[English] 日本語
Yorodumi
- PDB-3ln4: Crystal structure of HLA-B*4103 in complex with a 16mer self-pept... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ln4
TitleCrystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from heterogeneous nuclear ribonucleoproteins C1/C2
Components
  • 16-mer peptide from Heterogeneous nuclear ribonucleoproteins C1/C2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-41 alpha chain
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / Immune response / Major Histocompatibility Complex Class I / MHC-I peptide complex / peptide-binding motifs / Disulfide bond
Function / homology
Function and homology information


N6-methyladenosine-containing RNA reader activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / SUMOylation of RNA binding proteins / telomerase RNA binding / telomerase holoenzyme complex / regulation of interleukin-6 production / RHOBTB1 GTPase cycle / poly(U) RNA binding ...N6-methyladenosine-containing RNA reader activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / SUMOylation of RNA binding proteins / telomerase RNA binding / telomerase holoenzyme complex / regulation of interleukin-6 production / RHOBTB1 GTPase cycle / poly(U) RNA binding / 3'-UTR-mediated mRNA stabilization / nucleosomal DNA binding / negative regulation of telomere maintenance via telomerase / TAP binding / Processing of Capped Intron-Containing Pre-mRNA / 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 / detection of bacterium / RHOBTB2 GTPase cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / : / : / negative regulation of receptor binding / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / mRNA 3'-UTR binding / 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 / spliceosomal complex / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / defense response / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / mRNA splicing, via spliceosome / positive regulation of T cell cytokine production / 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 / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / positive regulation of protein binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / osteoblast differentiation / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / actin cytoskeleton / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / 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 / chromatin remodeling / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding
Similarity search - Function
Heterogeneous nuclear ribonucleoprotein C / : / 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 / RNA recognition motif / RNA recognition motif ...Heterogeneous nuclear ribonucleoprotein C / : / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / RNA-binding domain 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 / Nucleotide-binding alpha-beta plait domain superfamily / 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
ACETATE ION / HLA class I histocompatibility antigen, B alpha chain / Heterogeneous nuclear ribonucleoproteins C1/C2 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.296 Å
AuthorsTheodossis, A. / Gras, S. / Rossjohn, J.
CitationJournal: Haematologica / Year: 2011
Title: The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family
Authors: Bade-Doding, C. / Theodossis, A. / Gras, S. / Kjer-Nielsen, L. / Eiz-Vesper, B. / Seltsam, A. / Huyton, T. / Rossjohn, J. / McCluskey, J. / Blasczyk, R.
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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: HLA class I histocompatibility antigen, B-41 alpha chain
B: Beta-2-microglobulin
C: 16-mer peptide from Heterogeneous nuclear ribonucleoproteins C1/C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3965
Polymers45,2783
Non-polymers1182
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-17 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.777, 81.992, 109.810
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, B-41 alpha chain / HLA class I histocompatibility antigen / B*4103 alpha chain / MHC class I antigen B*41 / Bw-41


Mass: 31827.072 Da / Num. of mol.: 1 / Fragment: extracellular domains, UNP residues 25-298
Source method: isolated from a genetically manipulated source
Details: B*4103 allele (W95L polymorphic variant) / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcRT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P30479, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcRT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 16-mer peptide from Heterogeneous nuclear ribonucleoproteins C1/C2


Mass: 1702.859 Da / Num. of mol.: 1 / Fragment: UNP residues 102-117 / Source method: obtained synthetically / Details: Fmoc peptide synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P07910
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCYS A 101 AND 164 IN ALTERNATIVE CONFORMATION B & C ARE IN REDUCED FORM.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M citrate pH 5.6, 14-20% PEG 4000, 0.2M NH4OAc, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.296→65.6 Å / Num. all: 110817 / Num. obs: 110817 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 12.19 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.8
Reflection shellResolution: 1.296→1.35 Å / Redundancy: 5 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.2 / Num. unique all: 9992 / % possible all: 88.6

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SYV

1syv


Resolution: 1.296→27.918 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.92 / SU ML: 0.11 / σ(F): 1.33 / Phase error: 14.2 / Stereochemistry target values: ML
Details: REFINEMENT OF REDUCED CONFORMERS CARRIED OUT IN PHENIX USING THE THREE LETTER CODE CSH.
RfactorNum. reflection% reflectionSelection details
Rfree0.1766 1110 1 %RANDOM
Rwork0.1547 109572 --
obs0.1549 110682 96.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.643 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 54.57 Å2 / Biso mean: 20.013 Å2 / Biso min: 4.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.296→27.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 8 604 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063392
X-RAY DIFFRACTIONf_angle_d1.1014628
X-RAY DIFFRACTIONf_dihedral_angle_d15.4061263
X-RAY DIFFRACTIONf_chiral_restr0.08473
X-RAY DIFFRACTIONf_plane_restr0.005618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2961-1.35510.18731080.171112312X-RAY DIFFRACTION88
1.3551-1.42650.20611280.151813647X-RAY DIFFRACTION98
1.4265-1.51590.17241600.124913763X-RAY DIFFRACTION98
1.5159-1.63290.15931410.10713923X-RAY DIFFRACTION99
1.6329-1.79720.13791520.110613940X-RAY DIFFRACTION99
1.7972-2.05720.14471390.115714094X-RAY DIFFRACTION100
2.0572-2.59160.15971440.146614164X-RAY DIFFRACTION100
2.5916-27.92480.19911380.187413729X-RAY DIFFRACTION94

+
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