Bahre, H. / Konig, M. / Seifert, R. / Lee, A.S.Y. / Cai, H. / Imler, J.L. / Kranzusch, P.J.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein MB21D2
B: Protein MB21D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4695
Polymers107,1812
Non-polymers2883
Water00
1
A: Protein MB21D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7823
Polymers53,5901
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein MB21D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6862
Polymers53,5901
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.170, 127.822, 198.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Protein MB21D2 / Mab-21 domain-containing protein 2


Mass: 53590.297 Da / Num. of mol.: 2 / Fragment: UNP residues 29-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MB21D2, C3orf59 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYB1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN
Has protein modificationY

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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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.2 M ammonium sulfate, 5 mM magnesium chloride, 100 mM MES, pH 6.2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→49.56 Å / Num. obs: 50814 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 61.02 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/av σ(I): 12.6 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.48 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4680 / CC1/2: 0.848 / Rpim(I) all: 0.823

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→46.13 Å / SU ML: 0.368 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.4946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2673 1982 3.94 %
Rwork0.2471 48367 -
obs0.2479 50349 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 15 0 6413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00156550
X-RAY DIFFRACTIONf_angle_d0.398856
X-RAY DIFFRACTIONf_chiral_restr0.0356984
X-RAY DIFFRACTIONf_plane_restr0.00281117
X-RAY DIFFRACTIONf_dihedral_angle_d14.73842438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.52841390.49983381X-RAY DIFFRACTION97.29
2.46-2.530.48531390.46213410X-RAY DIFFRACTION98.75
2.53-2.60.55251390.44993402X-RAY DIFFRACTION98.64
2.6-2.680.4181410.40893393X-RAY DIFFRACTION96.82
2.68-2.780.42921400.36153390X-RAY DIFFRACTION98.36
2.78-2.890.33861420.32533407X-RAY DIFFRACTION98.75
2.89-3.020.36371390.30363446X-RAY DIFFRACTION98.49
3.02-3.180.3561410.30293443X-RAY DIFFRACTION98.95
3.18-3.380.31441390.27753473X-RAY DIFFRACTION99.15
3.38-3.640.27231420.25173466X-RAY DIFFRACTION99.18
3.64-4.010.25841400.23253429X-RAY DIFFRACTION97.62
4.01-4.590.24411450.19663516X-RAY DIFFRACTION99.78
4.59-5.780.20771460.2083543X-RAY DIFFRACTION99.95
5.78-46.130.18411500.193668X-RAY DIFFRACTION98.99
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)
11.48039724809-0.2342267804460.6444592096990.463163395249-0.005277783618240.1910727825720.01167469760840.1533459946470.09490251601510.334278689263-0.387894090907-0.278436903023-0.855618972528-0.9971536594930.0002071816169121.360647206080.2510998732520.08644864740140.9729240158380.03415992159181.1080562655231.2971788627108.2592484233.92816052383
20.896204998675-0.822896512643-0.9227163521831.5214381850.2470658103980.6824221330370.263502741260.009886932546110.0298884569166-0.126354470862-0.3114875212640.000323918665106-0.106162447317-0.332243888458-8.21297218463E-50.9068081099270.14576877008-0.005315687659390.829637646328-0.05333309731750.79508052781527.027868275887.453119369824.1684439297
31.41783206102-0.619193375476-0.9226679320811.101448808170.2369583478822.636361877770.0124054340411-0.0162711510884-0.1328312412760.0203494774002-0.122616814886-0.06717018652820.00626266331614-0.2276486156341.37007290859E-50.627322978392-0.0266706089492-0.00390063060850.661016430129-0.03166155565720.70466024824730.880244457174.67440878825.3797629057
41.11523134173-0.557035085270.04858786896750.381567345302-0.1873481066482.33104114684-0.1195293220850.07547040123540.00788400279155-0.09249584973930.161023023864-0.0895225153408-0.36878435737-0.2479068425332.33293942909E-50.727866395370.0276595151180.0184951087160.6300494046-0.01554238117340.68768771484542.420728597888.11805861812.3053259672
50.76322667992-0.6679051972540.2871322102991.67010944968-0.01393769429490.9929034841290.02225954593080.135008334947-0.0513923305038-0.100261410486-0.0763514223268-0.0961054648083-0.30436590275-0.0227009391843-4.64180764873E-50.9637073619550.1143055821920.05321114574950.8586119970990.05777508994030.76111303549335.811520216794.08559859080.335401829187
60.841709884857-0.724955145980.1454050863710.464126668341-0.1430000986750.0949913055785-0.0746897243459-0.207166279664-0.362177427225-0.0534154262297-0.3278041421750.2427988110711.371153531950.819457705173-2.14721029974E-51.29210105901-0.2500631976220.06202735954290.973653238212-0.009204570845331.092636974231.90731099116.98174568531.3306015297
70.252267577126-0.7354499779320.3240055853742.19091771513-0.8705499792962.037801457920.223828065763-0.1858570846660.07001689704680.0719228518395-0.232041838436-0.0619817639231-0.3819776494760.193611482494-5.09951635114E-50.890739497795-0.2204249883560.2382477330980.877700961281-0.01592708502070.86521714148927.356382031547.126712785251.0695044211
80.5420413696880.00334955227024-1.073244330621.15811429160.6192085586791.52213463645-0.02248701665560.2333382176930.0789296038273-0.00136129877598-0.1255025158640.442620746492-0.0807742755321-0.31472397027-8.44611681029E-50.611233087424-0.1982073120960.04674223481750.9860495914970.02497835742940.99235125082919.809658275638.665563971541.9865542711
90.926323807705-2.0578057035-1.06290784571.665150181620.8572480894623.279768172320.0864547226944-0.105167443637-0.1208933938060.0898688178718-0.125835550897-0.101932783074-0.34605872233-0.329207613446-2.52771187012E-50.815956665141-0.06465688579530.05509171290680.970173464310.04442323940680.95362128097923.41106079439.181972489635.5685691132
102.48896418452-0.314403506865-0.2270521699750.3769186835090.1103280596231.394518646020.1896493825850.605556642767-0.0486824114429-0.509458421925-0.1690410634520.247952327668-0.116461172753-0.5536703999919.4105693637E-50.910858561353-0.1141037233180.003645985514780.989321404389-0.02335812480290.94504638842125.476015580935.625447706423.0030115112
110.0224253428714-0.2468237443370.4733028347860.239696894629-0.05625814571120.2467923656640.4782284162270.0289471660358-0.851997592066-0.4259406121280.486376650196-0.1695045313420.7264962172280.928527300395-0.0001933888497451.084271466340.002958329317410.09736209500631.106686697640.02609921749490.99456927715342.570306642121.955422537.9785112319
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 52 )AA28 - 521 - 25
22chain 'A' and (resid 53 through 127 )AA53 - 12726 - 100
33chain 'A' and (resid 128 through 242 )AA128 - 242101 - 215
44chain 'A' and (resid 243 through 341 )AA243 - 341216 - 314
55chain 'A' and (resid 342 through 430 )AA342 - 430315 - 403
66chain 'B' and (resid 28 through 52 )BB28 - 521 - 25
77chain 'B' and (resid 53 through 216 )BB53 - 21626 - 183
88chain 'B' and (resid 217 through 263 )BB217 - 263184 - 230
99chain 'B' and (resid 264 through 328 )BB264 - 328231 - 295
1010chain 'B' and (resid 329 through 406 )BB329 - 406296 - 368
1111chain 'B' and (resid 407 through 431 )BB407 - 431369 - 393

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