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- PDB-8d5f: The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd -

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Basic information

Entry
Database: PDB / ID: 8d5f
TitleThe complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Transcription initiation factor IIB
KeywordsIMMUNE SYSTEM / Complex / MHC
Function / homology
Function and homology information


RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Pre-transcription Events / positive regulation of core promoter binding / RNA polymerase II core complex assembly / transcriptional start site selection at RNA polymerase II promoter / Endosomal/Vacuolar pathway ...RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Pre-transcription Events / positive regulation of core promoter binding / RNA polymerase II core complex assembly / transcriptional start site selection at RNA polymerase II promoter / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / nuclear thyroid hormone receptor binding / transcription preinitiation complex / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein acetylation / regulation of membrane depolarization / RNA polymerase II complex binding / viral transcription / acetyltransferase activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / cellular defense response / beta-2-microglobulin binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / TBP-class protein binding / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / DNA-templated transcription initiation / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / lumenal side of endoplasmic reticulum membrane / protein-DNA complex / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / RNA polymerase II transcription regulator complex / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / chromosome / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / DNA-binding transcription factor binding / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / transcription by RNA polymerase II / learning or memory / nuclear body / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / DNA binding
Similarity search - Function
Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-D alpha chain / Transcription initiation factor IIB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsCustodio, J.M.F. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118166 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes.
Authors: Custodio, J.M. / Ayres, C.M. / Rosales, T.J. / Brambley, C.A. / Arbuiso, A.G. / Landau, L.M. / Keller, G.L.J. / Srivastava, P.K. / Baker, B.M.
History
DepositionJun 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Jan 17, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7744
Polymers44,6823
Non-polymers921
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-18 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.300, 68.860, 109.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein H-2 class I histocompatibility antigen, D-D alpha chain / H-2D(D)


Mass: 31876.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pMBIO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11791.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887
#3: Protein/peptide Transcription initiation factor IIB / General transcription factor TFIIB / RNA polymerase II alpha initiation factor


Mass: 1014.069 Da / Num. of mol.: 1 / Fragment: UNP residues 88-96 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P62915, histone acetyltransferase
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 309.15 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 20% PEG3350, 200 nM sodium tartrate dibasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.31→47.233 Å / Num. obs: 17756 / % possible obs: 99.2 % / Redundancy: 6 % / Biso Wilson estimate: 29.8 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.077 / Rrim(I) all: 0.143 / Net I/σ(I): 10.7
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 6 % / Rmerge(I) obs: 0.046 / Num. unique obs: 17756 / CC1/2: 0.996 / Rpim(I) all: 0.027 / Rrim(I) all: 0.054

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: {DB entry 5KD7

5kd7


Resolution: 2.31→47.233 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.983 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.207 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 891 5.018 %RANDOM
Rwork0.193 16864 --
all0.193 ---
obs-17755 98.875 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.492 Å2-0 Å20 Å2
2--0.358 Å20 Å2
3---0.134 Å2
Refinement stepCycle: LAST / Resolution: 2.31→47.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 6 129 3269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123232
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.6574387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.0911031
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25410525
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.55210173
X-RAY DIFFRACTIONr_chiral_restr0.1260.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022520
X-RAY DIFFRACTIONr_nbd_refined0.220.21292
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22134
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2158
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.210
X-RAY DIFFRACTIONr_mcbond_it1.7182.9351521
X-RAY DIFFRACTIONr_mcangle_it2.9374.3961896
X-RAY DIFFRACTIONr_scbond_it2.5083.2171711
X-RAY DIFFRACTIONr_scangle_it4.144.6882491
X-RAY DIFFRACTIONr_lrange_it7.20257.74812913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.312640.271231X-RAY DIFFRACTION98.7796
2.37-2.4350.257600.2361176X-RAY DIFFRACTION99.4368
2.435-2.5050.238620.2291167X-RAY DIFFRACTION98.9533
2.505-2.5820.239540.2091083X-RAY DIFFRACTION94.9082
2.582-2.6670.218560.2061102X-RAY DIFFRACTION99.4845
2.667-2.760.221720.2111063X-RAY DIFFRACTION99.7364
2.76-2.8640.219540.2111030X-RAY DIFFRACTION100
2.864-2.980.181540.212998X-RAY DIFFRACTION99.6212
2.98-3.1120.217460.215965X-RAY DIFFRACTION99.9012
3.112-3.2630.248580.189908X-RAY DIFFRACTION99.6904
3.263-3.4390.199520.199864X-RAY DIFFRACTION99.7821
3.439-3.6460.218370.203836X-RAY DIFFRACTION99.6575
3.646-3.8960.192390.18746X-RAY DIFFRACTION94.012
3.896-4.2060.168350.168741X-RAY DIFFRACTION100
4.206-4.6040.138270.129695X-RAY DIFFRACTION100
4.604-5.1410.125300.139621X-RAY DIFFRACTION99.8466
5.141-5.9250.162250.161566X-RAY DIFFRACTION100
5.925-7.2280.15300.192462X-RAY DIFFRACTION96.4706
7.228-10.1040.192220.156371X-RAY DIFFRACTION97.5186
10.104-47.2330.24140.237239X-RAY DIFFRACTION99.2157
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)
10.36190.13610.1080.3650.12170.4365-0.05240.04680.01-0.00020.03440.00730.02140.04870.0180.017-0.00080.0120.01040.00780.0267-3.61058.9151-25.7664
21.33051.04880.46540.94650.71561.3075-0.0417-0.030.0878-0.0016-0.02850.11410.0320.00160.07030.01430.00120.02750.0061-0.00550.0778-21.5892.6186-23.4022
31.1683-0.07080.00257.81411.30660.21870.0056-0.0819-0.0330.03490.0803-0.46940.00540.0122-0.08590.034-0.0025-0.00350.03150.02030.05059.681911.1841-9.9825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 180
2X-RAY DIFFRACTION1ALLA180 - 274

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