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- PDB-6nwx: Structure of mouse GILT, an enzyme involved in antigen processing -

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Basic information

Entry
Database: PDB / ID: 6nwx
TitleStructure of mouse GILT, an enzyme involved in antigen processing
ComponentsGamma-interferon-inducible lysosomal thiol reductase
KeywordsOXIDOREDUCTASE / Interferon gamma / thioreductase / antigen presentation
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors / Oxidoreductases; Acting on a sulfur group of donors / disulfide oxidoreductase activity / MHC class II antigen presentation / antigen processing and presentation of exogenous peptide antigen via MHC class I / negative regulation of fibroblast proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / cell junction / oxidoreductase activity / lysosome ...oxidoreductase activity, acting on a sulfur group of donors / Oxidoreductases; Acting on a sulfur group of donors / disulfide oxidoreductase activity / MHC class II antigen presentation / antigen processing and presentation of exogenous peptide antigen via MHC class I / negative regulation of fibroblast proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / cell junction / oxidoreductase activity / lysosome / protein stabilization / intracellular membrane-bounded organelle / extracellular region / cytosol
Similarity search - Function
Gamma interferon inducible lysosomal thiol reductase GILT / Gamma interferon inducible lysosomal thiol reductase (GILT)
Similarity search - Domain/homology
Gamma-interferon-inducible lysosomal thiol reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLi, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: Gamma-interferon-inducible lysosomal thiol reductase (GILT). Maturation, activity, and mechanism of action
Authors: Cresswell, P.
History
DepositionFeb 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-interferon-inducible lysosomal thiol reductase
B: Gamma-interferon-inducible lysosomal thiol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,84117
Polymers43,6002
Non-polymers3,24115
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-74 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.440, 44.720, 78.170
Angle α, β, γ (deg.)90.000, 111.070, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-573-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 52 through 68 or resid 70...
21(chain B and (resid 52 through 68 or resid 70...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 52 through 68 or resid 70...A52 - 68
121(chain A and (resid 52 through 68 or resid 70...A70 - 71
131(chain A and (resid 52 through 68 or resid 70...A73
141(chain A and (resid 52 through 68 or resid 70...A75 - 120
151(chain A and (resid 52 through 68 or resid 70...A52 - 301
161(chain A and (resid 52 through 68 or resid 70...A52 - 301
171(chain A and (resid 52 through 68 or resid 70...A176 - 190
181(chain A and (resid 52 through 68 or resid 70...A303 - 401
211(chain B and (resid 52 through 68 or resid 70...B52 - 68
221(chain B and (resid 52 through 68 or resid 70...B70 - 71
231(chain B and (resid 52 through 68 or resid 70...B73
241(chain B and (resid 52 through 68 or resid 70...B75 - 120
251(chain B and (resid 52 through 68 or resid 70...B48 - 301
261(chain B and (resid 52 through 68 or resid 70...B48 - 301
271(chain B and (resid 52 through 68 or resid 70...B176 - 190
281(chain B and (resid 52 through 68 or resid 70...B303 - 401

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Gamma-interferon-inducible lysosomal thiol reductase / Gamma-interferon-inducible protein IP-30 / Lysosomal thiol reductase IP30


Mass: 21800.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifi30, Gilt, Ip30 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9ESY9, Oxidoreductases; Acting on a sulfur group of donors

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 367 molecules

#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.42 % / Description: Plates
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5 / Details: 0.1 M HEPES 2.0% PEG400 2.0 M AmSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.85 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.85 Å / Relative weight: 1
ReflectionResolution: 2→29.388 Å / Num. obs: 37057 / % possible obs: 99.24 % / Redundancy: 3 % / Biso Wilson estimate: 35.99 Å2 / Rmerge(I) obs: 0.0784 / Rrim(I) all: 0.095 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 3685 / % possible all: 99.43

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SOLVEphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2→29.388 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.62
RfactorNum. reflection% reflection
Rfree0.2018 1866 5 %
Rwork0.168 --
obs0.1698 37057 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.36 Å2 / Biso mean: 47.5694 Å2 / Biso min: 18.95 Å2
Refinement stepCycle: final / Resolution: 2→29.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 205 356 3568
Biso mean--85.67 56.78 -
Num. residues----382
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1042X-RAY DIFFRACTION4TORSIONAL
12B1042X-RAY DIFFRACTION4TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.05410.30581420.2622704284699
2.0541-2.11450.26161440.248727252869100
2.1145-2.18270.26841410.217526792820100
2.1827-2.26070.27291440.21312735287999
2.2607-2.35120.22881420.20162703284599
2.3512-2.45810.24221440.195727282872100
2.4581-2.58770.22981440.180227402884100
2.5877-2.74970.24161420.18122702284499
2.7497-2.96180.22611440.177427392883100
2.9618-3.25950.21421440.16762739288399
3.2595-3.73040.17411440.1492720286499
3.7304-4.69680.14421440.12392750289499
4.6968-29.39120.19211470.16652796294398
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)
11.4011-0.2198-0.08360.5110.15741.0930.0579-0.2996-0.24230.12130.00550.01550.1504-0.0275-0.00040.2755-0.02360.00260.27820.03060.2977-35.7837-12.45835.1363
21.22580.25370.34420.72380.02430.2636-0.0759-0.3237-0.16120.1947-0.0319-0.14680.07040.00040.00020.3076-0.0014-0.00660.34510.0330.3406-26.7416-8.882438.4456
30.72760.2354-0.25890.7181-0.2940.80350.1069-0.0541-0.0767-0.35470.01240.50440.0182-0.41690.00070.2923-0.02730.0280.419-0.00510.3842-50.0425-6.731328.936
40.8067-0.0956-0.1930.3033-0.23260.2678-0.19320.16350.2151-0.1069-0.05350.06920.03380.134-0.00240.3197-0.0147-0.00270.24380.00560.2465-34.49599.032815.1922
50.3927-0.16610.1740.0714-0.0950.7546-0.06390.25450.145-0.21970.0210.0634-0.1440.10740.00130.3636-0.02390.02360.2840.03120.2781-26.981713.289412.8453
60.04930.0397-0.01240.1195-0.16860.289-0.03220.23680.2348-0.2509-0.0269-0.1425-0.27450.2712-00.3462-0.0279-0.03160.35880.03330.4346-20.328116.529718.7427
70.1494-0.0354-0.04940.0939-0.05880.07290.00730.0089-0.08120.38420.1749-0.46960.42490.2782-0.00010.3410.0419-0.02890.3291-0.00410.3404-24.8714.451620.9071
80.1751-0.2680.18290.4159-0.25140.2644-0.08-0.0651-0.0470.3097-0.1135-0.6351-0.19790.2901-0.00010.2918-0.03-0.01070.36390.06340.4391-15.52956.952723.6421
90.11760.05160.07650.1750.07330.0596-0.30930.23640.3761-0.23050.1933-0.6034-0.5260.48050.00340.4587-0.08370.0430.52610.12950.4319-19.249917.76887.8641
100.3703-0.02170.24910.4353-0.16820.2201-0.120.27350.1737-0.27490.04270.5599-0.0986-0.2841-0.02040.42540.0233-0.04890.37740.03410.3163-40.737812.71849.7283
110.0624-0.01880.01040.0066-0.01540.1114-0.22290.0068-0.1202-0.4363-0.12380.61510.7506-0.33410.00310.5985-0.0504-0.02730.4515-0.0520.3606-47.0752-5.857710.5986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 133 )A53 - 133
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 193 )A134 - 193
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 240 )A194 - 240
4X-RAY DIFFRACTION4chain 'B' and (resid 53 through 79 )B53 - 79
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 113 )B80 - 113
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 133 )B114 - 133
7X-RAY DIFFRACTION7chain 'B' and (resid 134 through 149 )B134 - 149
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 177 )B150 - 177
9X-RAY DIFFRACTION9chain 'B' and (resid 178 through 193 )B178 - 193
10X-RAY DIFFRACTION10chain 'B' and (resid 194 through 225 )B194 - 225
11X-RAY DIFFRACTION11chain 'B' and (resid 226 through 240 )B226 - 240

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