[English] 日本語
Yorodumi
- PDB-4cvz: COMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 10MER CHICKEN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cvz
TitleCOMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 10MER CHICKEN PEPTIDE
Components
  • BETA-2-MICROGLOBULIN
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B21
  • PEPTIDE
KeywordsIMMUNE SYSTEM / MHC / B21
Function / homology
Function and homology information


Transferrin endocytosis and recycling / Post-translational modification: synthesis of GPI-anchored proteins / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / cellular response to iron ion ...Transferrin endocytosis and recycling / Post-translational modification: synthesis of GPI-anchored proteins / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / 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 / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / positive regulation of cellular senescence / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / cytosol
Similarity search - Function
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 / : ...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 / MHC class I alpha chain 2
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsChappell, P.E. / Roversi, P. / Harrison, M.C. / Mears, L.E. / Kaufman, J.F. / Lea, S.M.
CitationJournal: Elife / Year: 2015
Title: Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding.
Authors: Chappell, P. / Meziane, e.l..K. / Harrison, M. / Magiera, L. / Hermann, C. / Mears, L. / Wrobel, A.G. / Durant, C. / Nielsen, L.L. / Buus, S. / Ternette, N. / Mwangi, W. / Butter, C. / Nair, ...Authors: Chappell, P. / Meziane, e.l..K. / Harrison, M. / Magiera, L. / Hermann, C. / Mears, L. / Wrobel, A.G. / Durant, C. / Nielsen, L.L. / Buus, S. / Ternette, N. / Mwangi, W. / Butter, C. / Nair, V. / Ahyee, T. / Duggleby, R. / Madrigal, A. / Roversi, P. / Lea, S.M. / Kaufman, J.
History
DepositionMar 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B21
B: BETA-2-MICROGLOBULIN
C: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6269
Polymers49,2543
Non-polymers3726
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-3.3 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.520, 69.030, 93.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B21


Mass: 36862.012 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 1-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Description: B21 HAPLOTYPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: Q95601
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11062.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HEAVY AND LIGHT CHAINS EXPRESSED SEPARATELY IN INCLUSION BODIES AND SUBSEQUENTLY RENATURED TOGETHER IN THE PRESENCE OF PEPTIDE.
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: P21611
#3: Protein/peptide PEPTIDE


Mass: 1329.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GALLUS GALLUS (chicken)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.93 % / Description: NONE
Crystal growpH: 5
Details: 0.1M SODIUM ACETATE, PH 5.0, 1.5M AMMONIUM SULFATE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorDate: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.39→50.84 Å / Num. obs: 16087 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 44.97 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.9
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSTHROUGH XIA2data reduction
AimlessTHROUGH XIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YF6

2yf6
PDB Unreleased entry


Resolution: 2.39→50.84 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.8704 / SU R Cruickshank DPI: 0.583 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.597 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.284
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 811 5.04 %RANDOM
Rwork0.2581 ---
obs0.2586 16086 99.77 %-
Displacement parametersBiso mean: 30.27 Å2
Baniso -1Baniso -2Baniso -3
1--2.6854 Å20 Å20 Å2
2--6.0234 Å20 Å2
3----3.338 Å2
Refine analyzeLuzzati coordinate error obs: 0.475 Å
Refinement stepCycle: LAST / Resolution: 2.39→50.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 24 42 3145
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073185HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.854315HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1075SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes463HARMONIC5
X-RAY DIFFRACTIONt_it3185HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.75
X-RAY DIFFRACTIONt_other_torsion17.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion386SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3402SEMIHARMONIC4
LS refinement shellResolution: 2.39→2.56 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3419 139 4.84 %
Rwork0.328 2732 -
all0.3287 2871 -
obs--99.77 %

+
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