[English] 日本語
Yorodumi
- PDB-8d5e: The complex of Gtf2b Peptide TGAASFDEF Presented by H2-Dd -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / nuclear thyroid hormone receptor binding / transcription preinitiation complex / protein acetylation / cell division site / transcription factor TFIID complex / acetyltransferase activity / RNA polymerase II general transcription initiation factor activity / regulation of membrane depolarization / viral transcription / RNA polymerase II complex binding / chromosome organization / protein-lysine-acetyltransferase activity / antigen processing and presentation of peptide antigen via MHC class I / RNA polymerase II core promoter sequence-specific DNA binding / cellular defense response / histone acetyltransferase / RNA polymerase II preinitiation complex assembly / condensed chromosome / spindle assembly / Neutrophil degranulation / TBP-class protein binding / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / iron ion transport / promoter-specific chromatin binding / DNA-templated transcription initiation / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / transcription initiation at RNA polymerase II promoter / positive regulation of T cell cytokine production / multicellular organismal-level iron ion homeostasis / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / protein-DNA complex / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / RNA polymerase II transcription regulator complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / gene expression / kinetochore / T cell differentiation in thymus / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / transcription by RNA polymerase II / negative regulation of neuron projection development / late endosome membrane / chromosome / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to lipopolysaccharide / protein refolding / antibacterial humoral response / DNA-binding transcription factor binding / amyloid fibril formation / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / nuclear body / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / innate immune response / lysosomal membrane / Golgi apparatus
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

-
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)44,7044
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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