[English] 日本語
Yorodumi
- PDB-1hdm: HISTOCOMPATIBILITY ANTIGEN HLA-DM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hdm
TitleHISTOCOMPATIBILITY ANTIGEN HLA-DM
Components
  • PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
  • PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)
KeywordsIMMUNE SYSTEM / HISTOCOMPATIBILITY PROTEIN
Function / homology
Function and homology information


MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of T cell proliferation / MHC class II antigen presentation / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation ...MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of T cell proliferation / MHC class II antigen presentation / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosomal membrane / intracellular membrane-bounded organelle / cell surface / membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DM alpha chain / HLA class II histocompatibility antigen, DM beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWiley, D.C. / Mosyak, L.
CitationJournal: Immunity / Year: 1998
Title: The structure of HLA-DM, the peptide exchange catalyst that loads antigen onto class II MHC molecules during antigen presentation.
Authors: Mosyak, L. / Zaller, D.M. / Wiley, D.C.
History
DepositionSep 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)44,4642
Polymers44,4642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-34 kcal/mol
Surface area18330 Å2
MethodPISA
2
A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)

A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)88,9284
Polymers88,9284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area14740 Å2
ΔGint-87 kcal/mol
Surface area32510 Å2
MethodPISA
3
A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)

A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)88,9284
Polymers88,9284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12710 Å2
ΔGint-84 kcal/mol
Surface area34530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.390, 109.930, 105.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN) / RING6 / HLA-DMA


Mass: 22855.598 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DROSOPHILA S2 INSECT CELLS / Cell: B-LYMPHOCYTE / Production host: Drosophila hydei (fry) / References: UniProt: P28067
#2: Protein PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN) / RING7 / HLA-DMB


Mass: 21608.482 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DROSOPHILA S2 INSECT CELLS / Cell: B-LYMPHOCYTE / Production host: Drosophila hydei (fry) / References: UniProt: P28068

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growpH: 5.4 / Details: pH 5.4
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
210 mMTris11
31 M12Li2SO4
40.5 Mammonium sulfate12
50.1 Msodium citrate12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→34 Å / Num. obs: 18729 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 40.7 Å2 / Rsym value: 0.55 / Net I/σ(I): 27.7
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 7 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.21 / % possible all: 96.3
Reflection
*PLUS
Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 96.3 % / Redundancy: 7 % / Num. unique obs: 1837 / Rmerge(I) obs: 0.213

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLH

1dlh


Resolution: 2.5→34 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL WAS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1842 9.8 %RANDOM
Rwork0.197 ---
obs0.197 18727 96.2 %-
Displacement parametersBiso mean: 32.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 0 0 2927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.69
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
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 299 9.7 %
Rwork0.31 2795 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.69
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.354 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.31

+
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://pdbjlvh1.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