[English] 日本語
Yorodumi
- PDB-1w0w: Crystal Structure Of HLA-B*2709 Complexed With the self-Peptide T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w0w
TitleCrystal Structure Of HLA-B*2709 Complexed With the self-Peptide TIS from EGF-response factor 1
Components
  • BETA-2-MICROGLOBULIN
  • BUTYRATE RESPONSE FACTOR 2
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
KeywordsIMMUNE SYSTEM / MHC / MAJOR HISTOCOMPATIBILITY COMPLEX / HLA- B*2705 / MHC I
Function / homology
Function and homology information


negative regulation of mitotic cell cycle phase transition / regulation of B cell differentiation / somatic stem cell division / 3'-UTR-mediated mRNA destabilization / cellular response to granulocyte macrophage colony-stimulating factor stimulus / regulation of interleukin-12 production / regulation of dendritic cell differentiation / negative regulation of stem cell differentiation / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors ...negative regulation of mitotic cell cycle phase transition / regulation of B cell differentiation / somatic stem cell division / 3'-UTR-mediated mRNA destabilization / cellular response to granulocyte macrophage colony-stimulating factor stimulus / regulation of interleukin-12 production / regulation of dendritic cell differentiation / negative regulation of stem cell differentiation / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / definitive hemopoiesis / regulation of T cell anergy / regulation of interleukin-6 production / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / cellular response to glucocorticoid stimulus / negative regulation of fat cell differentiation / mRNA catabolic process / TAP binding / hemopoiesis / protection from natural killer cell mediated cytotoxicity / 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 / somatic stem cell population maintenance / detection of bacterium / cellular response to transforming growth factor beta stimulus / cellular response to fibroblast growth factor stimulus / ERK1 and ERK2 cascade / regulation of mRNA stability / cellular response to epidermal growth factor stimulus / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / response to wounding / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / cellular response to tumor necrosis factor / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / protein-folding chaperone binding / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / ribonucleoprotein complex / Golgi membrane / signaling receptor binding / lysosomal membrane
Similarity search - Function
Tis11B-like protein, N-terminal / Tis11B like protein, N terminus / RNA-binding protein ZFP36-like / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Tis11B-like protein, N-terminal / Tis11B like protein, N terminus / RNA-binding protein ZFP36-like / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / 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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / mRNA decay activator protein ZFP36L2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsHulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Thermodynamic and Structural Equivalence of Two Hla-B27 Subtypes Complexed with a Self-Peptide
Authors: Hulsmeyer, M. / Welfle, K. / Pohlmann, T. / Misselwitz, R. / Alexiev, U. / Welfle, H. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A.
#1: Journal: J.Exp.Med. / Year: 2004
Title: Dual, Hla-B27 Subtype-Dependent Conformation of a Self-Peptide
Authors: Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Thermodynamic and Structural Analysis of Peptide- and Allele-Dependent Properties of Two Hla-B27 Subtypes Exhibiting Differential Disease Association
Authors: Hillig, R.C. / Hulsmeyer, M. / Saenger, W. / Welfle, K. / Misselwitz, R. / Welfle, H. / Kozerski, C. / Volz, A. / Uchanska-Ziegler, B. / Ziegler, A.
History
DepositionJun 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA-2-MICROGLOBULIN
C: BUTYRATE RESPONSE FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1755
Polymers44,9913
Non-polymers1842
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.175, 82.670, 110.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN / B27 ALPHA CHAIN PRECURSOR / MHC CLASS I ANTIGEN B*27


Mass: 31951.219 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03989, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769
#3: Protein/peptide BUTYRATE RESPONSE FACTOR 2 / EGF-RESPONSE FACTOR 2 / ERF-2 / TIS11D PROTEIN


Mass: 1160.436 Da / Num. of mol.: 1 / Fragment: RESIDUES 479-487 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P47974
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBETA-2-MICROGLOBULIN IS THE BETA-CHAIN OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULES. ...BETA-2-MICROGLOBULIN IS THE BETA-CHAIN OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULES. BUTYRATE RESPONSE FACTOR 2 REGULATORY PROTEIN INVOLVED IN REGULATING THE RESPONSE TO GROWTH FACTORS.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.5 / Details: 20% PEG8000, 0.1M TRIS PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.886
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 2.11→28.1 Å / Num. obs: 22935 / % possible obs: 87 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10
Reflection shellResolution: 2.11→2.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 86

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKLdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W0V

1w0v


Resolution: 2.11→65.94 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.551 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1224 5.1 %RANDOM
Rwork0.182 ---
obs0.186 22935 87.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.11→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 12 439 3624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213316
X-RAY DIFFRACTIONr_bond_other_d0.0010.022875
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9314497
X-RAY DIFFRACTIONr_angle_other_deg1.11236687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023695
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02731
X-RAY DIFFRACTIONr_nbd_refined0.1930.2514
X-RAY DIFFRACTIONr_nbd_other0.2510.23294
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0770.21899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5891.51932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11723130
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66631384
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8224.51367
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 90
Rwork0.213 1541
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)
10.3547-0.02320.01720.19190.00690.0614-0.00380.03570-0.01040.0013-0.00450.0013-0.00370.00250.021-0.0005-0.00010.0235-0.00220.00821.239912.97923.8895
20.10920.0187-0.10560.06340.08081.08530.0196-0.0053-0.01130.00730.0044-0.0121-0.0384-0.0308-0.02410.02070.00770.00230.0245-0.00010.0115-0.155515.389852.6353
30.49240.1144-0.15650.4757-0.10830.3297-0.0229-0.0191-0.04150.01820.01830.01150.0050.00030.00460.02240.00420.01110.01240.00570.006610.5128-2.361944.1239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B1 - 99

+
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