[English] 日本語
Yorodumi
- PDB-3bw9: Crystal Structure of HLA B*3508 in complex with a HCMV 12-mer pep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bw9
TitleCrystal Structure of HLA B*3508 in complex with a HCMV 12-mer peptide from the pp65 protein
Components
  • Beta-2-microglobulin
  • CPS peptide from 65 kDa lower matrix phosphoprotein
  • HLA class I histocompatibility antigen, B-35 alpha chain
KeywordsIMMUNE SYSTEM / HLA B*3508 / HCMV / pp65 / immunology / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Polymorphism / Transmembrane / Ubl conjugation / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Phosphoprotein / Tegument protein / Viral matrix protein / Virion
Function / homology
Function and homology information


viral tegument / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / 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 ...viral tegument / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / 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 / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 iron ion transport / regulation of erythrocyte differentiation / 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 / 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 / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / amyloid fibril formation / adaptive immune response / structural constituent of virion / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-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 ...Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-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
HLA class I histocompatibility antigen, B alpha chain / 65 kDa phosphoprotein / 65 kDa phosphoprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsWynn, K.K. / Marland, Z. / Cooper, L. / Silins, S.L. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Miles, J.J. / McCluskey, J. / Burrows, S.R. ...Wynn, K.K. / Marland, Z. / Cooper, L. / Silins, S.L. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Miles, J.J. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Khanna, R.
CitationJournal: Blood / Year: 2008
Title: Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection
Authors: Wynn, K.K. / Fulton, Z. / Cooper, L. / Silins, S.L. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Miles, J.J. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Khanna, R.
History
DepositionJan 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 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-35 alpha chain
B: Beta-2-microglobulin
C: CPS peptide from 65 kDa lower matrix phosphoprotein


Theoretical massNumber of molelcules
Total (without water)45,2803
Polymers45,2803
Non-polymers00
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-20.1 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.006, 82.086, 111.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / HLA B*3508 heavy chain / MHC class I antigen B*35


Mass: 31984.281 Da / Num. of mol.: 1 / Fragment: residues in database 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide CPS peptide from 65 kDa lower matrix phosphoprotein / CPS peptide from HCMV pp65 protein


Mass: 1416.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P06725, UniProt: P18139*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE IS VARIANT, B*3508.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.2M ammonium acetate, 16% PEG 3350, pH 7.6, vapor diffusion, hanging drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorDetector: CCD / Date: Nov 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 94441 / % possible obs: 98.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 27.4
Reflection shellResolution: 1.72→1.82 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.334 / % possible all: 92.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H6P

2h6p


Resolution: 1.75→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.618 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2395 5.1 %RANDOM
Rwork0.189 ---
obs0.192 47354 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.782 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 0 438 4092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213794
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9385218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06323210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49315638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5111544
X-RAY DIFFRACTIONr_chiral_restr0.0940.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023154
X-RAY DIFFRACTIONr_nbd_refined0.2320.31825
X-RAY DIFFRACTIONr_nbtor_refined0.3170.52580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5685
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.545
X-RAY DIFFRACTIONr_mcbond_it1.07722321
X-RAY DIFFRACTIONr_mcangle_it1.66833717
X-RAY DIFFRACTIONr_scbond_it1.74431695
X-RAY DIFFRACTIONr_scangle_it2.33541501
LS refinement shellResolution: 1.75→1.811 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.307 226 -
Rwork0.246 4207 -
all-4433 -
obs--97.17 %

+
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