[English] 日本語
Yorodumi
- PDB-1hsa: THE THREE-DIMENSIONAL STRUCTURE OF HLA-B27 AT 2.1 ANGSTROMS RESOL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hsa
TitleTHE THREE-DIMENSIONAL STRUCTURE OF HLA-B27 AT 2.1 ANGSTROMS RESOLUTION SUGGESTS A GENERAL MECHANISM FOR TIGHT PEPTIDE BINDING TO MHC
Components
  • BETA 2-MICROGLOBULIN
  • CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705)
  • MODEL PEPTIDE SEQUENCE - ARAAAAAAA
KeywordsHISTOCOMPATIBILITY ANTIGEN
Function / homology
Function and homology information


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 / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / secretory granule membrane ...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 / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMadden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC.
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
#1: Journal: Nature / Year: 1991
Title: The Structure of Hla-B27 Reveals Nonamer Self-Peptides Bound in an Extended Conformation
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
#2: Journal: Nature / Year: 1991
Title: Identification of Self Peptides Bound to Purified Hla-B27
Authors: Jardetzky, T.S. / Lane, W.S. / Robinson, R.A. / Madden, D.R. / Wiley, D.C.
#3: Journal: Proteins / Year: 1992
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Human Major Histocompatibility Antigen Hla-B27
Authors: Gorga, J.C. / Madden, D.R. / Prendergast, J.K. / Wiley, D.C. / Strominger, J.L.
#4: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution
Authors: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C.
#5: Journal: Nature / Year: 1989
Title: Specificity Pockets for the Side Chains of Peptide Antigens in Hla-Aw68
Authors: Garrett, T.P.J. / Saper, M.A. / Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C.
#6: Journal: Nature / Year: 1987
Title: Structure of the Human Class I Histocompatibility Antigen, Hla-A2
Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C.
#7: Journal: Nature / Year: 1987
Title: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens
Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C.
#8: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes
Authors: Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C.
History
DepositionAug 11, 1992Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE ...SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE SHEETS TWICE (DESIGNATED SHEETS SB1, SB2 AND SD1, SD2 RESPECTIVELY) WHERE THE TWO REPRESENTATIONS DIFFER IN THEIR LAST STRAND.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705)
B: BETA 2-MICROGLOBULIN
C: MODEL PEPTIDE SEQUENCE - ARAAAAAAA
D: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705)
E: BETA 2-MICROGLOBULIN
F: MODEL PEPTIDE SEQUENCE - ARAAAAAAA


Theoretical massNumber of molelcules
Total (without water)88,8406
Polymers88,8406
Non-polymers00
Water7,927440
1
A: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705)
B: BETA 2-MICROGLOBULIN
C: MODEL PEPTIDE SEQUENCE - ARAAAAAAA


Theoretical massNumber of molelcules
Total (without water)44,4203
Polymers44,4203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-13 kcal/mol
Surface area19150 Å2
MethodPISA
2
D: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705)
E: BETA 2-MICROGLOBULIN
F: MODEL PEPTIDE SEQUENCE - ARAAAAAAA


Theoretical massNumber of molelcules
Total (without water)44,4203
Polymers44,4203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-14 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.100, 69.800, 81.100
Angle α, β, γ (deg.)80.30, 88.60, 89.90
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES PRO A 210, PRO B 32, PRO D 210 AND PRO E 32 ARE CIS PROLINES.
2: SIDE CHAIN ATOMS OF ARG A 108, LYS A 268, LYS B 58 AND ARG D 108, LYS D 268, LYS E 58 ARE DISORDERED, AND HAVE OCCUPANCIES EQUAL TO ZERO IN THIS ENTRY.
3: THESE SOLVENT MOLECULES ARE LOCATED WITHIN THE PEPTIDE-BINDING SITE OF COMPLEX 1.
4: THESE SOLVENT MOLECULES ARE LOCATED WITHIN THE PEPTIDE-BINDING SITE OF COMPLEX 2.

-
Components

#1: Protein CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705)


Mass: 31928.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P03989, UniProt: P01889*PLUS
#2: Protein BETA 2-MICROGLOBULIN


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61769
#3: Protein/peptide MODEL PEPTIDE SEQUENCE - ARAAAAAAA


Mass: 743.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER ...SECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER (PROGRAM *DSSP*). THE FINAL MODEL REPORTED IN THE PAPER CITED ON JRNL RECORDS ABOVE INCLUDED A PEPTIDE MODEL WITH SEQUENCE ARAAAAAAA. AN ADDITIONAL MODEL (SEQUENCE RRIKAITLK) WAS SEPARATELY REFINED AND IS DISCUSSED IN THE SAME PUBLICATION BUT IS NOT INCLUDED IN THIS ENTRY.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growDetails: THE FRAGMENT CRYSTALLIZED WAS THE EXTRACELLULAR PORTION OF THE PROTEIN CLEAVED FROM DETERGENT MICELLES WITH PAPAIN
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 %polyethylen glycol 33501reservoir
2250 mMsodium acetate1reservoir
3100 mMTris1reservoir
425 mMMES1reservoir
50.1 %sodium azide1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / % possible obs: 92 % / Rmerge(I) obs: 0.077

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.203 / Rfactor obs: 0.203 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 0 440 6706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5.5 Å / Rfactor obs: 0.203 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.8
X-RAY DIFFRACTIONx_mcbond_it0.86
X-RAY DIFFRACTIONx_scbond_it1.41

+
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