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- PDB-8d5e: The complex of Gtf2b Peptide TGAASFDEF Presented by H2-Dd -

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Basic information

Entry
Database: PDB / ID: 8d5e
TitleThe complex of Gtf2b Peptide TGAASFDEF Presented by H2-Dd
Components
  • Beta-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 transcribes snRNA genes / 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 Pre-transcription Events / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle ...RNA polymerase II transcribes snRNA genes / 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 Pre-transcription Events / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / nuclear thyroid hormone receptor binding / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein acetylation / cell division site / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / acetyltransferase activity / RNA polymerase II complex binding / viral transcription / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / chromosome organization / cellular defense response / RNA polymerase II core promoter sequence-specific DNA binding / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / RNA polymerase II preinitiation complex assembly / spindle assembly / histone acetyltransferase / condensed chromosome / TBP-class protein binding / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / protein-DNA complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / kinetochore / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / chromosome / protein refolding / gene expression / protein homotetramerization / amyloid fibril formation / transcription by RNA polymerase II / intracellular iron ion homeostasis / learning or memory / nuclear body / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / DNA binding / extracellular space / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / 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. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
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: 2.46 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: 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: 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)44,7044
Polymers44,6123
Non-polymers921
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-18 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.750, 80.590, 100.020
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


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: 943.953 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


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


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 309.15 K / Method: vapor diffusion, hanging drop / Details: 15% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-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: 2.46→47.391 Å / Num. obs: 16346 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.084 / Rrim(I) all: 0.208 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.46-2.560.8131035218010.7820.3680.8952.799.5
8.87-47.350.07723044010.990.0340.08427.299.7

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Processing

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

5kd7


Resolution: 2.46→47.391 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.191 / SU B: 18.284 / SU ML: 0.202 / Average fsc free: 0.9542 / Average fsc work: 0.9711 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.276 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 821 5.023 %RANDOM
Rwork0.1993 15525 --
all0.201 ---
obs-16346 99.859 %-
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: 38.695 Å2
Baniso -1Baniso -2Baniso -3
1--1.572 Å2-0 Å20 Å2
2---0.761 Å2-0 Å2
3---2.333 Å2
Refinement stepCycle: LAST / Resolution: 2.46→47.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 6 94 3229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123222
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.6564376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.7711030
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47610521
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.04210171
X-RAY DIFFRACTIONr_chiral_restr0.0950.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022516
X-RAY DIFFRACTIONr_nbd_refined0.1960.21276
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2141
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.29
X-RAY DIFFRACTIONr_mcbond_it2.3062.8791525
X-RAY DIFFRACTIONr_mcangle_it3.7144.3131901
X-RAY DIFFRACTIONr_scbond_it3.2243.1391697
X-RAY DIFFRACTIONr_scangle_it5.1274.5612475
X-RAY DIFFRACTIONr_lrange_it7.87256.71512649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.5240.332490.2581124X-RAY DIFFRACTION99.1547
2.524-2.5930.31610.2491091X-RAY DIFFRACTION99.9133
2.593-2.6680.362600.2441061X-RAY DIFFRACTION99.9109
2.668-2.750.365600.2371030X-RAY DIFFRACTION99.9083
2.75-2.8390.296520.221035X-RAY DIFFRACTION100
2.839-2.9390.215510.215951X-RAY DIFFRACTION99.7015
2.939-3.0490.283590.202930X-RAY DIFFRACTION99.7982
3.049-3.1730.273520.213912X-RAY DIFFRACTION100
3.173-3.3140.206370.193878X-RAY DIFFRACTION100
3.314-3.4740.245530.209839X-RAY DIFFRACTION100
3.474-3.6610.192380.183804X-RAY DIFFRACTION100
3.661-3.8820.183440.175765X-RAY DIFFRACTION100
3.882-4.1480.263300.168714X-RAY DIFFRACTION100
4.148-4.4770.178350.152682X-RAY DIFFRACTION100
4.477-4.90.205460.156603X-RAY DIFFRACTION99.8462
4.9-5.4710.207270.169566X-RAY DIFFRACTION99.8316
5.471-6.3040.243200.222514X-RAY DIFFRACTION100
6.304-7.6870.32170.227451X-RAY DIFFRACTION100
7.687-10.7310.168170.194355X-RAY DIFFRACTION100
10.731-47.3910.237130.31220X-RAY DIFFRACTION100
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)
10.49570.23750.33690.20030.24080.31250.06050.1053-0.0407-0.0279-0.0389-0.0018-0.0260.0085-0.02150.07270.0485-0.01160.1285-0.02940.0285-10.865915.7307-22.1959
23.47842.65071.26492.31971.44241.23580.1869-0.2118-0.08960.1591-0.1595-0.08640.093-0.1165-0.02740.02730.012-0.03580.0836-0.05860.0707-28.699811.6041-17.1744
33.50250.0652-0.11040.0058-0.00370.00420.04870.04010.2521-0.0149-0.0271-0.00890.00550.0026-0.02170.0870.02190.02210.10520.05660.09232.084724.2681-8.3799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 180
2X-RAY DIFFRACTION1ALLA181 - 275

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