[English] 日本語
Yorodumi
- PDB-8d5f: The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d5f
TitleThe complex of Gtf2b neoantigen TGAARFDEF 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 / Endosomal/Vacuolar pathway ...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 / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / germinal vesicle / ER-Phagosome pathway / nuclear thyroid hormone receptor binding / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / protein acetylation / cell division site / acetyltransferase activity / viral transcription / RNA polymerase II complex binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / chromosome organization / cellular defense response / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / spindle assembly / condensed chromosome / Neutrophil degranulation / TBP-class protein binding / lumenal side of endoplasmic reticulum membrane / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / protein-DNA complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / positive regulation of receptor-mediated endocytosis / kinetochore / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / chromosome / protein refolding / protein homotetramerization / gene expression / amyloid fibril formation / intracellular iron ion homeostasis / transcription by RNA polymerase II / learning or memory / nuclear body / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / DNA binding / 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: 2.31 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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: 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


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.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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